Editorial

3 pages, 176 KiB

Open AccessEditorial

by Jen-Tsung Chen

Int. J. Mol. Sci. 2022, 23(12), 6823; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126823 - 19 Jun 2022

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In the Special Issue entitled “Orchid Biochemistry”, researchers explored the biochemistry and molecular mechanisms of pigment formation, flower scent, bioactive compounds, plant–microbial interaction, as well as aspects of biotechnology, and these studies have greatly enriched the understanding in the field of orchid biology [...] Read more.

In the Special Issue entitled “Orchid Biochemistry”, researchers explored the biochemistry and molecular mechanisms of pigment formation, flower scent, bioactive compounds, plant–microbial interaction, as well as aspects of biotechnology, and these studies have greatly enriched the understanding in the field of orchid biology [...] Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

3 pages, 172 KiB

Open AccessEditorial

Orchid Biochemistry

by Jen-Tsung Chen

Int. J. Mol. Sci. 2020, 21(7), 2338; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21072338 - 27 Mar 2020

Cited by 5 | Viewed by 2446

Abstract

Orchids belong to Orchidaceae which is one of the largest families in flowering plants [...] Full article

(This article belongs to the Special Issue Orchid Biochemistry)

Research

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19 pages, 8697 KiB

Open AccessArticle

Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae)

by Young-Kee Kim, Sangjin Jo, Se-Hwan Cheon, Ja-Ram Hong and Ki-Joong Kim

Int. J. Mol. Sci. 2023, 24(14), 11448; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241411448 - 14 Jul 2023

Cited by 2 | Viewed by 1290

Abstract

Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most [...] Read more.

Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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27 pages, 1933 KiB

Open AccessArticle

In Which Way Do the Flower Properties of the Specialist Orchid Goodyera repens Meet the Requirements of Its Generalist Pollinators?

by Emilia Brzosko, Andrzej Bajguz, Justyna Burzyńska and Magdalena Chmur

Int. J. Mol. Sci. 2023, 24(10), 8602; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24108602 - 11 May 2023

Viewed by 1246

Abstract

This article is the next part of a series of studies documenting the influence of flower traits on the reproductive success (RS) of orchids. Knowledge of factors influencing RS helps to understand the mechanisms and processes crucial for shaping plant–pollinator interactions. The aim [...] Read more.

This article is the next part of a series of studies documenting the influence of flower traits on the reproductive success (RS) of orchids. Knowledge of factors influencing RS helps to understand the mechanisms and processes crucial for shaping plant–pollinator interactions. The aim of the present study was to determine the role of flower structure and nectar composition in shaping the RS of the specialist orchid Goodyea repens, which is pollinated by generalist bumblebees. We found a high level of pollinaria removal (PR) and female reproductive success (fruiting, FRS) as well as a high level of variation between populations, although in certain populations pollination efficiency was low. Floral display traits, mainly inflorescence length, influenced FRS in certain populations. Among the flower traits, only the height of flowers was correlated with FRS in one population, suggesting that the flower structure of this orchid is well adapted to pollination by bumblebees. The nectar of G. repens is diluted and dominated by hexoses. Sugars were less important in shaping RS than amino acids. At the species level, twenty proteogenic and six non-proteogenic AAs were noted, along with their differentiated amounts and participation in particular populations. We found that distinct AAs or their groups mainly shaped PR, especially when correlations were considered at the species level. Our results suggest that both the individual nectar components and the ratios between them have an impact on G. repens RS. Because different nectar components influence the RS parameters in different ways (i.e., negatively or positively), we suggest that different Bombus species play the role of main pollinators in distinct populations. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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20 pages, 4911 KiB

Open AccessArticle

Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics

by Shi-Jie Ke, Ding-Kun Liu, Xiong-De Tu, Xin He, Meng-Meng Zhang, Meng-Jia Zhu, Di-Yang Zhang, Cui-Li Zhang, Si-Ren Lan and Zhong-Jian Liu

Int. J. Mol. Sci. 2023, 24(9), 7837; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24097837 - 25 Apr 2023

Cited by 4 | Viewed by 1522

Abstract

Apostasia shenzhenica belongs to the subfamily Apostasioideae and is a primitive group located at the base of the Orchidaceae phylogenetic tree. However, the A. shenzhenica mitochondrial genome (mitogenome) is still unexplored, and the phylogenetic relationships between monocots mitogenomes remain unexplored. In this study, [...] Read more.

Apostasia shenzhenica belongs to the subfamily Apostasioideae and is a primitive group located at the base of the Orchidaceae phylogenetic tree. However, the A. shenzhenica mitochondrial genome (mitogenome) is still unexplored, and the phylogenetic relationships between monocots mitogenomes remain unexplored. In this study, we discussed the genetic diversity of A. shenzhenica and the phylogenetic relationships within its monocotyledon mitogenome. We sequenced and assembled the complete mitogenome of A. shenzhenica, resulting in a circular mitochondrial draft of 672,872 bp, with an average read coverage of 122× and a GC content of 44.4%. A. shenzhenica mitogenome contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis revealed a large number of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high mitogenome conservation in related species. RNA editing identified 416 sites in the protein-coding region. Furthermore, we found 44 chloroplast genomic DNA fragments that were transferred from the chloroplast to the mitogenome of A. shenzhenica, with five plastid-derived genes remaining intact in the mitogenome. Finally, the phylogenetic analysis of the mitogenomes from A. shenzhenica and 28 other monocots showed that the evolution and classification of most monocots were well determined. These findings enrich the genetic resources of orchids and provide valuable information on the taxonomic classification and molecular evolution of monocots. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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28 pages, 2828 KiB

Open AccessArticle

Does Reproductive Success in Natural and Anthropogenic Populations of Generalist Epipactis helleborine Depend on Flower Morphology and Nectar Composition?

by Emilia Brzosko, Andrzej Bajguz, Justyna Burzyńska and Magdalena Chmur

Int. J. Mol. Sci. 2023, 24(5), 4276; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24054276 - 21 Feb 2023

Cited by 2 | Viewed by 1498

Abstract

The purpose of our study was to determine the role of flower structure and nectar composition in shaping the reproductive success (RS) of the generalist orchid Epipactis helleborine in natural and anthropogenic populations. We supposed that the distinct character of two groups of [...] Read more.

The purpose of our study was to determine the role of flower structure and nectar composition in shaping the reproductive success (RS) of the generalist orchid Epipactis helleborine in natural and anthropogenic populations. We supposed that the distinct character of two groups of habitats creates different conditions for plant–pollinator relationships, thus influencing reproductive success in E. helleborine populations. Both pollinaria removal (PR) and fruiting (FRS) were differentiated between the populations. On average, FRS was almost two times higher in the anthropogenic than in the natural populations. The difference between the two population groups in PR was smaller but still statistically significant. RS parameters were correlated with some floral display and flower traits. Floral display influenced RS only in three anthropogenic populations. Flower traits had a weak influence on RS (10 of the 192 cases analyzed). The more important trait in shaping RS was nectar chemistry. The nectar of E. helleborine is relatively diluted with a lower sugar concentration in the anthropogenic than in the natural populations. In the natural populations, domination of sucrose over hexoses was found, while in the anthropogenic populations, hexoses were more abundant and the participation of sugars was balanced. In some populations, sugars influenced RS. In E. helleborine nectar, 20 proteogenic and 7 non-proteogenic amino acids (AAs) were found with a clear domination of glutamic acid. We noted relationships between some AAs and RS, but distinct AAs shaped RS in different populations, and their impact was independent of their participation. Our results indicate that the flower structure and nectar composition of E. helleborine reflect its generalistic character and meet the requirements of a wide range of pollinators. Simultaneously, the differentiation of flower traits suggests a variation in pollinator assemblages in particular populations. Knowledge about the factors influencing RS in distinct habitats helps to understand the evolutionary potential of species and to understand mechanisms and processes crucial for shaping interactions between plants and pollinators. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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20 pages, 3237 KiB

Open AccessArticle

Evolutionary Patterns of the Chloroplast Genome in Vanilloid Orchids (Vanilloideae, Orchidaceae)

by Young-Kee Kim, Se-Hwan Cheon, Ja-Ram Hong and Ki-Joong Kim

Int. J. Mol. Sci. 2023, 24(4), 3808; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24043808 - 14 Feb 2023

Cited by 2 | Viewed by 1693

Abstract

The Vanilloideae (vanilloids) is one of five subfamilies of Orchidaceae and is composed of fourteen genera and approximately 245 species. In this study, the six new chloroplast genomes (plastomes) of vanilloids (two Lecanorchis, two Pogonia, and two Vanilla species) were decoded, [...] Read more.

The Vanilloideae (vanilloids) is one of five subfamilies of Orchidaceae and is composed of fourteen genera and approximately 245 species. In this study, the six new chloroplast genomes (plastomes) of vanilloids (two Lecanorchis, two Pogonia, and two Vanilla species) were decoded, and then the evolutionary patterns of plastomes were compared to all available vanilloid plastomes. Pogonia japonica has the longest plastome, with 158,200 bp in genome size. In contrast, Lecanorchis japonica has the shortest plastome with 70,498 bp in genome size. The vanilloid plastomes have regular quadripartite structures, but the small single copy (SSC) region was drastically reduced. Two different tribes of Vanilloideae (Pogonieae and Vanilleae) showed different levels of SSC reductions. In addition, various gene losses were observed among the vanilloid plastomes. The photosynthetic vanilloids (Pogonia and Vanilla) showed signs of stage 1 degradation and had lost most of their ndh genes. The other three species (one Cyrotsia and two Lecanorchis), however, had stage 3 or stage 4 degradation and had lost almost all the genes in their plastomes, except for some housekeeping genes. The Vanilloideae were located between the Apostasioideae and Cypripedioideae in the maximum likelihood tree. A total of ten rearrangements were found among ten Vanilloideae plastomes when compared to the basal Apostasioideae plastomes. The four sub-regions of the single copy (SC) region shifted into an inverted repeat (IR) region, and the other four sub-regions of the IR region shifted into the SC regions. Both the synonymous (dS) and nonsynonymous (dN) substitution rates of IR in-cooperated SC sub-regions were decelerated, while the substitution rates of SC in-cooperated IR sub-regions were accelerated. A total of 20 protein-coding genes remained in mycoheterotrophic vanilloids. Almost all these protein genes show accelerated base substitution rates compared to the photosynthetic vanilloids. Two of the twenty genes in the mycoheterotrophic species faced strong “relaxed selection” pressure (p-value < 0.05). Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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16 pages, 3669 KiB

Open AccessArticle

Genome-Wide Identification Analysis of the R2R3-MYB Transcription Factor Family in Cymbidium sinense for Insights into Drought Stress Responses

by Mengjia Zhu, Qianqian Wang, Song Tu, Shijie Ke, Yuanyang Bi, Sagheer Ahmad, Diyang Zhang, Dingkun Liu and Siren Lan

Int. J. Mol. Sci. 2023, 24(4), 3235; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24043235 - 06 Feb 2023

Cited by 4 | Viewed by 1542

Abstract

Cymbidium sinense represents a distinctive Orchidaceae plant that is more tolerant than other terrestrial orchids. Studies have shown that many members of the MYB transcription factor (TF) family, especially the R2R3-MYB subfamily, are responsive to drought stress. This study identified 103 CsMYBs; [...] Read more.

Cymbidium sinense represents a distinctive Orchidaceae plant that is more tolerant than other terrestrial orchids. Studies have shown that many members of the MYB transcription factor (TF) family, especially the R2R3-MYB subfamily, are responsive to drought stress. This study identified 103 CsMYBs; phylogenetic analysis classified these genes into 22 subgroups with Arabidopsis thaliana. Structural analysis showed that most CsMYB genes contained the same motifs, three exons and two introns, and showed a helix-turn-helix 3D structure in each R repeat. However, the members of subgroup 22 contained only one exon and no intron. Collinear analysis revealed that C. sinense had more orthologous R2R3-MYB genes with wheat than A. thaliana and rice. Ka/Ks ratios indicated that most CsMYB genes were under purifying negative selection pressure. Cis-acting elements analysis revealed that drought-related elements were mainly focused on subgroups 4, 8, 18, 20, 21, and 22, and Mol015419 (S20) contained the most. The transcriptome analysis results showed that expression patterns of most CsMYB genes were upregulated in leaves in response to slight drought stress and downregulated in roots. Among them, members in S8 and S20 significantly responded to drought stress in C. sinense. In addition, S14 and S17 also participated in these responses, and nine genes were selected for the real-time reverse transcription quantitative PCR (RT-qPCR) experiment. The results were roughly consistent with the transcriptome. Our results, thus, provide an important contribution to understanding the role of CsMYBs in stress-related metabolic processes. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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18 pages, 4554 KiB

Open AccessArticle

The Integrated mRNA and miRNA Approach Reveals Potential Regulators of Flowering Time in Arundina graminifolia

by Sagheer Ahmad, Chuqiao Lu, Jie Gao, Yonglu Wei, Qi Xie, Jianpeng Jin, Genfa Zhu and Fengxi Yang

Int. J. Mol. Sci. 2023, 24(2), 1699; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24021699 - 15 Jan 2023

Cited by 4 | Viewed by 1937

Abstract

Orchids are among the most precious flowers in the world. Regulation of flowering time is one of the most important targets to enhance their ornamental value. The beauty of Arundina graminifolia is its year-round flowering, although the molecular mechanism of this flowering ability [...] Read more.

Orchids are among the most precious flowers in the world. Regulation of flowering time is one of the most important targets to enhance their ornamental value. The beauty of Arundina graminifolia is its year-round flowering, although the molecular mechanism of this flowering ability remains masked. Therefore, we performed a comprehensive assessment to integrate transcriptome and miRNA sequencing to disentangle the genetic regulation of flowering in this valuable species. Clustering analyses provided a set of molecular regulators of floral transition and floral morphogenesis. We mined candidate floral homeotic genes, including FCA, FPA, GI, FT, FLC, AP2, SOC1, SVP, GI, TCP, and CO, which were targeted by a variety of miRNAs. MiR11091 targeted the highest number of genes, including candidate regulators of phase transition and hormonal control. The conserved miR156-miR172 pathway of floral time regulation was evident in our data, and we found important targets of these miRNAs in the transcriptome. Moreover, endogenous hormone levels were determined to decipher the hormonal control of floral buds in A. graminifolia. The qRT-PCR analysis of floral and hormonal integrators validated the transcriptome expression. Therefore, miRNA-mediated mining of candidate genes with hormonal regulation forms the basis for comprehending the complex regulatory network of perpetual flowering in precious orchids. The findings of this study can do a great deal to broaden the breeding programs for flowering time manipulation of orchids. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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22 pages, 5797 KiB

Open AccessArticle

A Comparison of the Flavonoid Biosynthesis Mechanisms of Dendrobium Species by Analyzing the Transcriptome and Metabolome

by Sian Liu, Hanyue Zhang and Yingdan Yuan

Int. J. Mol. Sci. 2022, 23(19), 11980; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911980 - 09 Oct 2022

Cited by 11 | Viewed by 1965

Abstract

Dendrobium huoshanense, Dendrobium officinale, and Dendrobium moniliforme, as precious Chinese medicinal materials, have a variety of medicinal properties. Flavonoids are important medicinal components of Dendrobium, but their accumulation rules and biosynthesis mechanisms remain unclear. To explore the similarities and [...] Read more.

Dendrobium huoshanense, Dendrobium officinale, and Dendrobium moniliforme, as precious Chinese medicinal materials, have a variety of medicinal properties. Flavonoids are important medicinal components of Dendrobium, but their accumulation rules and biosynthesis mechanisms remain unclear. To explore the similarities and differences of flavonoid accumulation and biosynthesis in these three Dendrobium species, we performed flavonoid content determination, widely-targeted metabolomics and transcriptome sequencing on 1–4 years old Dendrobium species. The results showed that in different growth years, D. huoshanense stems had the highest flavonoid content in the second year of growth, while D. officinale and D. moniliforme stems had the highest flavonoid content in the third year of growth. A total of 644 differentially accumulated metabolites (DAMs) and 10,426 differentially expressed genes (DEGs) were identified by metabolomic and transcriptomic analysis. It was found that DAMs and DEGs were not only enriched in the general pathway of “flavonoid biosynthesis”, but also in multiple sub-pathways such as “Flavone biosynthesis”, and “Flavonol biosynthesis” and “Isoflavonoid biosynthesis”. According to a combined transcriptome and metabolome analysis, the expression levels of the F3′H gene (LOC110096779) and two F3′5′H genes (LOC110101765 and LOC110103762) may be the main genes responsible for the differences in flavonoid accumulation. As a result of this study, we have not only determined the optimal harvesting period for three Dendrobium plants, but also identified the key genes involved in flavonoid biosynthesis and provided a basis for further study of the molecular mechanism of flavonoid synthesis. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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18 pages, 14695 KiB

Open AccessArticle

Genome-Wide Identification and Expression Patterns of the SWEET Gene Family in Bletilla striata and its Responses to Low Temperature and Oxidative Stress

by Chan Lu, Jun Ye, Yuanqing Chang, Zeyuan Mi, Shuai Liu, Donghao Wang, Zhezhi Wang and Junfeng Niu

Int. J. Mol. Sci. 2022, 23(17), 10057; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231710057 - 02 Sep 2022

Cited by 5 | Viewed by 1858

Abstract

SWEETs (sugars will eventually be exported transporters), a well-known class of sugar transporters, are involved in plant growth and development, sugar transport, biotic and abiotic stresses, etc. However, to date, there have been few investigations of SWEETs in Orchidaceae. In this study, 23 [...] Read more.

SWEETs (sugars will eventually be exported transporters), a well-known class of sugar transporters, are involved in plant growth and development, sugar transport, biotic and abiotic stresses, etc. However, to date, there have been few investigations of SWEETs in Orchidaceae. In this study, 23 SWEET genes were identified in Bletilla striata for the first time, with an MtN3/saliva conserved domain, and were divided into four subgroups by phylogenetic tree. The same subfamily members had similar gene structures and motifs. Multiple cis-elements related to sugar and environmental stresses were found in the promoter region. Further, 21 genes were localized on 11 chromosomes and 2 paralogous pairs were found via intraspecific collinearity analysis. Expression profiling results showed that BsSWEETs were tissue-specific. It also revealed that BsSWEET10 and BsSWEET18 were responsive to low temperature and oxidative stresses. In addition, subcellular localization study indicated that BsSWEET15 and BsSWEET16 were localized in the cell membrane. This study provided important clues for the in-depth elucidation of the sugar transport mechanism of BsSWEET genes and their functional roles in response to abiotic stresses. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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29 pages, 3068 KiB

Open AccessArticle

Nectar Chemistry or Flower Morphology—What Is More Important for the Reproductive Success of Generalist Orchid Epipactis palustris in Natural and Anthropogenic Populations?

by Emilia Brzosko, Andrzej Bajguz, Justyna Burzyńska and Magdalena Chmur

Int. J. Mol. Sci. 2021, 22(22), 12164; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212164 - 10 Nov 2021

Cited by 3 | Viewed by 1982

Abstract

The aim of this study was to determine the level of reproductive success (RS) in natural and anthropogenic populations of generalist orchid Epipactis palustris and its dependence on flower structure and nectar composition, i.e., amino acids and sugars. We found that both pollinaria [...] Read more.

The aim of this study was to determine the level of reproductive success (RS) in natural and anthropogenic populations of generalist orchid Epipactis palustris and its dependence on flower structure and nectar composition, i.e., amino acids and sugars. We found that both pollinaria removal and female reproductive success were high and similar in all populations, despite differences in flower traits and nectar chemistry. Flower structures were weakly correlated with parameters of RS. Nectar traits were more important in shaping RS; although, we noted differentiated selection on nectar components in distinct populations. Individuals in natural populations produced nectar with a larger amount of sugars and amino acids. The sucrose to (fructose and glucose) ratio in natural populations was close to 1, while in anthropogenic ones, a clear domination of fructose and glucose was noted. Our results indicate that the flower traits and nectar composition of E. palustris reflect its generalist character and meet the requirements of a wide range of pollinators, differing according to body sizes, mouth apparatus, and dietary needs. Simultaneously, differentiation of nectar chemistry suggests a variation of pollinator assemblages in particular populations or domination of their some groups. To our knowledge, a comparison of nectar chemistry between natural and anthropogenic populations of orchids is reported for the first time in this paper. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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18 pages, 3333 KiB

Open AccessArticle

Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development

by Francesca Lucibelli, Maria Carmen Valoroso, Günter Theißen, Susanne Nolden, Mariana Mondragon-Palomino and Serena Aceto

Int. J. Mol. Sci. 2021, 22(13), 7025; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22137025 - 29 Jun 2021

Cited by 8 | Viewed by 5133

Abstract

The molecular basis of orchid flower development is accomplished through a specific regulatory program in which the class B MADS-box AP3/DEF genes play a central role. In particular, the differential expression of four class B AP3/DEF genes is responsible for specification [...] Read more.

The molecular basis of orchid flower development is accomplished through a specific regulatory program in which the class B MADS-box AP3/DEF genes play a central role. In particular, the differential expression of four class B AP3/DEF genes is responsible for specification of organ identities in the orchid perianth. Other MADS-box genes (AGL6 and SEP-like) enrich the molecular program underpinning the orchid perianth development, resulting in the expansion of the original “orchid code” in an even more complex gene regulatory network. To identify candidates that could interact with the AP3/DEF genes in orchids, we conducted an in silico differential expression analysis in wild-type and peloric Phalaenopsis. The results suggest that a YABBY DL-like gene could be involved in the molecular program leading to the development of the orchid perianth, particularly the labellum. Two YABBY DL/CRC homologs are present in the genome of Phalaenopsis equestris, PeDL1 and PeDL2, and both express two alternative isoforms. Quantitative real-time PCR analyses revealed that both genes are expressed in column and ovary. In addition, PeDL2 is more strongly expressed the labellum than in the other tepals of wild-type flowers. This pattern is similar to that of the AP3/DEF genes PeMADS3/4 and opposite to that of PeMADS2/5. In peloric mutant Phalaenopsis, where labellum-like structures substitute the lateral inner tepals, PeDL2 is expressed at similar levels of the PeMADS2-5 genes, suggesting the involvement of PeDL2 in the development of the labellum, together with the PeMADS2-PeMADS5 genes. Although the yeast two-hybrid analysis did not reveal the ability of PeDL2 to bind the PeMADS2-PeMADS5 proteins directly, the existence of regulatory interactions is suggested by the presence of CArG-boxes and other MADS-box transcription factor binding sites within the putative promoter of the orchid DL2 gene. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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21 pages, 3575 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of the APETALA2 (AP2) Transcription Factor in Dendrobium officinale

by Danqi Zeng, Jaime A. Teixeira da Silva, Mingze Zhang, Zhenming Yu, Can Si, Conghui Zhao, Guangyi Dai, Chunmei He and Jun Duan

Int. J. Mol. Sci. 2021, 22(10), 5221; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105221 - 14 May 2021

Cited by 13 | Viewed by 2757

Abstract

The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 [...] Read more.

The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 DoAP2 TFs that were identified from the D. officinale genome and named DoAP2-1 to DoAP2-14 were divided into three clades: euAP2, euANT, and basalANT. The promoters of all DoAP2 genes contained cis-regulatory elements related to plant development and also responsive to plant hormones and stress. qRT-PCR analysis showed the abundant expression of DoAP2-2, DoAP2-5, DoAP2-7, DoAP2-8 and DoAP2-12 genes in protocorm-like bodies (PLBs), while DoAP2-3, DoAP2-4, DoAP2-6, DoAP2-9, DoAP2-10 and DoAP2-11 expression was strong in plantlets. In addition, the expression of some DoAP2 genes was down-regulated during flower development. These results suggest that DoAP2 genes may play roles in plant regeneration and flower development in D. officinale. Four DoAP2 genes (DoAP2-1 from euAP2, DoAP2-2 from euANT, and DoAP2-6 and DoAP2-11 from basal ANT) were selected for further analyses. The transcriptional activation of DoAP2-1, DoAP2-2, DoAP2-6 and DoAP2-11 proteins, which were localized in the nucleus of Arabidopsis thaliana mesophyll protoplasts, was further analyzed by a dual-luciferase reporter gene system in Nicotiana benthamiana leaves. Our data showed that pBD-DoAP2-1, pBD-DoAP2-2, pBD-DoAP2-6 and pBD-DoAP2-11 significantly repressed the expression of the LUC reporter compared with the negative control (pBD), suggesting that these DoAP2 proteins may act as transcriptional repressors in the nucleus of plant cells. Our findings on AP2 genes in D. officinale shed light on the function of AP2 genes in this orchid and other plant species. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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27 pages, 1792 KiB

Open AccessArticle

How Are the Flower Structure and Nectar Composition of the Generalistic Orchid Neottia ovata Adapted to a Wide Range of Pollinators?

by Emilia Brzosko, Andrzej Bajguz, Magdalena Chmur, Justyna Burzyńska, Edyta Jermakowicz, Paweł Mirski and Piotr Zieliński

Int. J. Mol. Sci. 2021, 22(4), 2214; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22042214 - 23 Feb 2021

Cited by 9 | Viewed by 3056

Abstract

Plant-pollinator interactions significantly influence reproductive success (RS) and drive the evolution of pollination syndromes. In the context of RS, mainly the role of flower morphology is touched. The importance of nectar properties is less studied, despite its significance in pollination effectiveness. Therefore, the [...] Read more.

Plant-pollinator interactions significantly influence reproductive success (RS) and drive the evolution of pollination syndromes. In the context of RS, mainly the role of flower morphology is touched. The importance of nectar properties is less studied, despite its significance in pollination effectiveness. Therefore, the aim of this study was to test selection on flower morphology and nectar chemistry in the generalistic orchid Neottia ovata. In 2019–2020, we measured three floral displays and six flower traits, pollinaria removal (PR), female reproductive success (FRS), and determined the soil properties. The sugars and amino acids (AAs) were analyzed using the HPLC method. Data were analyzed using multiple statistical methods (boxplots, ternary plot, one-way ANOVA, Kruskal-Wallis test, and PCA). Variation of flower structure and nectar chemistry and their weak correlation with RS confirms the generalistic character of N. ovata. In particular populations, different traits were under selection. PR was high and similar in all populations in both years, while FRS was lower and varied among populations. Nectar was dominated by glucose, fructose, and included 28 AAs (Ala and Glu have the highest content). Sugars and AAs influenced mainly FRS. Among soil parameters, carbon and carbon:nitrogen ratio seems to be the most important in shaping flower structure and nectar chemistry. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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15 pages, 2914 KiB

Open AccessArticle

Functional Characterization of a Dendrobium officinale Geraniol Synthase DoGES1 Involved in Floral Scent Formation

by Conghui Zhao, Zhenming Yu, Jaime A. Teixeira da Silva, Chunmei He, Haobin Wang, Can Si, Mingze Zhang, Danqi Zeng and Jun Duan

Int. J. Mol. Sci. 2020, 21(19), 7005; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21197005 - 23 Sep 2020

Cited by 23 | Viewed by 4107

Abstract

Floral scent is a key ornamental trait that determines the quality and commercial value of orchids. Geraniol, an important volatile monoterpene in orchids that attracts pollinators, is also involved in responses to stresses but the geraniol synthase (GES) responsible for its synthesis in [...] Read more.

Floral scent is a key ornamental trait that determines the quality and commercial value of orchids. Geraniol, an important volatile monoterpene in orchids that attracts pollinators, is also involved in responses to stresses but the geraniol synthase (GES) responsible for its synthesis in the medicinal orchid Dendrobium officinale has not yet been identified. In this study, three potential geraniol synthases were mined from the D. officinale genome. DoGES1, which was localized in chloroplasts, was characterized as a geraniol synthase. DoGES1 was highly expressed in flowers, especially in petals. DoGES1 transcript levels were high in the budding stage of D. officinale flowers at 11:00 a.m. DoGES1 catalyzed geraniol in vitro, and transient expression of DoGES1 in Nicotiana benthamiana leaves resulted in the accumulation of geraniol in vivo. These findings on DoGES1 advance our understanding of geraniol biosynthesis in orchids, and lay the basis for genetic modification of floral scent in D. officinale or in other ornamental orchids. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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17 pages, 3861 KiB

Open AccessArticle

DoRWA3 from Dendrobium officinale Plays an Essential Role in Acetylation of Polysaccharides

by Can Si, Jaime A. Teixeira da Silva, Chunmei He, Zhenming Yu, Conghui Zhao, Haobin Wang, Mingze Zhang and Jun Duan

Int. J. Mol. Sci. 2020, 21(17), 6250; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21176250 - 28 Aug 2020

Cited by 12 | Viewed by 3174

Abstract

The acetylation or deacetylation of polysaccharides can influence their physical properties and biological activities. One main constituent of the edible medicinal orchid, Dendrobium officinale, is water-soluble polysaccharides (WSPs) with substituted O-acetyl groups. Both O-acetyl groups and WSPs show a similar [...] Read more.

The acetylation or deacetylation of polysaccharides can influence their physical properties and biological activities. One main constituent of the edible medicinal orchid, Dendrobium officinale, is water-soluble polysaccharides (WSPs) with substituted O-acetyl groups. Both O-acetyl groups and WSPs show a similar trend in different organs, but the genes coding for enzymes that transfer acetyl groups to WSPs have not been identified. In this study, we report that REDUCED WALL ACETYLATION (RWA) proteins may act as acetyltransferases. Three DoRWA genes were identified, cloned, and sequenced. They were sensitive to abscisic acid (ABA), but there were no differences in germination rate and root length between wild type and 35S::DoRWA3 transgenic lines under ABA stress. Three DoRWA proteins were localized in the endoplasmic reticulum. DoRWA3 had relatively stronger transcript levels in organs where acetyl groups accumulated than DoRWA1 and DoRWA2, was co-expressed with polysaccharides synthetic genes, so it was considered as a candidate acetyltransferase gene. The level of acetylation of polysaccharides increased significantly in the seeds, leaves and stems of three 35S::DoRWA3 transgenic lines compared to wild type plants. These results indicate that DoRWA3 can transfer acetyl groups to polysaccharides and is a candidate protein to improve the biological activity of other edible and medicinal plants. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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23 pages, 3676 KiB

Open AccessArticle

Symbiotic and Asymbiotic Germination of Dendrobium officinale (Orchidaceae) Respond Differently to Exogenous Gibberellins

by Juan Chen, Bo Yan, Yanjing Tang, Yongmei Xing, Yang Li, Dongyu Zhou and Shunxing Guo

Int. J. Mol. Sci. 2020, 21(17), 6104; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21176104 - 25 Aug 2020

Cited by 17 | Viewed by 3470

Abstract

Seeds of almost all orchids depend on mycorrhizal fungi to induce their germination in the wild. The regulation of this symbiotic germination of orchid seeds involves complex crosstalk interactions between mycorrhizal establishment and the germination process. The aim of this study was to [...] Read more.

Seeds of almost all orchids depend on mycorrhizal fungi to induce their germination in the wild. The regulation of this symbiotic germination of orchid seeds involves complex crosstalk interactions between mycorrhizal establishment and the germination process. The aim of this study was to investigate the effect of gibberellins (GAs) on the symbiotic germination of Dendrobium officinale seeds and its functioning in the mutualistic interaction between orchid species and their mycobionts. To do this, we used liquid chromatograph-mass spectrometer to quantify endogenous hormones across different development stages between symbiotic and asymbiotic germination of D. officinale, as well as real-time quantitative PCR to investigate gene expression levels during seed germination under the different treatment concentrations of exogenous gibberellic acids (GA₃). Our results showed that the level of endogenous GA₃ was not significantly different between the asymbiotic and symbiotic germination groups, but the ratio of GA₃ and abscisic acids (ABA) was significantly higher during symbiotic germination than asymbiotic germination. Exogenous GA₃ treatment showed that a high concentration of GA₃ could inhibit fungal colonization in the embryo cell and decrease the seed germination rate, but did not significantly affect asymbiotic germination or the growth of the free-living fungal mycelium. The expression of genes involved in the common symbiotic pathway (e.g., calcium-binding protein and calcium-dependent protein kinase) responded to the changed concentrations of exogenous GA₃. Taken together, our results demonstrate that GA₃ is probably a key signal molecule for crosstalk between the seed germination pathway and mycorrhiza symbiosis during the orchid seed symbiotic germination. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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17 pages, 3530 KiB

Open AccessArticle

Upregulation of the MYB2 Transcription Factor is Associated with Increased Accumulation of Anthocyanin in the Leaves of Dendrobium bigibbum

by Gah-Hyun Lim, Se Won Kim, Jaihyunk Ryu, Si-Yong Kang, Jin-Baek Kim and Sang Hoon Kim

Int. J. Mol. Sci. 2020, 21(16), 5653; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21165653 - 06 Aug 2020

Cited by 12 | Viewed by 2933

Abstract

Orchids with colorful leaves and flowers have significant ornamental value. Here, we used γ-irradiation-based mutagenesis to produce a Dendrobium bigibbum mutant that developed purple instead of the normal green leaves. RNA sequencing of the mutant plant identified 2513 differentially expressed genes, including 1870 [...] Read more.

Orchids with colorful leaves and flowers have significant ornamental value. Here, we used γ-irradiation-based mutagenesis to produce a Dendrobium bigibbum mutant that developed purple instead of the normal green leaves. RNA sequencing of the mutant plant identified 2513 differentially expressed genes, including 1870 up- and 706 downregulated genes. The purple leaf color of mutant leaves was associated with increased expression of genes that encoded key biosynthetic enzymes in the anthocyanin biosynthetic pathway. In addition, the mutant leaves also showed increased expression of several families of transcription factors including the MYB2 gene. Transient overexpression of D. biggibumMYB2 in Nicotiana benthamiana was associated with increased expression of endogenous anthocyanin biosynthesis genes. Interestingly, transient overexpression of orthologous MYB2 genes from other orchids did not upregulate expression of endogenous anthocyanin biosynthesis genes. Together, these results suggest that the purple coloration of D. biggibum leaves is at least associated with increased expression of the MYB2 gene, and the MYB2 orthologs from orchids likely function differently, regardless of their high level of similarity. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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22 pages, 13695 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profile of TPS Gene Family in Dendrobium officinale and the Role of DoTPS10 in Linalool Biosynthesis

by Zhenming Yu, Conghui Zhao, Guihua Zhang, Jaime A. Teixeira da Silva and Jun Duan

Int. J. Mol. Sci. 2020, 21(15), 5419; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21155419 - 30 Jul 2020

Cited by 52 | Viewed by 5675

Abstract

Terpene synthase (TPS) is a critical enzyme responsible for the biosynthesis of terpenes, which possess diverse roles in plant growth and development. Although many terpenes have been reported in orchids, limited information is available regarding the genome-wide identification and characterization of the TPS [...] Read more.

Terpene synthase (TPS) is a critical enzyme responsible for the biosynthesis of terpenes, which possess diverse roles in plant growth and development. Although many terpenes have been reported in orchids, limited information is available regarding the genome-wide identification and characterization of the TPS family in the orchid, Dendrobium officinale. By integrating the D. officinale genome and transcriptional data, 34 TPS genes were found in D. officinale. These were divided into four subfamilies (TPS-a, TPS-b, TPS-c, and TPS-e/f). Distinct tempospatial expression profiles of DoTPS genes were observed in 10 organs of D. officinale. Most DoTPS genes were predominantly expressed in flowers, followed by roots and stems. Expression of the majority of DoTPS genes was enhanced following exposure to cold and osmotic stresses. Recombinant DoTPS10 protein, located in chloroplasts, uniquely converted geranyl diphosphate to linalool in vitro. The DoTPS10 gene, which resulted in linalool formation, was highly expressed during all flower developmental stages. Methyl jasmonate significantly up-regulated DoTPS10 expression and linalool accumulation. These results simultaneously provide valuable insight into understanding the roles of the TPS family and lay a basis for further studies on the regulation of terpenoid biosynthesis by DoTPS in D. officinale. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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17 pages, 4671 KiB

Open AccessArticle

Comparative Metabolomic Analysis Reveals Distinct Flavonoid Biosynthesis Regulation for Leaf Color Development of Cymbidium sinense ‘Red Sun’

by Jie Gao, Rui Ren, Yonglu Wei, Jianpeng Jin, Sagheer Ahmad, Chuqiao Lu, Jieqiu Wu, Chuanyuan Zheng, Fengxi Yang and Genfa Zhu

Int. J. Mol. Sci. 2020, 21(5), 1869; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21051869 - 09 Mar 2020

Cited by 26 | Viewed by 3859

Abstract

The colorful leaf is an important ornamental character of Cymbidium sinense (C. sinense), especially the red leaf, which has always been attracted by breeders and consumers. However, little is documented on the formation mechanism of the red leaf of C. sinense [...] Read more.

The colorful leaf is an important ornamental character of Cymbidium sinense (C. sinense), especially the red leaf, which has always been attracted by breeders and consumers. However, little is documented on the formation mechanism of the red leaf of C. sinense. In this study, the changing patterns of flavonoid-related metabolites, corresponding enzyme activities and genes expression in the leaves of C. sinense ‘Red Sun’ from red to yellow and finally to green was investigated. A total of 196 flavonoid-related metabolites including 11 anthocyanins metabolites were identified using UPLC-MS/MS-based approach. In the process of leaf color change, 42 metabolites were identified as having significantly different contents and the content of 28 differential metabolites turned to zero. In anthocyanin biosynthetic pathway, content of all 15 identified metabolites showed downregulation trend in the process of leaf color change. Among the 15 metabolites, the contents of Naringenin chalcone, Pelargonidin O-acetylhexoside and Anthocyanin 3-O-beta-d-glucoside decreased to zero in the green leaf stage. The changing pattern of enzyme activity of 10 enzymes involved in the anthocyanin biosynthetic pathway showed different trends from red leaves that have turned yellow and finally green, while the expression of genes encoding these enzymes was all down-regulated in the process of leaf color change. The results of this study revealed the types of flavonoid-related metabolites and the comprehensive analysis of metabolites content, enzyme activities and genes expression providing a new reference for breeders to improve the leaf color of C. sinense ‘Red Sun’. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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20 pages, 9945 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways

by Yingdan Yuan, Bo Zhang, Xinggang Tang, Jinchi Zhang and Jie Lin

Int. J. Mol. Sci. 2020, 21(3), 861; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21030861 - 29 Jan 2020

Cited by 23 | Viewed by 6238

Abstract

Dendrobium is widely used in traditional Chinese medicine, which contains many kinds of active ingredients. In recent years, many Dendrobium transcriptomes have been sequenced. Hence, weighted gene co-expression network analysis (WGCNA) was used with the gene expression profiles of active ingredients to identify [...] Read more.

Dendrobium is widely used in traditional Chinese medicine, which contains many kinds of active ingredients. In recent years, many Dendrobium transcriptomes have been sequenced. Hence, weighted gene co-expression network analysis (WGCNA) was used with the gene expression profiles of active ingredients to identify the modules and genes that may associate with particular species and tissues. Three kinds of Dendrobium species and three tissues were sampled for RNA-seq to generate a high-quality, full-length transcriptome database. Based on significant changes in gene expression, we constructed co-expression networks and revealed 19 gene modules. Among them, four modules with properties correlating to active ingredients regulation and biosynthesis, and several hub genes were selected for further functional investigation. This is the first time the WGCNA method has been used to analyze Dendrobium transcriptome data. Further excavation of the gene module information will help us to further study the role and significance of key genes, key signaling pathways, and regulatory mechanisms between genes on the occurrence and development of medicinal components of Dendrobium. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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10 pages, 1092 KiB

Open AccessCommunication

Identification of (Z)-8-Heptadecene and n-Pentadecane as Electrophysiologically Active Compounds in Ophrys insectifera and Its Argogorytes Pollinator

by Björn Bohman, Alyssa M. Weinstein, Raimondas Mozuraitis, Gavin R. Flematti and Anna-Karin Borg-Karlson

Int. J. Mol. Sci. 2020, 21(2), 620; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21020620 - 17 Jan 2020

Cited by 10 | Viewed by 3019

Abstract

Sexually deceptive orchids typically depend on specific insect species for pollination, which are lured by sex pheromone mimicry. European Ophrys orchids often exploit specific species of wasps or bees with carboxylic acid derivatives. Here, we identify the specific semiochemicals present in O. insectifera [...] Read more.

Sexually deceptive orchids typically depend on specific insect species for pollination, which are lured by sex pheromone mimicry. European Ophrys orchids often exploit specific species of wasps or bees with carboxylic acid derivatives. Here, we identify the specific semiochemicals present in O. insectifera, and in females of one of its pollinator species, Argogorytes fargeii. Headspace volatile samples and solvent extracts were analysed by GC-MS and semiochemicals were structurally elucidated by microderivatisation experiments and synthesis. (Z)-8-Heptadecene and n-pentadecane were confirmed as present in both O. insectifera and A. fargeii female extracts, with both compounds being found to be electrophysiologically active to pollinators. The identified semiochemicals were compared with previously identified Ophrys pollinator attractants, such as (Z)-9 and (Z)-12-C₂₇-C₂₉ alkenes in O. sphegodes and (Z)-9-octadecenal, octadecanal, ethyl linoleate and ethyl oleate in O. speculum, to provide further insights into the biosynthesis of semiochemicals in this genus. We propose that all these currently identified Ophrys semiochemicals can be formed biosynthetically from the same activated carboxylic acid precursors, after a sequence of elongation and decarbonylation reactions in O. sphegodes and O. speculum, while in O. insectifera, possibly by decarbonylation without preceding elongation. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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21 pages, 6153 KiB

Open AccessArticle

Combined Metabolome and Transcriptome Analyses Reveal the Effects of Mycorrhizal Fungus Ceratobasidium sp. AR2 on the Flavonoid Accumulation in Anoectochilus roxburghii during Different Growth Stages

by Ying Zhang, Yuanyuan Li, Xiaomei Chen, Zhixia Meng and Shunxing Guo

Int. J. Mol. Sci. 2020, 21(2), 564; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21020564 - 15 Jan 2020

Cited by 31 | Viewed by 4011

Abstract

Anoectochilus roxburghii is a traditional Chinese herb with high medicinal value, with main bioactive constituents which are flavonoids. It commonly associates with mycorrhizal fungi for its growth and development. Moreover, mycorrhizal fungi can induce changes in the internal metabolism of host plants. However, [...] Read more.

Anoectochilus roxburghii is a traditional Chinese herb with high medicinal value, with main bioactive constituents which are flavonoids. It commonly associates with mycorrhizal fungi for its growth and development. Moreover, mycorrhizal fungi can induce changes in the internal metabolism of host plants. However, its role in the flavonoid accumulation in A. roxburghii at different growth stages is not well studied. In this study, combined metabolome and transcriptome analyses were performed to investigate the metabolic and transcriptional profiling in mycorrhizal A. roxburghii (M) and non-mycorrhizal A. roxburghii (NM) growth for six months. An association analysis revealed that flavonoid biosynthetic pathway presented significant differences between the M and NM. Additionally, the structural genes related to flavonoid synthesis and different flavonoid metabolites in both groups over a period of six months were validated using quantitative real-time polymerase chain reaction (qRT-PCR) and high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). The results showed that Ceratobasidium sp. AR2 could increase the accumulation of five flavonol-glycosides (i.e., narcissin, rutin, isorhamnetin-3-O-beta-d-glucoside, quercetin-7-O-glucoside, and kaempferol-3-O-glucoside), two flavonols (i.e., quercetin and isorhamnetin), and two flavones (i.e., nobiletin and tangeretin) to some degrees. The qRT-PCR showed that the flavonoid biosynthetic genes (PAL, 4CL, CHS, GT, and RT) were significantly differentially expressed between the M and NM. Overall, our findings indicate that AR2 induces flavonoid metabolism in A. roxburghii during different growth stages, especially in the third month. This shows great potential of Ceratobasidium sp. AR2 for the quality improvement of A. roxburghii. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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16 pages, 2195 KiB

Open AccessArticle

Molecular Identification of Endophytic Fungi and Their Pathogenicity Evaluation Against Dendrobium nobile and Dendrobium officinale

by Surendra Sarsaiya, Archana Jain, Qi Jia, Xiaokuan Fan, Fuxing Shu, Zhongwen Chen, Qinian Zhou, Jingshan Shi and Jishuang Chen

Int. J. Mol. Sci. 2020, 21(1), 316; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010316 - 02 Jan 2020

Cited by 44 | Viewed by 8576

Abstract

Dendrobium are tropical orchid plants that host diverse endophytic fungi. The role of these fungi is not currently well understood in Dendrobium plants. We morphologically and molecularly identified these fungal endophytes, and created an efficient system for evaluating the pathogenicity and symptoms of [...] Read more.

Dendrobium are tropical orchid plants that host diverse endophytic fungi. The role of these fungi is not currently well understood in Dendrobium plants. We morphologically and molecularly identified these fungal endophytes, and created an efficient system for evaluating the pathogenicity and symptoms of endophytic fungi on Dendrobium nobile and Dendrobium officinale though in vitro co-culturing. ReThe colony morphological traits of Dendrobium myco-endophytes (DMEs) were recorded for their identification. Molecular identification revealed the presence of Colletotrichum tropicicola, Fusarium keratoplasticum, Fusarium oxysporum, Fusarium solani, and Trichoderma longibrachiatum. The pathogenicity results revealed that T. longibrachiatum produced the least pathogenic effects against D. nobile protocorms. In seedlings, T. longibrachiatum showed the least pathogenic effects against D. officinale seedlings after seven days. C. tropicicola produced highly pathogenic effects against both Dendrobium seedlings. The results of histological examination of infected tissues revealed that F. keratoplasticum and T. longibrachiatum fulfill Koch’s postulates for the existence of endophytes inside the living tissues. The DMEs are cross-transmitted inside the host plant cells, playing an important role in plant host development, resistance, and alkaloids stimulation. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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18 pages, 4598 KiB

Open AccessArticle

Comparative Transcriptomics Provides Insight into Floral Color Polymorphism in a Pleione limprichtii Orchid Population

by Yiyi Zhang, Tinghong Zhou, Zhongwu Dai, Xiaoyu Dai, Wei Li, Mengxia Cao, Chengru Li, Wen-Chieh Tsai, Xiaoqian Wu, Junwen Zhai, Zhongjian Liu and Shasha Wu

Int. J. Mol. Sci. 2020, 21(1), 247; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010247 - 30 Dec 2019

Cited by 29 | Viewed by 4468

Abstract

Floral color polymorphism can provide great insight into species evolution from a genetic and ecological standpoint. Color variations between species are often mediated by pollinators and are fixed characteristics, indicating their relevance to adaptive evolution, especially between plants within a single population or [...] Read more.

Floral color polymorphism can provide great insight into species evolution from a genetic and ecological standpoint. Color variations between species are often mediated by pollinators and are fixed characteristics, indicating their relevance to adaptive evolution, especially between plants within a single population or between similar species. The orchid genus Pleione has a wide variety of flower colors, from violet, rose-purple, pink, to white, but their color formation and its evolutionary mechanism are unclear. Here, we selected the P. limprichtii population in Huanglong, Sichuan Province, China, which displayed three color variations: Rose-purple, pink, and white, providing ideal material for exploring color variations with regard to species evolution. We investigated the distribution pattern of the different color morphs. The ratio of rose-purple:pink:white-flowered individuals was close to 6:3:1. We inferred that the distribution pattern may serve as a reproductive strategy to maintain the population size. Metabolome analysis was used to reveal that cyanindin derivatives and delphidin are the main color pigments involved. RNA sequencing was used to characterize anthocyanin biosynthetic pathway-related genes and reveal different color formation pathways and transcription factors in order to identify differentially-expressed genes and explore their relationship with color formation. In addition, qRT-PCR was used to validate the expression patterns of some of the genes. The results show that PlFLS serves as a crucial gene that contributes to white color formation and that PlANS and PlUFGT are related to the accumulation of anthocyanin which is responsible for color intensity, especially in pigmented flowers. Phylogenetic and co-expression analyses also identified a R2R3-MYB gene PlMYB10, which is predicted to combine with PlbHLH20 or PlbHLH26 along with PlWD40-1 to form an MBW protein complex (MYB, bHLH, and WDR) that regulates PlFLS expression and may serve as a repressor of anthocyanin accumulation-controlled color variations. Our results not only explain the molecular mechanism of color variation in P. limprichtii, but also contribute to the exploration of a flower color evolutionary model in Pleione, as well as other flowering plants. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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15 pages, 3646 KiB

Open AccessArticle

Comparative Analysis and Expression Patterns of the PLP_deC Genes in Dendrobium officinale

by Lei Zhang, Chunyan Jiao, Yunpeng Cao, Xi Cheng, Jian Wang, Qing Jin and Yongping Cai

Int. J. Mol. Sci. 2020, 21(1), 54; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21010054 - 20 Dec 2019

Cited by 4 | Viewed by 2652

Abstract

Studies have shown that the type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) genes produce secondary metabolites and flavor volatiles in plants, and TDC (tryptophan decarboxylase), a member of the PLP_deC family, plays an important role in the biosynthesis of terpenoid indole alkaloids [...] Read more.

Studies have shown that the type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) genes produce secondary metabolites and flavor volatiles in plants, and TDC (tryptophan decarboxylase), a member of the PLP_deC family, plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs). In this study, we identified eight PLP_deC genes in Dendrobium officinale (D. officinale) and six in Phalaenopsis equestris (P. equestris), and their structures, physicochemical properties, response elements, evolutionary relationships, and expression patterns were preliminarily predicted and analyzed. The results showed that PLP_deC genes play important roles in D. officinale and respond to different exogenous hormone treatments; additionally, the results support the selection of appropriate candidates for further functional characterization of PLP_deC genes in D. officinale. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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18 pages, 2612 KiB

Open AccessArticle

Coelonin, an Anti-Inflammation Active Component of Bletilla striata and Its Potential Mechanism

by Fusheng Jiang, Meiya Li, Hongye Wang, Bin Ding, Chunchun Zhang, Zhishan Ding, Xiaobo Yu and Guiyuan Lv

Int. J. Mol. Sci. 2019, 20(18), 4422; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20184422 - 08 Sep 2019

Cited by 54 | Viewed by 4248

Abstract

Ethanol extract of Bletilla striata has remarkable anti-inflammatory and anti-pulmonary fibrosis activities in the rat silicosis model. However, its active substances and molecular mechanism are still unclear. To uncover the active ingredients and potential molecular mechanism of the Bletilla striata extract, the lipopolysaccharide [...] Read more.

Ethanol extract of Bletilla striata has remarkable anti-inflammatory and anti-pulmonary fibrosis activities in the rat silicosis model. However, its active substances and molecular mechanism are still unclear. To uncover the active ingredients and potential molecular mechanism of the Bletilla striata extract, the lipopolysaccharide (LPS)-induced macrophage inflammation model and phospho antibody array were used. Coelonin, a dihydrophenanthrene compound was isolated and identified. It significantly inhibited LPS-induced interleukin-1β (IL-1β), interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) expression at 2.5 μg/mL. The microarray data indicate that the phosphorylation levels of 32 proteins in the coelonin pre-treated group were significantly down-regulated. In particular, the phosphorylation levels of the key inflammatory regulators factor nuclear factor-kappa B (NF-κB) were significantly reduced, and the negative regulator phosphatase and tensin homologue on chromosome ten (PTEN) was reduced. Moreover, the phosphorylation level of cyclin dependent kinase inhibitor 1B (p27^Kip1), another downstream molecule regulated by PTEN was also reduced significantly. Western blot and confocal microscopy results confirmed that coelonin inhibited LPS-induced PTEN phosphorylation in a dose-dependent manner, then inhibited NF-κB activation and p27^Kip1 degradation by regulating the phosphatidylinositol-3-kinases/ v-akt murine thymoma viral oncogene homolog (PI3K/AKT) pathway negatively. However, PTEN inhibitor co-treatment analysis indicated that the inhibition of IL-1β, IL-6 and TNF-α expression by coelonin was independent of PTEN, whereas the inhibition of p27^Kip1 degradation resulted in cell-cycle arrest in the G1 phase, which was dependent on PTEN. The anti-inflammatory activity of coelonin in vivo, which is one of the main active ingredients of Bletilla striata, deserves further study. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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15 pages, 3172 KiB

Open AccessArticle

mRNA and miRNA Expression Analysis Reveal the Regulation for Flower Spot Patterning in Phalaenopsis ‘Panda’

by Anjin Zhao, Zheng Cui, Tingge Li, Huiqin Pei, Yuhui Sheng, Xueqing Li, Ying Zhao, Yang Zhou, Wenjun Huang, Xiqiang Song, Ting Peng and Jian Wang

Int. J. Mol. Sci. 2019, 20(17), 4250; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms20174250 - 30 Aug 2019

Cited by 19 | Viewed by 4223

Abstract

Phalaenopsis cultivar ‘Panda’ is a beautiful and valuable ornamental for its big flower and unique big spots on the petals and sepals. Although anthocyanins are known as the main pigments responsible for flower colors in Phalaenopsis, and the anthocyanins biosynthetic pathway in [...] Read more.

Phalaenopsis cultivar ‘Panda’ is a beautiful and valuable ornamental for its big flower and unique big spots on the petals and sepals. Although anthocyanins are known as the main pigments responsible for flower colors in Phalaenopsis, and the anthocyanins biosynthetic pathway in Phalaenopsis is generally well known, the detailed knowledge of anthocynins regulation within the spot and non-spot parts in ‘Panda’ flower is limited. In this study, transcriptome and small RNA libraries analysis from spot and non-spot sepal tissues of ‘Panda’ were performed, and we found PeMYB7, PeMYB11, and miR156g, miR858 is associated with the purple spot patterning in its sepals. Transcriptome analyses showed a total 674 differentially expressed genes (DEGs), with 424 downregulated and 250 upregulated (Non-spot-VS-Spot), and 10 candidate DEGs involved in anthocyanin biosynthetic pathway. The qPCR analysis confirmed that seven candidate structure genes (PeANS, PeF3′H, PeC4H, PeF3H, PeF3H1, Pe4CL2, and PeCHI) have significantly higher expressing levels in spot tissues than non-spot tissues. A total 1552 differentially expressed miRNAs (DEMs) were detected with 676 downregulated and 876 upregulated. However, microRNA data showed no DEMs targeting on anthocyanin biosynthesis structure gene, while a total 40 DEMs target transcription factor (TF) genes, which expressed significantly different level in spot via non-spot sepal, including 2 key MYB regulator genes. These results indicated that the lack of anthocyanidins in non-spot sepal may not directly be caused by microRNA suppressing anthocyanidin synthesis genes rather than the MYB genes. Our findings will help in understanding the role of miRNA molecular mechanisms in the spot formation pattern of Phalaenopsis, and would be useful to provide a reference to similar research in other species. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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35 pages, 2620 KiB

Open AccessReview

Active Compounds with Medicinal Potential Found in Maxillariinae Benth. (Orchidaceae Juss.) Representatives—A Review

by Monika M. Lipińska, Łukasz P. Haliński, Marek Gołębiowski and Agnieszka K. Kowalkowska

Int. J. Mol. Sci. 2023, 24(1), 739; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24010739 - 01 Jan 2023

Cited by 2 | Viewed by 2566

Abstract

Orchids are widely used in traditional medicine for the treatment of a whole range of different health conditions, and representatives of the Neotropical subtribe Maxillariinae are not an exception. They are utilized, for instance, for their spasmolytic and anti-inflammatory activities. In this work, [...] Read more.

Orchids are widely used in traditional medicine for the treatment of a whole range of different health conditions, and representatives of the Neotropical subtribe Maxillariinae are not an exception. They are utilized, for instance, for their spasmolytic and anti-inflammatory activities. In this work, we analyze the literature concerning the chemical composition of the plant extracts and secretions of this subtribe’s representatives published between 1991 and 2022. Maxillariinae is one of the biggest taxa within the orchid family; however, to date, only 19 species have been investigated in this regard and, as we report, they produce 62 semiochemicals of medical potential. The presented review is the first summary of biologically active compounds found in Maxillariinae. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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19 pages, 7512 KiB

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Evolution of Terpene Synthases in Orchidaceae

by Li-Min Huang, Hsin Huang, Yu-Chen Chuang, Wen-Huei Chen, Chun-Neng Wang and Hong-Hwa Chen

Int. J. Mol. Sci. 2021, 22(13), 6947; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22136947 - 28 Jun 2021

Cited by 18 | Viewed by 3986

Abstract

Terpenoids are the largest class of plant secondary metabolites and are one of the major emitted volatile compounds released to the atmosphere. They have functions of attracting pollinators or defense function, insecticidal properties, and are even used as pharmaceutical agents. Because of the [...] Read more.

Terpenoids are the largest class of plant secondary metabolites and are one of the major emitted volatile compounds released to the atmosphere. They have functions of attracting pollinators or defense function, insecticidal properties, and are even used as pharmaceutical agents. Because of the importance of terpenoids, an increasing number of plants are required to investigate the function and evolution of terpene synthases (TPSs) that are the key enzymes in terpenoids biosynthesis. Orchidacea, containing more than 800 genera and 28,000 species, is one of the largest and most diverse families of flowering plants, and is widely distributed. Here, the diversification of the TPSs evolution in Orchidaceae is revealed. A characterization and phylogeny of TPSs from four different species with whole genome sequences is available. Phylogenetic analysis of orchid TPSs indicates these genes are divided into TPS-a, -b, -e/f, and g subfamilies, and their duplicated copies are increased in derived orchid species compared to that in the early divergence orchid, A. shenzhenica. The large increase of both TPS-a and TPS-b copies can probably be attributed to the pro-duction of different volatile compounds for attracting pollinators or generating chemical defenses in derived orchid lineages; while the duplications of TPS-g and TPS-e/f copies occurred in a species-dependent manner. Full article

(This article belongs to the Special Issue Orchid Biochemistry 2.0)

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19 pages, 3380 KiB

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Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

by Mummadireddy Ramya, Seonghoe Jang, Hye-Ryun An, Su-Young Lee, Pil-Man Park and Pue Hee Park

Int. J. Mol. Sci. 2020, 21(3), 1160; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21031160 - 10 Feb 2020

Cited by 45 | Viewed by 7807

Abstract

Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color [...] Read more.

Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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32 pages, 1816 KiB

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An Overview of Orchid Protocorm-Like Bodies: Mass Propagation, Biotechnology, Molecular Aspects, and Breeding

by Jean Carlos Cardoso, Cesar Augusto Zanello and Jen-Tsung Chen

Int. J. Mol. Sci. 2020, 21(3), 985; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21030985 - 02 Feb 2020

Cited by 60 | Viewed by 13817

Abstract

The process through induction, proliferation and regeneration of protocorm-like bodies (PLBs) is one of the most advantageous methods for mass propagation of orchids which applied to the world floricultural market. In addition, this method has been used as a tool to identify genes [...] Read more.

The process through induction, proliferation and regeneration of protocorm-like bodies (PLBs) is one of the most advantageous methods for mass propagation of orchids which applied to the world floricultural market. In addition, this method has been used as a tool to identify genes of interest associated with the production of PLBs, and also in breeding techniques that use biotechnology to produce new cultivars, such as to obtain transgenic plants. Most of the molecular studies developed have used model plants as species of Phalaenopsis, and interestingly, despite similarities to somatic embryogenesis, some molecular differences do not yet allow to characterize that PLB induction is in fact a type of somatic embryogenesis. Despite the importance of species for conservation and collection purposes, the flower market is supported by hybrid cultivars, usually polyploid, which makes more detailed molecular evaluations difficult. Studies on the effect of plant growth regulators on induction, proliferation, and regeneration of PLBs are the most numerous. However, studies of other factors and new technologies affecting PLB production such as the use of temporary immersion bioreactors and the use of lighting-emitting diodes have emerged as new tools for advancing the technique with increasing PLB production efficiency. In addition, recent studies on Phalaenopsis equestris genome sequencing have enabled more detailed molecular studies and the molecular characterization of plantlets obtained from this technique currently allow the technique to be evaluated in a more comprehensive way regarding its real applications and main limitations aiming at mass propagation, such as somaclonal variation. Full article

(This article belongs to the Special Issue Orchid Biochemistry)

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