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Evolution and Biodiversity of the Plant Genome Architecture
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Evolution and Biodiversity of the Plant Genome Architecture

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2017) | Viewed by 55197

Special Issue Editor

Dr. Aureliano Bombarely

E-Mail Website
Guest Editor
Department of Biosciences, University of Milan (UNIMI), 20122 Milano MI, Italy
Interests: plant genomics; evolutionary genomics; polyploidy; bioinformatics; databases; sequence assembly; solanacea; domestication
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since the publication of the Arabidopsis genome in 2000, more than 200 genomes have been published. In the last 17 years, we have learned that Whole Genome Duplications (WGD) have been common in the plant lineages, that they have by average much more genes than any animal, that they have plastic genomes full of repeats strongly regulated by epigenetic mechanisms or that how the 3D chromatin structure is organized is different that in animals. We are entering in the golden age of the study of plant genome architecture. Soon, these studies will give us a more complete understanding about how organisms adapt, survive and evolve to the changing environment.

The study of the plant genome architecture goes beyond the whole genome sequencing of novel species. It also targets the evolution of the repeat content of a genus, the impact of the heterozygosity and/or polyploidy across different accessions, populations or species. It could target the genomic changes occurred under a process of local adaptation or since the appearance of the Angiosperms. In last instance these studies target anything related with our understanding of how genetic elements are organized and regulated in a genome or genomes and how they change in time and space.

With this Special Issue, we would like to invite submissions of high quality original research or review articles on any topic related to “Evolution and Biodiversity of Plant Genome Architecture”. Please join us submitting your genomic research to this exciting travel across space and time through plant genomes.

Dr. Aureliano Bombarely
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genome architecture.
  • Genome size variation.
  • Gene space
  • Repeat content
  • Whole genome duplications
  • Polyploidy
  • Aneuploidy
  • Hybridization
  • Heterozygosity
  • Gene conversions
  • Homologous exchanges
  • Chromatin organization and gene expression
  • Epigenetic modifications
  • Transcriptome variation
  • Comparative genomics

Published Papers (7 papers)

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Research

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16 pages, 32129 KiB  
Article
Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
by Sergei Kliver, Mike Rayko, Alexey Komissarov, Evgeny Bakin, Daria Zhernakova, Kasavajhala Prasad, Catherine Rushworth, R. Baskar, Dmitry Smetanin, Jeremy Schmutz, Daniel S. Rokhsar, Thomas Mitchell-Olds, Ueli Grossniklaus and Vladimir Brukhin
Genes 2018, 9(4), 185; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9040185 - 28 Mar 2018
Cited by 20 | Viewed by 8385
Abstract
Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. [...] Read more.
Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species. Full article
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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1564 KiB  
Article
Comparative Transcriptome Analysis of Male and Female Conelets and Development of Microsatellite Markers in Pinus bungeana, an Endemic Conifer in China
by Dong Duan, Yun Jia, Jie Yang and Zhong-Hu Li
Genes 2017, 8(12), 393; https://0-doi-org.brum.beds.ac.uk/10.3390/genes8120393 - 19 Dec 2017
Cited by 18 | Viewed by 4552
Abstract
The sex determination in gymnosperms is still poorly characterized due to the lack of genomic/transcriptome resources and useful molecular genetic markers. To enhance our understanding of the molecular mechanisms of the determination of sexual recognition of reproductive structures in conifers, the transcriptome of [...] Read more.
The sex determination in gymnosperms is still poorly characterized due to the lack of genomic/transcriptome resources and useful molecular genetic markers. To enhance our understanding of the molecular mechanisms of the determination of sexual recognition of reproductive structures in conifers, the transcriptome of male and female conelets were characterized in a Chinese endemic conifer species, Pinus bungeana Zucc. ex Endl. The 39.62 Gb high-throughput sequencing reads were obtained from two kinds of sexual conelets. After de novo assembly of the obtained reads, 85,305 unigenes were identified, 53,944 (63.23%) of which were annotated with public databases. A total of 12,073 differentially expressed genes were detected between the two types of sexes in P. bungeana, and 5766 (47.76%) of them were up-regulated in females. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched analysis suggested that some of the genes were significantly associated with the sex determination process of P. bungeana, such as those involved in tryptophan metabolism, zeatin biosynthesis, and cysteine and methionine metabolism, and the phenylpropanoid biosynthesis pathways. Meanwhile, some important plant hormone pathways (e.g., the gibberellin (GA) pathway, carotenoid biosynthesis, and brassinosteroid biosynthesis (BR) pathway) that affected sexual determination were also induced in P. bungeana. In addition, 8791 expressed sequence tag-simple sequence repeats (EST-SSRs) from 7859 unigenes were detected in P. bungeana. The most abundant repeat types were dinucleotides (1926), followed by trinucleotides (1711). The dominant classes of the sequence repeat were A/T (4942) in mononucleotides and AT/AT (1283) in dinucleotides. Among these EST-SSRs, 84 pairs of primers were randomly selected for the characterization of potential molecular genetic markers. Finally, 19 polymorphic EST-SSR primers were characterized. We found low to moderate levels of genetic diversity (NA = 1.754; HO = 0.206; HE = 0.205) across natural populations of P. bungeana. The cluster analysis revealed two distinct genetic groups for the six populations that were sampled in this endemic species, which might be caused by the fragmentation of habitats and long-term geographic isolation among different populations. Taken together, this work provides important insights into the molecular mechanisms of sexual identity in the reproductive organs of P. bungeana. The molecular genetic resources that were identified in this study will also facilitate further studies in functional genomics and population genetics in the Pinus species. Full article
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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4661 KiB  
Article
Comparative Analysis of the Complete Chloroplast Genome of Four Known Ziziphus Species
by Jian Huang, Ruihong Chen and Xingang Li
Genes 2017, 8(12), 340; https://0-doi-org.brum.beds.ac.uk/10.3390/genes8120340 - 24 Nov 2017
Cited by 37 | Viewed by 5718
Abstract
Ziziphus Mill. (Rhamnaceae) is comprised of about 170 species that are mainly distributed in tropical to subtropical regions, with few in the temperate zone. Several Ziziphus fruit tree species are important energy, nutrient, and medicinal resources for human populations, particularly for those living [...] Read more.
Ziziphus Mill. (Rhamnaceae) is comprised of about 170 species that are mainly distributed in tropical to subtropical regions, with few in the temperate zone. Several Ziziphus fruit tree species are important energy, nutrient, and medicinal resources for human populations, particularly for those living in rural regions. To date, limited genomic information is available for this genus. Here, we assembled the complete chloroplast genomes of four best known Ziziphus species, i.e., Ziziphus jujuba, Ziziphus acidojujuba, Ziziphus mauritiana, and Ziziphus spina-christi, based on the Illumina Paired-end sequencing method. The chloroplast genomes of the four Ziziphus species are all very similar to one another, and exhibit structural, gene content, and order characteristics that are similar to other flowering plants. The entire chloroplast genome encodes 113 predicted unique genes (85 protein-coding genes, 8 rRNA, and 37 tRNA), 17 of which are duplicated in the inverted repeat regions. Rich single sequence repeats loci (217) were detected in Z. jujuba and 106 SSR loci, composed of A/T, displayed polymorphism across the four species by comparative genomic analysis. We found only four genes under positive selection between Z. jujuba and Z. acidojujuba, and two genes for Z. mauritiana vs. Z. spina-christi, respectively, while half of the 78 protein-coding genes experienced positive selection between the two groups. Phylogenetic analyses revealed that Ziziphus (Rhamnaceae) was sister to Elaeagnaceae, and the four species of Ziziphus were clustered into two groups (Z. jujuba and Z. acidojujuba, Z. mauritiana and Z. spina-christi). Our results provide genomic resources for intrageneric classifications of Ziziphus, and valuable genetic markers for investigating the population genetics and biogeography of closely related Ziziphus species. Full article
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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6245 KiB  
Article
Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea)
by Zhiliang Xiao, Yang Hu, Xiaoli Zhang, Yuqian Xue, Zhiyuan Fang, Limei Yang, Yangyong Zhang, Yumei Liu, Zhansheng Li, Xing Liu, Zezhou Liu, Honghao Lv and Mu Zhuang
Genes 2017, 8(6), 147; https://0-doi-org.brum.beds.ac.uk/10.3390/genes8060147 - 05 Jun 2017
Cited by 15 | Viewed by 7789
Abstract
Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage (Brassica oleracea) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that [...] Read more.
Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage (Brassica oleracea) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2, respectively. We also applied RNA-Seq to analyze hybrid lethality in cabbage. In the region of BoHL1, seven differentially expressed genes (DEGs) and five resistance (R)-related genes (two in common, i.e., Bo1g153320 and Bo1g153380) were found, whereas in the region of BoHL2, two DEGs and four R-related genes (two in common, i.e., Bo4g173780 and Bo4g173810) were found. Along with studies in which R genes were frequently involved in hybrid lethality in other plants, these interesting R-DEGs may be good candidates associated with hybrid lethality. We also used SNP/InDel analyses and quantitative real-time PCR to confirm the results. This work provides new insight into the mechanisms of hybrid lethality in cabbage. Full article
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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6678 KiB  
Article
Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium
by Jiao Yang, Ming Yue, Chuan Niu, Xiong-Feng Ma and Zhong-Hu Li
Genes 2017, 8(4), 124; https://0-doi-org.brum.beds.ac.uk/10.3390/genes8040124 - 19 Apr 2017
Cited by 43 | Viewed by 6971
Abstract
Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete [...] Read more.
Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing. We investigated the gene organization, order, size and repeat sequences of the cp genome and constructed the phylogenetic relationships of Notopterygium species based on the chloroplast DNA and nuclear internal transcribed spacer (ITS) sequences. Comparative analysis of plastid genome showed that the cp DNA are the standard double-stranded molecule, ranging from 157,462 bp (N. oviforme) to 159,607 bp (N. forrestii) in length. The circular DNA each contained a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs). The cp DNA of four species contained 85 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes, respectively. We determined the marked conservation of gene content and sequence evolutionary rate in the cp genome of four Notopterygium species. Three genes (psaI, psbI and rpoA) were possibly under positive selection among the four sampled species. Phylogenetic analysis showed that four Notopterygium species formed a monophyletic clade with high bootstrap support. However, the inconsistent interspecific relationships with the genus Notopterygium were identified between the cp DNA and ITS markers. The incomplete lineage sorting, convergence evolution or hybridization, gene infiltration and different sampling strategies among species may have caused the incongruence between the nuclear and cp DNA relationships. The present results suggested that Notopterygium species may have experienced a complex evolutionary history and speciation process. Full article
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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Review

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14 pages, 1879 KiB  
Review
Genome Size Diversity and Its Impact on the Evolution of Land Plants
by Jaume Pellicer, Oriane Hidalgo, Steven Dodsworth and Ilia J. Leitch
Genes 2018, 9(2), 88; https://0-doi-org.brum.beds.ac.uk/10.3390/genes9020088 - 14 Feb 2018
Cited by 211 | Viewed by 15159
Abstract
Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our understanding of the implications and significance of [...] Read more.
Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our understanding of the implications and significance of this remarkable genome size diversity in land plants grows, it is becoming increasingly evident that this trait plays not only an important role in shaping the evolution of plant genomes, but also in influencing plant community assemblages at the ecosystem level. Recent advances and improvements in novel sequencing technologies, as well as analytical tools, make it possible to gain critical insights into the genomic and epigenetic mechanisms underpinning genome size changes. In this review we provide an overview of our current understanding of genome size diversity across the different land plant groups, its implications on the biology of the genome and what future directions need to be addressed to fill key knowledge gaps. Full article
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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Other

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2109 KiB  
Brief Report
Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Bread Wheat (Triticum aestivum L.)
by Haoshuang Zhan, Hong Yue, Xian Zhao, Meng Wang, Weining Song and Xiaojun Nie
Genes 2017, 8(10), 284; https://doi.org/10.3390/genes8100284 - 20 Oct 2017
Cited by 39 | Viewed by 5553
Abstract
The mitogen-activated protein kinase (MAPK) cascade is a universal signal transduction module that plays a vital role in regulating growth and development, as well as environmental stress responses in plants. Wheat is one of the most important crops worldwide. Although the MAPK kinase [...] Read more.
The mitogen-activated protein kinase (MAPK) cascade is a universal signal transduction module that plays a vital role in regulating growth and development, as well as environmental stress responses in plants. Wheat is one of the most important crops worldwide. Although the MAPK kinase kinase (MAP3K) family in wheat has been investigated, the MAPK and MAPK kinase (MAP2K) gene families remain unknown at present. Here, 54 MAPK and 18 MAPKK genes were identified in wheat using recent genomic information. Phylogenetic analysis of Triticum aestivum L. MAPKs and MAPKKs (TaMAPKs and TaMAPKKs) together with homologous genes from other species classified them into four groups, and the clustering was consistent with the genomic exon/intron structures. Conserved motif analysis found that MAPK proteins contained a typical TXY phosphorylation site and MAPKK proteins contained an S/T-X5-S/T motif. RNA-seq data mapping analysis showed that MAPK and MAPKK genes in group IV had tissue-specific expression profiles, whereas each group I member showed relatively high expression in all organs. Expression patterns of TaMAPK and TaMAPKK genes under stress conditions were also investigated and stress-responsive candidates were identified. Co-expression network analysis identified 11 TaMAPK genes and 6 TaMAPKK genes involved in the interaction network pathway. Overall, this study provided useful information for evolutionary and functional surveys of MAPK and MAPKK gene families in wheat and beyond. Full article
(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
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