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Comparative Genomics and Functional Genomics Analysis in Plants 2.0
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Comparative Genomics and Functional Genomics Analysis in Plants 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 4863

Special Issue Editors

Prof. Dr. Quan Zou

grade E-Mail Website
Guest Editor
Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
Interests: bioinformatics; machine learning; parallel computing
Special Issues, Collections and Topics in MDPI journals
Dr. Ran Su

E-Mail Website
Guest Editor
School of Computer Software, Tianjin University, Tianjin 300350, China
Interests: biomedical image analysis; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since the first plant genome Arabidopsis thaliana was published in December 2000, over 1000 plant genomes, representing different plant species or subspecies, have been sequenced and published. With the development of sequencing technology, increasing numbers of omics datasets have been released, such as pan-genomics, proteomics, transcriptomics, and metabolomics datasets. It is important to highlight that the quick accumulation of omics datasets has greatly promoted the development of plant science, especially crop genetics and breeding. In recent years, even though many bioinformatic tools have been developed for omics analyses, there are still many challenges, from the construction of complex plant genomes to multi-omics analyses; hence, more advanced algorithms, more powerful pan-genome analysis tools, and more comprehensive databases still need to be developed.

Polyploidy, heterozygosity, and large genomes in plants are still the main obstacles to plant genome sequencing and assembly. We believe that future studies about omics analyses in plants can progress by incorporating more advanced technologies. Therefore, we have organized this Special Issue on “Comparative Genomics and Functional Genomics Analysis in Plants 2.0” to help us to better understand plant genome or gene function and evolution and provide resources for decoding the molecular mechanism of complex agronomic traits. 

We are pleased to invite you to participate to this Special Issue on “Comparative Genomics and Functional Genomics Analysis in Plants”. Research papers, up-to-date review articles, and commentaries are all welcome.

Prof. Dr. Quan Zou
Dr. Ran Su
Guest Editors

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • de novo genome sequencing
  • pan-genomic analyses
  • genome re-sequencing
  • WAS analyses
  • RNA-seq
  • metabolomics
  • gene family analyses
  • plant evolutionary analyses
  • bioinformatics
  • database
 

Related Special Issue

Published Papers (3 papers)

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Research

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23 pages, 2861 KiB  
Article
Transcriptomic Analyses Reveal the Role of Cytokinin and the Nodal Stem in Microtuber Sprouting in Potato (Solanum tuberosum L.)
by Xia Zhang, Kaien Fujino and Hanako Shimura
Int. J. Mol. Sci. 2023, 24(24), 17534; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms242417534 - 15 Dec 2023
Viewed by 914
Abstract
In potatoes, tuber secondary growth, especially sprouting, deforms the tubers and severely lowers their commercial value. Tuber sprouting is induced by signal substances, such as gibberellin (GA), which are transported to the tuber from the plant body. The molecular mechanism underlying GA-induced sprouting [...] Read more.
In potatoes, tuber secondary growth, especially sprouting, deforms the tubers and severely lowers their commercial value. Tuber sprouting is induced by signal substances, such as gibberellin (GA), which are transported to the tuber from the plant body. The molecular mechanism underlying GA-induced sprouting remains ambiguous. Here, we tried to recreate tuber secondary growth using in vitro stemmed microtubers (MTs) (with the nodal stem attached) and MT halves (with the nodal stem entirely removed). Our experiments showed that GA alone could initiate the sprouting of stemmed microtubers; however, GA failed to initiate MT halves unless 6-benzyladenine, a synthetic cytokinin CK, was co-applied. Here, we analyzed the transcriptional profiles of sprouting buds using these in vitro MTs. RNA-seq analysis revealed a downregulation of cytokinin-activated signaling but an upregulation of the “Zeatin biosynthesis” pathway, as shown by increased expression of CYP735A, CISZOG, and UGT85A1 in sprouting buds; additionally, the upregulation of genes, such as IAA15, IAA22, and SAUR50, associated with auxin-activated signaling and one abscisic acid (ABA) negative regulator, PLY4, plays a vital role during sprouting growth. Our findings indicate that the role of the nodal stem is synonymous with CK in sprouting growth, suggesting that CK signaling and homeostasis are critical to supporting GA-induced sprouting. To effectively control tuber sprouting, more effort is required to be devoted to these critical genes. Full article
(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants 2.0)
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14 pages, 3602 KiB  
Article
Transcriptomic and Metabolomic Analyses Reveal the Roles of Flavonoids and Auxin on Peanut Nodulation
by Jianguo Wang, Ruining Diao, Zhengfeng Wu, Shubo Wan, Sha Yang and Xinguo Li
Int. J. Mol. Sci. 2023, 24(12), 10152; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241210152 - 15 Jun 2023
Viewed by 1284
Abstract
Rhizobia form symbiotic relationships with legumes, fixing atmospheric nitrogen into a plant-accessible form within their root nodules. Nitrogen fixation is vital for sustainable soil improvements in agriculture. Peanut (Arachis hypogaea) is a leguminous crop whose nodulation mechanism requires further elucidation. In [...] Read more.
Rhizobia form symbiotic relationships with legumes, fixing atmospheric nitrogen into a plant-accessible form within their root nodules. Nitrogen fixation is vital for sustainable soil improvements in agriculture. Peanut (Arachis hypogaea) is a leguminous crop whose nodulation mechanism requires further elucidation. In this study, comprehensive transcriptomic and metabolomic analyses were conducted to assess the differences between a non-nodulating peanut variety and a nodulating peanut variety. Total RNA was extracted from peanut roots, then first-strand and second-strand cDNA were synthesized and purified. After sequencing adaptors were added to the fragments, the cDNA libraries were sequenced. Our transcriptomic analysis identified 3362 differentially expressed genes (DEGs) between the two varieties. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that the DEGs were mainly involved in metabolic pathways, hormone signal transduction, secondary metabolic biosynthesis, phenylpropanoid biosynthesis, or ABC transport. Further analyses indicated that the biosynthesis of flavonoids, such as isoflavones, flavonols, and flavonoids, was important for peanut nodulation. A lack of flavonoid transport into the rhizosphere (soil) could prevent rhizobial chemotaxis and the activation of their nodulation genes. The downregulation of AUXIN-RESPONSE FACTOR (ARF) genes and lower auxin content could reduce rhizobia’s invasion of peanut roots, ultimately reducing nodule formation. Auxin is the major hormone that influences the cell-cycle initiation and progression required for nodule initiation and accumulates during different stages of nodule development. These findings lay the foundation for subsequent research into the nitrogen-fixation efficiency of peanut nodules. Full article
(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants 2.0)
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Review

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21 pages, 6150 KiB  
Review
Genetic and Epigenetic Mechanisms of Longevity in Forest Trees
by Anastasia Y. Batalova and Konstantin V. Krutovsky
Int. J. Mol. Sci. 2023, 24(12), 10403; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241210403 - 20 Jun 2023
Cited by 4 | Viewed by 2085
Abstract
Trees are unique in terms of development, sustainability and longevity. Some species have a record lifespan in the living world, reaching several millennia. The aim of this review is to summarize the available data on the genetic and epigenetic mechanisms of longevity in [...] Read more.
Trees are unique in terms of development, sustainability and longevity. Some species have a record lifespan in the living world, reaching several millennia. The aim of this review is to summarize the available data on the genetic and epigenetic mechanisms of longevity in forest trees. In this review, we have focused on the genetic aspects of longevity of a few well-studied forest tree species, such as Quercus robur, Ginkgo biloba, Ficus benghalensis and F. religiosa, Populus, Welwitschia and Dracaena, as well as on interspecific genetic traits associated with plant longevity. A key trait associated with plant longevity is the enhanced immune defense, with the increase in gene families such as RLK, RLP and NLR in Quercus robur, the expansion of the CC-NBS-LRR disease resistance families in Ficus species and the steady expression of R-genes in Ginkgo biloba. A high copy number ratio of the PARP1 family genes involved in DNA repair and defense response was found in Pseudotsuga menziesii, Pinus sylvestris and Malus domestica. An increase in the number of copies of the epigenetic regulators BRU1/TSK/MGO3 (maintenance of meristems and genome integrity) and SDE3 (antiviral protection) was also found in long-lived trees. CHG methylation gradually declines in the DAL 1 gene in Pinus tabuliformis, a conservative age biomarker in conifers, as the age increases. It was shown in Larix kaempferi that grafting, cutting and pruning change the expression of age-related genes and rejuvenate plants. Thus, the main genetic and epigenetic mechanisms of longevity in forest trees were considered, among which there are both general and individual processes. Full article
(This article belongs to the Special Issue Comparative Genomics and Functional Genomics Analysis in Plants 2.0)
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