Special Issue "Comparative Omics Analyses in Plant Evolution"

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: closed (28 February 2020).

Special Issue Editor

Dr. Marek Mutwil
E-Mail Website
Guest Editor
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
Interests: comparative transcriptomics; plant evolution; co-expression; specialized metabolism
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Studying plant evolution can reveal principles of the emergence of novel traits, such as multicellularity, adaptation to terrestrial growth, sexual reproduction, and hormone signaling. Typically, the evolution of these traits is studied through comparative genomic and phylogenomic analyses, which assume that the traits emerge and evolve as gene families. However, genes and gene families form higher-order functional units (gene modules), such as protein complexes and enzymatic pathways, which employ multiple genes from different gene families. These gene modules can be identified by analyzing omics data, such as protein–protein interaction networks, and by identifying transcriptionally co-regulated (co-expressed) genes, among others. Therefore, a more rewarding approach to explain the evolution of new traits, adaptations, and gene functions should by necessity compare omics data across different experiments and species. However, the methods to compare omics data across experiments and species are still not fully developed.

This Special Issue is poised to address the studies, approaches, and databases that compare omics data, such as genomics, transcriptomics, proteomics, and metabolomics, across members of the Archaeplastida.

Dr. Marek Mutwil
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 papers will be 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. Plants 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 1800 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

  • Gene function prediction
  • Comparative omics
  • Evolution of traits
  • Comparative databases
  • Reverse genetics

Published Papers (1 paper)

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Review

Review
Co-regulation of Clustered and Neo-functionalized Genes in Plant-Specialized Metabolism
Plants 2020, 9(5), 622; https://doi.org/10.3390/plants9050622 - 13 May 2020
Cited by 4 | Viewed by 1360
Abstract
Current findings of neighboring genes involved in plant specialized metabolism provide the genomic signatures of metabolic evolution. Two such genomic features, namely, (i) metabolic gene cluster and (ii) neo-functionalization of tandem gene duplications, represent key factors corresponding to the creation of metabolic diversity [...] Read more.
Current findings of neighboring genes involved in plant specialized metabolism provide the genomic signatures of metabolic evolution. Two such genomic features, namely, (i) metabolic gene cluster and (ii) neo-functionalization of tandem gene duplications, represent key factors corresponding to the creation of metabolic diversity of plant specialized metabolism. So far, several terpenoid and alkaloid biosynthetic genes have been characterized with gene clusters in some plants. On the other hand, some modification genes involved in flavonoid and glucosinolate biosynthesis were found to arise via gene neo-functionalization. Although the occurrence of both types of metabolic evolution are different, the neighboring genes are generally regulated by the same or related regulation factors. Therefore, the translation-based approaches associated with genomics, and transcriptomics are able to be employed for functional genomics focusing on plant secondary metabolism. Here, we present a survey of the current understanding of neighboring genes involved in plant secondary metabolism. Additionally, a genomic overview of neighboring genes of four model plants and transcriptional co-expression network neighboring genes to detect metabolic gene clusters in Arabidopsis is provided. Finally, the insights functional genomics have provided concerning the evolution and mechanistic regulation of both the formation and operation of metabolic neighboring clusters is discussed. Full article
(This article belongs to the Special Issue Comparative Omics Analyses in Plant Evolution)
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