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Diversity
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Phylogenetics of Stress Regulators in Plants
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Phylogenetics of Stress Regulators in Plants

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Plant Diversity".

Deadline for manuscript submissions: closed (15 August 2022) | Viewed by 10547

Special Issue Editors

Dr. Xiang Yu

E-Mail Website
Guest Editor
Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
Interests: RNA modification; RNA silencing; RNA degradation; post-transcriptional regulation; plant-stress response
Special Issues, Collections and Topics in MDPI journals
Dr. Yan Bao

E-Mail Website
Guest Editor
School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: plant stress response; drought; autophagy; gene evolution; vitamin metabolism

Special Issue Information

Dear Colleagues,

Multiple layers of molecular regulators that play a role in plant tolerance to environmental stresses have been revealed in model plants and some crops. For example, stress-responsive transcriptional factors (transcriptional regulators), writers, readers, and erasers of RNA modifications (post-transcriptional regulators), proteins involved in phosphorylation and autophagy (post-translational regulators) and metabolic enzymes function in plant resistance to abiotic and biotic stress. However, the phylogenetics of these stress regulators in crop species and horticultural plants, including vegetables, flowers, and trees, remain largely unexplored. Gene families undergo duplication or depletion among different species and evolve diverse molecular functions under environmental pressure. With the advance of high-throughput sequencing, many plant genomes have been assembled, and substantial transcriptome profiling has been performed in these plants under stress conditions. This information opens a window for us to identify and characterize gene families and their expression pattern response to stress.

For this Special Issue, we invite submissions that address phylogenetics of stress regulators, focusing on the gain and loss of particular gene families in plants, and how these genes respond to variant environmental cues, which potentially contribute to plant defense and stress tolerance.

This Special Issue “Phylogenetics of Stress Regulators in Plants" is a platform for the transfer of current knowledge from model plants to broader plant species, and to reveal diverse stress response of regulatory genes in plants.

Dr. Xiang Yu
Dr. Yan Bao
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. Diversity 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

  • Phylogenetics
  • Stress response
  • Plant tolerance
  • Transcriptional regulators
  • Post-transcriptional regulation
  • Autophagy
  • Horticulture
  • Gene evolution
  • Metabolic evolution

Published Papers (4 papers)

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Editorial

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4 pages, 182 KiB  
Editorial
Phylogenetics of Molecular Regulators Contributing to Plant Stress Tolerance
by Xiang Yu and Yan Bao
Diversity 2020, 12(10), 407; https://doi.org/10.3390/d12100407 - 21 Oct 2020
Viewed by 2142
Abstract
Genetic studies on model plants and crops in the last few decades have uncovered numerous genes that play vital roles in plant tolerance to adverse environments. These genes could be used as targets for genetic engineering to improve plant tolerance to abiotic and [...] Read more.
Genetic studies on model plants and crops in the last few decades have uncovered numerous genes that play vital roles in plant tolerance to adverse environments. These genes could be used as targets for genetic engineering to improve plant tolerance to abiotic and biotic stresses. Recent advances in CRISPR-based genome editing have accelerated modern plant breeding and wild-species domestication. However, the stress regulators in many crops and horticultural cultivars and their wild species remain largely unexplored. Thus, transferring the accumulated knowledge of these molecular regulators from model plants to a wider range of other species is critical for modern plant breeding. Phylogenetic analysis is one of the powerful strategies for studying the functional conservation and diversity of homologous gene families among different species with complete genome sequences available. In addition, many transcriptome datasets of plants under stress conditions have been publicly released, providing a useful resource for addressing the stress response of given gene families. This Special Issue aims to illustrate the phylogenetics of molecular regulators with potential in contributing to plant stress tolerance and their stress response diversity in multiple non-model plants. Full article
(This article belongs to the Special Issue Phylogenetics of Stress Regulators in Plants)

Research

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17 pages, 4410 KiB  
Article
Genome-Wide Analysis and Expression Profiling of HD-ZIP III Genes in Three Brassica Species
by Han Wang, Wenna Shao, Min Yan, Ye Xu, Shaohua Liu and Renlei Wang
Diversity 2021, 13(12), 684; https://doi.org/10.3390/d13120684 - 20 Dec 2021
Cited by 1 | Viewed by 2534
Abstract
Class III homeodomain-leucine zipper (HD-ZIP III) genes encode plant-specific transcription factors that play pivotal roles in plant growth and development. There is no systematic report on HD-ZIP III members in Brassica plants and their responses to stress are largely unknown. In this study, [...] Read more.
Class III homeodomain-leucine zipper (HD-ZIP III) genes encode plant-specific transcription factors that play pivotal roles in plant growth and development. There is no systematic report on HD-ZIP III members in Brassica plants and their responses to stress are largely unknown. In this study, a total of 10, 9 and 16 HD-ZIP III genes were identified from B. rapa, B. oleracea and B. napus, respectively. The phylogenetic analysis showed that HD-ZIP III proteins were grouped into three clades: PHB/PHV, REV and CNA/HB8. Genes in the same group tended to have similar exon–intron structures. Various phytohormone-responsive elements and stress-responsive elements were detected in the promoter regions of HD-ZIP III genes. Gene expression levels in different tissues, as well as under different stress conditions, were investigated using public transcription profiling data. The HD-ZIP III genes were constitutively expressed among all the tested tissues and were highly accumulated in root and stem. In B. rapa, only one BrREV gene especially responded to heat stress, BrPHB and BrREV members were downregulated upon cold stress and most HD-ZIP III genes exhibited divergent responses to drought stress. In addition, we investigated the genetic variation at known miR165/166 complementary sites of the identified HD-ZIP III genes and found one single nucleotide polymorphism (SNP) in PHB members and two SNPs in REV members, which were further confirmed using Sanger sequencing. Taken together, these results provide information for the genome-wide characterization of HD-ZIP III genes and their stress response diversity in Brassica species. Full article
(This article belongs to the Special Issue Phylogenetics of Stress Regulators in Plants)
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14 pages, 2907 KiB  
Article
Global Characterization of XRN 5′-3′ Exoribonucleases and Their Responses to Environmental Stresses in Plants
by Weimeng Song, Yanjie Li, Yue Niu, You Wu, Yan Bao and Xiang Yu
Diversity 2021, 13(12), 612; https://doi.org/10.3390/d13120612 - 24 Nov 2021
Cited by 1 | Viewed by 1942
Abstract
The XRN family of 5′-3′ Exoribonucleases is functionally conserved in eukaryotic organisms. However, the molecular evolution of XRN proteins in plants and their functions in plant response to environment stresses remain largely unexplored. In this study, we identified 23 XRN proteins in 6 [...] Read more.
The XRN family of 5′-3′ Exoribonucleases is functionally conserved in eukaryotic organisms. However, the molecular evolution of XRN proteins in plants and their functions in plant response to environment stresses remain largely unexplored. In this study, we identified 23 XRN proteins in 6 representative plant species. Polygenetic analysis revealed that XRN2 was Arabidopsis-specific among these species, and additional branches outside the clades of XRN3 and XRN4 proteins, which we named as XRN5, were found in rice, maize, and soybean. However, XRN5 in soybean lost their entire 5′-3′ XRN Exoribonuclease domain. Protein conserved sequence analysis showed that XRN3/XRN2 contained potential bipartite nuclear-localization signals (NLS) while all the XRN4 proteins lost their second KR/RR motif of NLS, potentially leading to their cytoplasm localization. SIXRN3-2 contained one mutation in this second KR/RR motif, which may change their sub-cellular localization. The promoter cis-element analysis indicated that these XRN genes responded to multiple stresses and plant hormones diversely at transcriptional level. Finally, transcriptomic analysis suggested that OsXRN3 and ZmXRN3-1 were induced by low temperature, SIXRN4 and ZmXRN4 was inhibited by heat shock, and OsXRN5 and GmXRN5-2 were repressed by drought. However, in general, the expression patterns revealed the response diversity of XRNs to environment stimuli in different plant species. Taken together, this study characterized 23 XRNs with NLS variation that contributed to their sub-cellular localization and provided an overview of the XRNs response diversity to multiple environmental stresses, suggesting that XRNs could be used as potential gene editing candidates for precise stress-tolerant crop breeding. Full article
(This article belongs to the Special Issue Phylogenetics of Stress Regulators in Plants)
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18 pages, 2930 KiB  
Article
Genome-Wide Identification and Characterization of Cysteine-Rich Receptor-Like Protein Kinase Genes in Tomato and Their Expression Profile in Response to Heat Stress
by Yahui Liu, Zhengxiang Feng, Weimin Zhu, Junzhong Liu and Yingying Zhang
Diversity 2021, 13(6), 258; https://doi.org/10.3390/d13060258 - 10 Jun 2021
Cited by 13 | Viewed by 2955
Abstract
During plant growth, development and stress adaption, receptor-like protein kinases (RLKs) are essential components in perceiving and integrating extracellular stimuli and transmitting the signals to activate the downstream signaling pathways. Cysteine-rich receptor-like protein kinases (CRKs) are a large subfamily of RLKs and their [...] Read more.
During plant growth, development and stress adaption, receptor-like protein kinases (RLKs) are essential components in perceiving and integrating extracellular stimuli and transmitting the signals to activate the downstream signaling pathways. Cysteine-rich receptor-like protein kinases (CRKs) are a large subfamily of RLKs and their roles in modulating plant disease resistance are well elucidated. However, the roles of CRKs in plant abiotic stress responses, especially heat stress, are largely unknown. In this study, 35 SlCRK genes were identified in tomato (Solanum lycopersicum) based on the multiple sequence alignment and phylogenetic relationships. SlCRK genes are tandemly distributed on seven chromosomes and have similar exon–intron organization and common conserved motifs. Various phytohormone responsive, stress responsive cis-regulatory elements and heat shock elements are predicted in the promoter regions of SlCRK genes. Transcriptome analysis of tomato fruits under heat stress revealed that most SlCRK genes were downregulated upon heat treatment. GO enrichment analyses of genes that were co-expressed with SlCRK members have identified various stress responses related and proteasomal protein catabolic process related genes, which may be involved in heat stress signaling. Overall, our results provide valuable information for further research on the roles of SlCRKs in response to abiotic stress, especially heat stress. Full article
(This article belongs to the Special Issue Phylogenetics of Stress Regulators in Plants)
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