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Life
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Genome Evolution Mechanism of Plant Polyploids
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Genome Evolution Mechanism of Plant Polyploids

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Plant Science".

Deadline for manuscript submissions: closed (30 December 2022) | Viewed by 6063

Special Issue Editors

Prof. Dr. Xiaoming Song

E-Mail Website
Guest Editor
School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
Interests: plant genome evolution; comparative genomics; gene family; RNA-seq; expression network; non-coding RNA; database construction
Special Issues, Collections and Topics in MDPI journals
Dr. Weike Duan

E-Mail Website
Guest Editor
College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China
Interests: plant genome; gene family; comparative genomics; evolution; expression pattern analysis
Dr. Peng Wu

E-Mail Website
Guest Editor
School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225000, China
Interests: plant genome; adaptive evolution; polyploidization; metabolomics; transcriptome

Special Issue Information

Dear Colleagues,

Polyploidy or whole-genome duplication/triplication (WGD/T) is widespread in plants, and more than 70% of flowering plants are polyploids. Generally, polyploids are classified into autopolyploids and allopolyploids based on their origin and chromosomal composition. Polyploidization is an important driving force for plant evolution, speciation and domestication. Polyploidy is often accompanied by changes in genome structure, chromosomal rearrangement, gene duplication or loss and gene expression bias. Therefore, the study of the formation mechanism of plant polyploidy and the series of changes after polyploidy has important guiding significance for crop genetics and breeding guided by genomics in the future. With the completion of more and more plant genome and pan-genome sequencing, it provides us with rich genomic data resources to study the generation and impact of plant polyploidy. Meanwhile, based on a large number of transcriptomic and metabolomic data, the effects of plant polyploidy on gene expression, metabolism and complex trait regulatory networks can be explored. Together with the rich omics resources and advanced bioinformatics tools, we hope to further explore plant genome evolution. Therefore, we organized this Special Issue about “Genome Evolution Mechanism of Plant Polyploids”. This Special Issue will be devoted to the evolution of polyploidization in plants, and especially for horticultural plants. This Special Issue will mainly collect articles on aspects including, but not limited to : (a) exploration of the formation factors and modes of plant genome polyploidy; (b) effects of plant polyploidy on genome structure and gene retention or loss; (c) effects of plant genome polyploidization on the expansion or contraction of important functional gene families on a large scale; (d) effects of plant genome polyploidization on gene regulatory networks of complex agronomic traits; (e) omics data resource databases, pipelines or tools that can promote the study of plant genome evolution.

Dr. Xiaoming Song
Dr. Weike Duan
Dr. Peng Wu
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. Life 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 evolution
  • plant polyploids
  • comparative genomics
  • gene family
  • expression patterns
  • regulatory networks
  • database construction

Published Papers (4 papers)

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Research

17 pages, 2153 KiB  
Article
Allopolyploidy: An Underestimated Driver in Juniperus Evolution
by Perla Farhat, Sonja Siljak-Yakovlev, Najat Takvorian, Magda Bou Dagher Kharrat and Thierry Robert
Life 2023, 13(7), 1479; https://doi.org/10.3390/life13071479 - 30 Jun 2023
Viewed by 878
Abstract
Allopolyploidy is considered as a principal driver that shaped angiosperms’ evolution in terms of diversification and speciation. Despite the unexpected high frequency of polyploidy that was recently discovered in the coniferous genus Juniperus, little is known about the origin of these polyploid [...] Read more.
Allopolyploidy is considered as a principal driver that shaped angiosperms’ evolution in terms of diversification and speciation. Despite the unexpected high frequency of polyploidy that was recently discovered in the coniferous genus Juniperus, little is known about the origin of these polyploid taxa. Here, we conducted the first study devoted to deciphering the origin of the only hexaploid taxon in Juniperus along with four of its closely related tetraploid taxa using AFLP markers with four primers combinations. Phylogenetic analysis revealed that the 10 studied species belong to 2 major clusters. J. foetidissima appeared to be more related to J. thurifera, J. sabina, and J. chinensis. The Bayesian clustering analysis showing a slight variation in genetic admixture between the studied populations of J. foetidissima, suggesting an allopolyploid origin of this species involving J. thurifera and J. sabina lineages, although a purely autopolyploidy origin of both J. thurifera and J. foetidissima cannot be ruled out. The admixed genetic pattern revealed for J. seravschanica showed that the tetraploid cytotypes of this species originated from allopolyploidy, whereas no clear evidence of hybridization in the origin of the tetraploid J. thurifera and J. chinensis was detected. This study provides first insights into the polyploidy origin of the Sabina section and highlights the potential implication of allopolyploidy in the evolution of the genus Juniperus. Further analyses are needed for a more in-depth understanding of the evolutionary scenarios that produced the observed genetic patterns. Full article
(This article belongs to the Special Issue Genome Evolution Mechanism of Plant Polyploids)
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17 pages, 7750 KiB  
Article
iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions
by Xu Yang, Zheng Jiang, Jie He and Lei Shen
Life 2023, 13(6), 1399; https://doi.org/10.3390/life13061399 - 15 Jun 2023
Cited by 3 | Viewed by 1008
Abstract
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein [...] Read more.
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose–bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress. Full article
(This article belongs to the Special Issue Genome Evolution Mechanism of Plant Polyploids)
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17 pages, 63618 KiB  
Article
Genome-Wide Analysis of the NAC Family Associated with Two Paleohexaploidization Events in the Tomato
by Jiale Yuan, Ying Liu, Zhenyi Wang, Tianyu Lei, Yanfang Hu, Lan Zhang, Min Yuan, Jinpeng Wang and Yuxian Li
Life 2022, 12(8), 1236; https://doi.org/10.3390/life12081236 - 15 Aug 2022
Cited by 2 | Viewed by 1567
Abstract
NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (S. lycopersicum) and 88 [...] Read more.
NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (S. lycopersicum) and 88 (S. pennellii) members of the NAC family were present in two tomatoes, and most of them were amplified from two paleohexaploidizations. We differentiated NAC family members from the different paleohexaploidizations and found that the SWGT-derived NAC genes had more rearrangement events, so it was different from the DWGT-derived NAC genes in terms of physicochemical properties, phylogeny, and gene location. The results of selection pressure show that DWGT-derived NAC genes tended to be positively selected in S. lycopersicum and negatively selected in S. pennellii. A comprehensive analysis of paleopolyploidization and expression reveals that DWGT-derived NAC genes tend to promote fruit ripening, and are expressed at the early and middle stages, whereas SWGT-derived NAC genes tend to terminate fruit growth and are expressed at the late stages of fruit ripening. This study obtained NAC genes from different sources that can be used as materials for tomato fruit development, and the method in the study can be extended to the study of other plants. Full article
(This article belongs to the Special Issue Genome Evolution Mechanism of Plant Polyploids)
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10 pages, 2507 KiB  
Communication
LSAP: A Machine Learning Method for Leaf-Senescence-Associated Genes Prediction
by Zhidong Li, Wei Tang, Xiong You and Xilin Hou
Life 2022, 12(7), 1095; https://doi.org/10.3390/life12071095 - 21 Jul 2022
Cited by 3 | Viewed by 1676
Abstract
Plant leaves, which convert light energy into chemical energy, serve as a major food source on Earth. The decrease in crop yield and quality is caused by plant leaf premature senescence. It is important to detect senescence-associated genes. In this study, we collected [...] Read more.
Plant leaves, which convert light energy into chemical energy, serve as a major food source on Earth. The decrease in crop yield and quality is caused by plant leaf premature senescence. It is important to detect senescence-associated genes. In this study, we collected 5853 genes from a leaf senescence database and developed a leaf-senescence-associated genes (SAGs) prediction model using the support vector machine (SVM) and XGBoost algorithms. This is the first computational approach for predicting SAGs with the sequence dataset. The SVM-PCA-Kmer-PC-PseAAC model achieved the best performance (F1score = 0.866, accuracy = 0.862 and receiver operating characteristic = 0.922), and based on this model, we developed a SAGs prediction tool called “SAGs_Anno”. We identified a total of 1,398,277 SAGs from 3,165,746 gene sequences from 83 species, including 12 lower plants and 71 higher plants. Interestingly, leafy species showed a higher percentage of SAGs, while leafless species showed a lower percentage of SAGs. Finally, we constructed the Leaf SAGs Annotation Platform using these available datasets and the SAGs_Anno tool, which helps users to easily predict, download, and search for plant leaf SAGs of all species. Our study will provide rich resources for plant leaf-senescence-associated genes research. Full article
(This article belongs to the Special Issue Genome Evolution Mechanism of Plant Polyploids)
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