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15th Anniversary of Genes: Feature Papers in the “Plant...
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15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section

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

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 4063

Special Issue Editors

Prof. Dr. Jacqueline Batley

grade E-Mail Website
Guest Editor
School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
Interests: crop genomics; brassica; disease resistance; pan genomics; evolutionary genomics; population genomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Roberto Tuberosa

E-Mail
Guest Editor
Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
Interests: crop genomics; quantitative trait loci cloning; maize; durum wheat; barley; tilling; wheat pangenome: drought resistance; disease resistance; root system architecture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, “15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section”, will gather high-quality research articles, reviews, and communications on advances in research in plant genetics and genomics, celebrating the 15th anniversary of Genes and the 10th anniversary of the journal receiving its first impact factor. As our aim for this Special Issue is to illustrate, through selected works, frontier research in the field of plant genetics and genomics, we encourage Editorial Board Members for the “Plant Genetics and Genomics” Section to contribute feature papers reflecting the latest progress in their research field or to invite relevant senior experts and colleagues to contribute to this Special Issue. We aim to showcase our Section as an attractive open access publishing platform for plant genetics research.

Possible topics include, but are not limited to, the following:

  • Mechanisms of plant gene regulation;
  • Phylogenomics and evolutionary plant genetics;
  • Gene silencing and miRNAs;
  • QTL mapping and cloning;
  • Chromatin organization;
  • Epigenetics and epigenomics;
  • Plastid genomic studies;
  • Genetic engineering for crop production;
  • Pangenomes.

Prof. Dr. Jacqueline Batley
Prof. Dr. Roberto Tuberosa
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 250 words) can be sent to the Editorial Office for assessment.

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

  • epigenetic editing
  • genetics
  • genomics
  • pangenome
  • plants
  • QTL mapping
  • QTL cloning
  • regulation of gene expression
  • transcriptome

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

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Research

16 pages, 2393 KB  
Article
Plastome Evolution in Viburnum (Adoxaceae): Comparative Genomics Reveals Hypervariable Markers and Relaxed Selection on Protein Import Genes
by Lanruo Mou, Qiang Zhang, Bingyue Zhu, Chao Shi and Jing Yang
Genes 2026, 17(2), 196; https://doi.org/10.3390/genes17020196 - 6 Feb 2026
Viewed by 372
Abstract
Background: Viburnum (Adoxaceae) is a species-rich woody genus whose taxonomy is complicated by morphological convergence and hybridization. Methods: We assembled complete plastomes of eight species representing five sections and analyzed their structural variation, sequence divergence, and molecular evolution. Results: All plastomes displayed the [...] Read more.
Background: Viburnum (Adoxaceae) is a species-rich woody genus whose taxonomy is complicated by morphological convergence and hybridization. Methods: We assembled complete plastomes of eight species representing five sections and analyzed their structural variation, sequence divergence, and molecular evolution. Results: All plastomes displayed the conserved quadripartite structure typical of angiosperms, with limited size variation attributable primarily to intergenic spacer-length polymorphisms. Sequence divergence was unevenly distributed, with single-copy regions exhibiting substantially higher nucleotide diversity than inverted repeat regions. We identified multiple hypervariable intergenic spacers such as the region trnK-UUU–rps16, suitable as molecular markers for population genetics and species identification. Selection pressure analysis revealed that while most protein-coding genes evolved under strong purifying selection, three genes involved in fatty acid biosynthesis and protein import—accD, ycf1, and ycf2—showed significantly relaxed constraints, suggesting ongoing functional divergence. Phylogenetic analysis recovered well-supported relationships consistent with previous classifications, while clarifying the positions of Viburnum amplificatum and Viburnum tinus. Conclusions: These findings provide molecular resources for Viburnum systematics and offer insights into the evolutionary dynamics of plastome genes with non-photosynthetic functions. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section)
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16 pages, 3384 KB  
Article
Cloning and Characterization of IbHQT1: A BAHD Acyltransferase Gene That Positively Regulates Chlorogenic Acid Biosynthesis in Sweet Potato
by Lien Xiang, Xintong Wang, Jiaqi Zhao, Sheng Li and Quanlu Zhou
Genes 2026, 17(2), 123; https://doi.org/10.3390/genes17020123 - 25 Jan 2026
Viewed by 395
Abstract
Background: Hydroxycinnamoyl-CoA quinate hydroxycinnamoyl-transferase (HQT) is an essential enzyme for chlorogenic acid (CGA) biosynthesis in plants. Multiple HQT-encoding genes potentially involved in CGA synthesis in sweet potato (Ipomoea batatas) have been predicted. However, the functions of these genes have not [...] Read more.
Background: Hydroxycinnamoyl-CoA quinate hydroxycinnamoyl-transferase (HQT) is an essential enzyme for chlorogenic acid (CGA) biosynthesis in plants. Multiple HQT-encoding genes potentially involved in CGA synthesis in sweet potato (Ipomoea batatas) have been predicted. However, the functions of these genes have not been verified. Methods: In this study, the gene IbHQT1 was isolated from the sweet potato cultivar ‘Nanshu-88’ and functionally characterized using transgenic technology. Results: IbHQT1 encodes a protein comprising 431 amino acids, with conserved HXXXD and DFGWG motifs characteristic of BAHD acyltransferase family members. A phylogenetic analysis indicated that IbHQT1 has a close evolutionary relationship with StHQT in Solanum tuberosum. According to qPCR data, IbHQT1 is highly expressed in young leaves, and its expression is affected by exogenous MeJA (100 µM), ABA (100 µM), GA3 (50 µM), and SA (100 µM). Analyses of cis-acting regulatory elements indicated that the IbHQT1 promoter contains multiple elements responsive to MeJA, ABA, SA, GA3, and light. In plants overexpressing IbHQT1, CGA contents in mature leaves and storage roots increased 1.30- to 1.44-fold and 1.28- to 1.43-fold, respectively. Conversely, in IbHQT1-RNAi lines, CGA contents in mature leaves and storage roots decreased by 16–38% and 18–40%, respectively. Conclusions: These findings indicate that IbHQT1 positively regulates CGA biosynthesis in sweet potato plants. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section)
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26 pages, 5576 KB  
Article
The Complete Chloroplast Genome of Encyclia tampensis (Orchidaceae): Structural Variation and Heterogeneous Evolutionary Dynamics in Epidendreae
by Bing Liu, Ju Huang, Zishuo Wang, Dong Li, Zhangxi Yuan and Yi Yao
Genes 2025, 16(12), 1418; https://doi.org/10.3390/genes16121418 - 28 Nov 2025
Cited by 1 | Viewed by 600
Abstract
Background: The epiphytic orchids of the tribe Epidendreae represent a remarkably evolutionary radiation, yet their phylogenetic relationships and plastome evolutionary dynamics are still not fully resolved. Methods: This study has sequenced, assembled, and annotated the complete chloroplast genome of Encyclia tampensis. Through [...] Read more.
Background: The epiphytic orchids of the tribe Epidendreae represent a remarkably evolutionary radiation, yet their phylogenetic relationships and plastome evolutionary dynamics are still not fully resolved. Methods: This study has sequenced, assembled, and annotated the complete chloroplast genome of Encyclia tampensis. Through comparative analyses of a curated dataset of 40 Epidendreae plastomes, we investigated codon usage bias, evolutionary selection pressures (Ka/Ks), and phylogenetic relationships. Results: The plastome of E. tampensis (160,650 bp) has a typical quadripartite structure, with a significant AT bias (62.09%), and contains 124 annotated genes. Comparative genomic analysis across 40 Epidendreae species revealed substantial plastome size variation (123,455 to 160,650 bp), pronounced small single copy (SSC) contraction in E. tampensis (608 bp), and atypical long simple sequence repeats (SSRs) accumulation. Natural selection dominated codon usage, with strongest purifying selection in rbcL (average Ka/Ks = 0.205). Phylogenetic analyses confirmed subtribal monophyly and detected evolutionary rate heterogeneity correlated with life history strategies. Conclusions: These results establish that plastome evolution in Epidendreae has been principally driven by structural reorganization through SSC contraction and long SSR accumulation, selective constraints maintaining functional genes under purifying selection, and life history-strategy-mediated evolutionary rate diversification. These processes collectively account for the tribe’s extensive genomic diversity and phylogenetic complexity, thereby providing a theoretical framework for understanding orchid plastome evolution and a molecular basis for the systematic classification and conservation of this economically significant plant group. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section)
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16 pages, 6878 KB  
Article
Cotton STARD Gene Family: Characterization, Evolution, and Expression Profiles During Salt Stress
by Ruifeng Cui, Jiuguang Sun, Shuyan Li, Yupeng Cui, Cun Rui, Minshan Sun and Wuwei Ye
Genes 2025, 16(7), 813; https://doi.org/10.3390/genes16070813 - 11 Jul 2025
Viewed by 1123
Abstract
Background: Cotton, a key global economic crop, suffers yield and quality losses due to salt stress. This study aims to analyze the cotton STARD gene family and its role in salt stress responses. Methods: We conducted a genome-wide analysis of the [...] Read more.
Background: Cotton, a key global economic crop, suffers yield and quality losses due to salt stress. This study aims to analyze the cotton STARD gene family and its role in salt stress responses. Methods: We conducted a genome-wide analysis of the STARD gene family in four cotton species, using phylogenetic trees, chromosomal mapping, and collinearity analyses to explore their evolutionary relationships and expansion mechanisms. We also examined gene structures, conserved motifs, and promoter cis-elements. Results: STARD genes are evenly distributed across the four cotton species. Segmental duplication was found to be the main driver of gene expansion, with most pairs undergoing purifying selection. Distinct structural features and potential roles in plant growth and stress responses were identified. Notably, 11 GhSTARD genes showed significant expression changes under salt stress, especially GhSTARD45 in root tissues. Conclusions: This study provides new insights into the function and salt stress response mechanisms of the cotton STARD gene family, suggesting GhSTARD45 plays a key role in root-mediated salt tolerance and highlighting the potential of STARD genes in enhancing cotton’s salt tolerance. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section)
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13 pages, 1907 KB  
Article
Comprehensive Assembly and Comparative Analysis of Chloroplast Genome and Mitogenome of Prunus salicina var. cordata
by Ruyu Liao, Mengshi Zhao, Qin Lan, Song Peng, Fengqiang Lin and Zhaolong Li
Genes 2025, 16(6), 660; https://doi.org/10.3390/genes16060660 - 29 May 2025
Cited by 1 | Viewed by 1060
Abstract
Background: Prunus plants are widely distributed across Asia and Europe, yet their intricate phylogenetic relationships pose significant challenges for systematic studies and interspecies identification. Objectives: To clarify the mitochondrial and chloroplast genomes of Prunus salicina var. cordata, and to reveal [...] Read more.
Background: Prunus plants are widely distributed across Asia and Europe, yet their intricate phylogenetic relationships pose significant challenges for systematic studies and interspecies identification. Objectives: To clarify the mitochondrial and chloroplast genomes of Prunus salicina var. cordata, and to reveal its evolutionary relationship and historical gene flow with domesticated cherries. Methods: In this study, we assembled, annotated, and analyzed the first mitochondrial and chloroplast genomes of P. salicina var. cordata, a species within the Prunus genus. Results: The mitochondrial genome was found to be 484,858 base pairs in length, exhibiting a typical circular conformation. Phylogenetic analysis revealed a close evolutionary relationship between P. domestica and P. salicina, suggesting historical gene flow between these two species last genomes; mitochondrial genomes; phylogeny analysis. Conclusions: To provide a genomic basis for resolving the phylogenetic controversies within the Li-associated plants, elucidating their evolutionary mechanisms, and formulating breeding strategies. Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in the “Plant Genetics and Genomics” Section)
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