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Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 4193

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
Dr. Qiangguo Jin

E-Mail Website
Guest Editor
School of Software, Northwestern Polytechnical University, Xi’an 710129, China
Interests: medical image analysis; AI in healthcare; computer-aided diagnosis; AI in drug design; anticancer peptides analysis
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 and subspecies have been sequenced and published. With the development of sequencing technology, an increasing number of omics datasets have been released, such as pan-genomics, proteomics, transcriptomics, and metabolomics. It is important to highlight that the rapid accumulation of omics datasets has greatly promoted the development of plant science, especially crop genetics and breeding. In recent years, even many bioinformatic tools have been developed for omics analyses, but there are still many challenges remaining, 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 regarding omics analyses in plants can make progress by incorporating more advanced technologies. Therefore, we organized this Special Issue, ‘Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition’, to help us better understand the plant genome, gene function, and their evolution, as well as to provide a resource for decoding the molecular mechanisms of complex agronomic traits.  

I am pleased to invite you to participate in this Special Issue. Research papers, up-to-date review articles, and commentaries are all welcome.

You can read the publications in the first and second volumes of this Special Issue here:

https://www.mdpi.com/journal/cimb/special_issues/LBJL2665KM

https://www.mdpi.com/journal/cimb/special_issues/Comparative_Genomics

Prof. Dr. Quan Zou
Dr. Ran Su
Dr. Qiangguo Jin
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. Current Issues in Molecular Biology 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 2200 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

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

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Published Papers (7 papers)

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16 pages, 3716 KiB  
Article
Genome-Wide Analysis of Oxidosqualene Cyclase Genes in Artemisia annua: Evolution, Expression, and Potential Roles in Triterpenoid Biosynthesis
by Changfeng Guo, Si Xu and Xiaoyun Guo
Curr. Issues Mol. Biol. 2025, 47(7), 545; https://doi.org/10.3390/cimb47070545 - 14 Jul 2025
Viewed by 268
Abstract
Plant triterpenoids are structurally diverse specialized metabolites with significant ecological, medicinal, and agricultural importance. Oxidosqualene cyclases (OSCs) catalyze the crucial cyclization step in triterpenoid biosynthesis, generating the fundamental carbon skeletons that determine their structural diversity and biological functions. Genome-wide identification of OSC genes [...] Read more.
Plant triterpenoids are structurally diverse specialized metabolites with significant ecological, medicinal, and agricultural importance. Oxidosqualene cyclases (OSCs) catalyze the crucial cyclization step in triterpenoid biosynthesis, generating the fundamental carbon skeletons that determine their structural diversity and biological functions. Genome-wide identification of OSC genes was performed using bioinformatics tools, including HMMER and BLASTP, followed by phylogenetic analysis, gene structure analysis, conserved domain and motifs identification, cis-regulatory element prediction, protein–protein interaction analysis, and expression profiling using publicly available transcriptome data from UV-B treated A. annua six-week-old seedlings. We identified 24 AaOSC genes, classified into CAS, LAS, LUS, and unknown subfamilies. Phylogenetic analysis revealed evolutionary relationships with OSCs from other plant species. Gene structure analysis showed variations in exon–intron organization. Promoter analysis identified cis-regulatory elements related to light responsiveness, plant growth and development, hormone signaling, and stress response. Expression profiling revealed differential expression patterns of AaOSC genes under UV-B irradiation. This genome-wide characterization provides insights into the evolution and functional diversification of the OSC gene family in A. annua. The identified AaOSC genes and their regulatory elements lay the foundation for future studies aimed at manipulating triterpenoid biosynthesis for medicinal and biotechnological applications, particularly focusing on enhancing stress tolerance and artemisinin production. Full article
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition)
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17 pages, 2055 KiB  
Article
Genome-Wide Identification and Characterization of TaCRY Gene Family and Its Expression in Seed Aging Process of Wheat
by Guoqing Cui, Xiuyan Cui, Junjie Wang, Menglin Lei, Xia Liu, Yanzhen Wang, Haigang Wang, Longlong Liu, Zhixin Mu and Xia Xin
Curr. Issues Mol. Biol. 2025, 47(7), 522; https://doi.org/10.3390/cimb47070522 - 6 Jul 2025
Viewed by 240
Abstract
Cryptochromes (CRYs), as essential blue-light photoreceptors, play pivotal roles in modulating plant growth, development, and stress responses. Although CRY-mediated light signaling has been extensively studied in model species, their functions remain limited in wheat. In this work, a comprehensive analysis of the [...] Read more.
Cryptochromes (CRYs), as essential blue-light photoreceptors, play pivotal roles in modulating plant growth, development, and stress responses. Although CRY-mediated light signaling has been extensively studied in model species, their functions remain limited in wheat. In this work, a comprehensive analysis of the TaCRY gene family was performed in wheat, identifying 12 TaCRY members localized to distinct chromosomes 2, 6, and 7. TaCRYs contain the conserved PHR and CCT domains and diverse gene structures. Collinearity relationships indicated their dynamic evolution patterns during polyploidization. Cis-acting elements of TaCRY members associated with light responsiveness, phytohormone signaling, and abiotic stress were also identified. Transcriptome analysis revealed that the differential expression patterns of TaCRY members under seed vigor process. This study expands our understanding of TaCRY diversity and provides valuable molecular information for marker-assisted selection in wheat improvement. Full article
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition)
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21 pages, 6590 KiB  
Article
Comparative Analysis of the Complete Chloroplast Genomes of Eight Salvia Medicinal Species: Insights into the Deep Phylogeny of Salvia in East Asia
by Yan Du, Yang Luo, Yuanyuan Wang, Jiaxin Li, Chunlei Xiang and Meiqing Yang
Curr. Issues Mol. Biol. 2025, 47(7), 493; https://doi.org/10.3390/cimb47070493 - 27 Jun 2025
Viewed by 317
Abstract
Salvia, a medicinally and economically important genus, is widely used in traditional medicine, agriculture, and horticulture. This study compares the chloroplast genomes of eight East Asian Salvia species to assess genetic diversity, structural features, and evolutionary relationships. Complete chloroplast genomes were sequenced, [...] Read more.
Salvia, a medicinally and economically important genus, is widely used in traditional medicine, agriculture, and horticulture. This study compares the chloroplast genomes of eight East Asian Salvia species to assess genetic diversity, structural features, and evolutionary relationships. Complete chloroplast genomes were sequenced, annotated, and analyzed for gene content, codon usage, and repetitive sequences. Phylogenetic relationships were reconstructed using Maximum Likelihood, Maximum Parsimony and Bayesian inference. The genomes exhibited a conserved quadripartite structure (151,081–152,678 bp, GC content 37.9–38.1%), containing 114 unique genes with consistent arrangement. Codon usage favored A/T endings, with leucine (Leu) most frequent and cysteine (Cys) least. We identified 281 long sequence repeats (LSRs) and 345 simple sequence repeats (SSRs), mostly in non-coding regions. Comparative analysis revealed five hypervariable regions (trnH-psbA, rbcL-accD, petA-psbJ, rpl32-trnL, ycf1) as potential molecular markers. Phylogenetic analysis confirmed the monophyly of East Asian Salvia, dividing them into five clades, with Sect. Sonchifoliae basal. While G1, G3, and G8 were monophyletic, G5 and G6 were paraphyletic, and the G7-G8 relationship challenged traditional classifications. The genomic evidence provides crucial insights for resolving long-standing taxonomic uncertainties and refining the classification system of Salvia. These findings suggest a complex evolutionary history involving hybridization and incomplete lineage sorting, providing valuable genomic insights for Salvia phylogeny, taxonomy, and conservation. Full article
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition)
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16 pages, 2719 KiB  
Article
A Transcriptomic Study on the Toxic Effects of Iodide (I−) Wet Deposition on Pepper (Capsicum annuum) Leaves
by Rui Yu, Zhu-Ling Ma, Min Wang and Jie Jin
Curr. Issues Mol. Biol. 2025, 47(5), 313; https://doi.org/10.3390/cimb47050313 - 28 Apr 2025
Viewed by 448
Abstract
Radioactive iodine (129I), released into the environment from human nuclear activities, poses significant health risks to the biosphere due to its long half-life and mobility. This study investigates the toxic effects of wet-deposited iodine on the growth of chili pepper seedlings [...] Read more.
Radioactive iodine (129I), released into the environment from human nuclear activities, poses significant health risks to the biosphere due to its long half-life and mobility. This study investigates the toxic effects of wet-deposited iodine on the growth of chili pepper seedlings (Capsicum annuum L.) under soil cultivation conditions. Using sodium iodide (NaI) as the exposure agent, transcriptomic analysis was conducted to evaluate the molecular responses of chili pepper leaves to iodine at concentrations of 2, 4, and 8 ppm. The study identified 2440 and 1543 differentially expressed genes (DEGs) in leaves exposed to 2 ppm vs. 4 ppm iodine and 2 ppm vs. 8 ppm iodine, respectively. GO enrichment analysis showed that DEGs at 4 ppm were significantly associated with protein–chromophore linkage, extracellular region, and iron ion binding, while those at 8 ppm were enriched in defense response, cell wall components, and iron ion binding. Iodine stress disrupted key pathways associated with photosynthesis, antioxidant defense, and cuticle biosynthesis. In particular, the downregulation of key genes related to protein–chromophore binding, lipid metabolism, and cell wall organization indicated reduced photosynthetic efficiency and weakened stress resistance. This study provides molecular-level insights into the ecological risks of iodine stress in plants and offers a scientific basis for managing iodine contamination and breeding iodine-tolerant chili pepper cultivars. Full article
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition)
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24 pages, 3157 KiB  
Article
Comparative Transcriptome Analysis of Two Types of Rye Under Low-Temperature Stress
by Haonan Li, Jiahuan Zhao, Weiyong Zhang, Ting He, Dexu Meng, Yue Lu, Shuge Zhou, Xiaoping Wang and Haibin Zhao
Curr. Issues Mol. Biol. 2025, 47(3), 171; https://doi.org/10.3390/cimb47030171 - 3 Mar 2025
Cited by 1 | Viewed by 1056
Abstract
Wheat is a crucial food crop, and low-temperature stress can severely disrupt its growth and development, ultimately leading to a substantial reduction in wheat yield. Understanding the cold-resistant genes of wheat and their action pathways is essential for revealing the cold-resistance mechanism of [...] Read more.
Wheat is a crucial food crop, and low-temperature stress can severely disrupt its growth and development, ultimately leading to a substantial reduction in wheat yield. Understanding the cold-resistant genes of wheat and their action pathways is essential for revealing the cold-resistance mechanism of wheat, enhancing its yield and quality in low-temperature environments, and ensuring global food security. Rye (Secale cereale L.), on the other hand, has excellent cold resistance in comparison to some other crops. By studying the differential responses of different rye varieties to low-temperature stress at the transcriptome level, we aim to identify key genes and regulatory mechanisms related to cold tolerance. This knowledge can not only deepen our understanding of the molecular basis of rye’s cold resistance but also provide valuable insights for improving the cold tolerance of other crops through genetic breeding strategies. In this study, young leaves of two rye varieties, namely “winter” rye and “victory” rye, were used as experimental materials. Leaf samples of both types were treated at 4 °C for 0, 6, 24, and 72 h and then underwent RNA-sequencing. A total of 144,371 Unigenes were reconstituted. The Unigenes annotated in the NR, GO, KEGG, and KOG databases accounted for 79.39%, 55.98%, 59.90%, and 56.28%, respectively. A total of 3013 Unigenes were annotated as transcription factors (TFs), mainly belonging to the MYB family and the bHLH family. A total of 122,065 differentially expressed genes (DEGs) were identified and annotated in the GO pathways and KEGG pathways. For DEG analysis, 0 h 4 °C treated samples were controls. With strict criteria (p < 0.05, fold-change > 2 or <0.5, |log2(fold-change)| > 1), 122,065 DEGs were identified and annotated in GO and KEGG pathways. Among them, the “Chloroplast thylakoid membrane” and “Chloroplast” pathways were enriched in both the “winter” rye and “victory” rye groups treated with low temperatures, but the degrees of significance were different. Compared with “victory” rye, “winter” rye has more annotated pathways such as the “hydrogen catabolic process”. Although the presence of more pathways does not directly prove a more extensive cold-resistant mechanism, these pathways are likely associated with cold tolerance. Our subsequent analysis of gene expression patterns within these pathways, as well as their relationships with known cold-resistance-related genes, suggests that they play important roles in “winter” rye’s response to low-temperature stress. For example, genes in the “hydrogen catabolic process” pathway may be involved in regulating cellular redox balance, which is crucial for maintaining cell function under cold stress. Full article
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition)
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13 pages, 2282 KiB  
Article
Ammonium Transporter 1 (AMT1) Gene Family in Pomegranate: Genome-Wide Analysis and Expression Profiles in Response to Salt Stress
by Fatima Omari Alzahrani
Curr. Issues Mol. Biol. 2025, 47(1), 59; https://doi.org/10.3390/cimb47010059 - 16 Jan 2025
Cited by 1 | Viewed by 1062
Abstract
Understanding the ammonium (NH4+) uptake and transport systems, particularly AMT1 genes, is important for plant growth and defense. However, there is a lack of research on identifying and analyzing AMT1 genes in pomegranate, emphasizing the need for further investigation in [...] Read more.
Understanding the ammonium (NH4+) uptake and transport systems, particularly AMT1 genes, is important for plant growth and defense. However, there is a lack of research on identifying and analyzing AMT1 genes in pomegranate, emphasizing the need for further investigation in this area. Five AMT1 genes (PgAMT1-1 to PgAMT1-5) were identified, all of which contain the PF00909 domain, a feature of ammonium transporters. Various characteristics of these genes, including gene length, coding sequence length, and chromosomal locations, were examined. This study evaluated the isoelectric point, hydropathicity, conserved domains, motifs, and synteny of the PgAMT1 proteins. Phylogenetic analysis confirmed the homology of PgAMT1 genes with previously reported AMT in Arabidopsis and tomato. The tissue-specific expression analysis of PgAMT1 genes revealed distinct patterns: PgAMT1-1 and PgAMT1-2 were predominantly expressed in flowers, PgAMT1-3 exhibited notable expression in roots, leaves, and flowers, PgAMT1-4 was primarily expressed in leaf tissue, while the expression of PgAMT1-5 was detected in both leaves and roots. The impact of salt-induced stress on AMT1 gene expression was also examined, revealing that PgAMT1-1, PgAMT1-2, and PgAMT1-4 expression is reduced under increased salt stress. These expression modifications can help regulate NH4+ assimilation in conditions of elevated salinity, maintaining cellular homeostasis and ion balance. This study contributes to the comprehensive identification of the AMT1s gene family in pomegranate; however, further research on the functional characterization of the identified PgAMT1s is needed. Full article
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition)
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7 pages, 585 KiB  
Brief Report
The Superoxide Dismutase Family in Balloon Flower (Platycodon grandiflorus): Phylogenetic Relationships, Structural Characteristics, and Expression Patterns
by Tae Kyung Hyun
Curr. Issues Mol. Biol. 2025, 47(5), 351; https://doi.org/10.3390/cimb47050351 - 12 May 2025
Viewed by 422
Abstract
Superoxide dismutases (SODs) are essential antioxidant enzymes that protect plant cells from oxidative stress, thereby preserving cellular integrity. This study presents a comprehensive genome-wide analysis of the SOD gene family in Platycodon grandiflorus, identifying seven genes classified into three distinct groups based [...] Read more.
Superoxide dismutases (SODs) are essential antioxidant enzymes that protect plant cells from oxidative stress, thereby preserving cellular integrity. This study presents a comprehensive genome-wide analysis of the SOD gene family in Platycodon grandiflorus, identifying seven genes classified into three distinct groups based on phylogenetic relationships. Detailed bioinformatics analyses revealed variations in structural characteristics and physicochemical properties. PlgSODs were predicted to localize primarily to the chloroplast and mitochondria. Tissue-specific expression patterns indicate that PlgSOD genes play important roles in plant growth and development. Furthermore, promoter analysis identified several potential transcription factors (TFs), including members of the B3, Dof, and MYB-related families, which are known for their involvement in stress responses. These TFs are likely to regulate multiple PlgSOD genes, suggesting a coordinated transcriptional regulation mechanism under specific physiological or stress conditions. Taken together, these findings provide valuable insights into the functional roles of SODs in P. grandiflorus and lay the groundwork for future genetic and biotechnological strategies aimed at enhancing stress tolerance in this species. Full article
(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 3rd Edition)
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