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Functional Genomics and Comparative Genomics Analysis in Plants, 4th Edition

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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 October 2026 | Viewed by 2268

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Editors

Prof. Dr. Quan Zou

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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

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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

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Guest Editor

: School of Software, Northwestern Polytechnical University, Xian 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, many bioinformatic tools have been developed for omics analyses; however, there are still many challenges that remain, 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 contribute to this Special Issue. Research papers, up-to-date review articles, and commentaries are all welcome.

You may read the publications in three 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

https://www.mdpi.com/journal/cimb/special_issues/JR24B11C29

Prof. Dr. Quan Zou
Dr. Ran Su
Dr. Qiangguo Jin
Guest Editors

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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 (5 papers)

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Research

18 pages, 2808 KB

Open AccessArticle

Genome-Wide Identification and Expression Profiling of the Oxidosqualene Cyclase Gene Family in Akebia trifoliata Across Fruit Development and Disease-Susceptibility Groups

by Hefei Rao, Hao Liu, Jie Li, Xiaoxiao Yi, Yunfeng Deng, Chen Chen, Feiquan Tan and Peigao Luo

Curr. Issues Mol. Biol. 2026, 48(8), 795; https://doi.org/10.3390/cimb48080795 - 6 Aug 2026

Viewed by 137

Abstract

Akebia trifoliata is an important Chinese traditional medicinal plant, and its abundant triterpenoids are the primary active medicinal components. However, the oxidosqualene cyclase (OSC) gene family responsible for constructing their triterpenoid skeletons has not yet been systematically characterized. In this study, nine AktOSC genes were identified genome-wide in A. trifoliata. Phylogenetic analysis revealed that most AktOSC members formed independent evolutionary subclades. Synteny and selective pressure analyses indicated that multiple duplication modes collectively contributed to the expansion of the AktOSC family, and all members were subjected to strong purifying selection. Sequence alignment showed that all members possess the characteristic motifs of the OSC family, whereas amino acid substitutions at critical active-site residues hinted at potential catalytic product diversity. Cis-acting element prediction revealed an abundance of environmental and phytohormone responsiveness elements within the AktOSC promoter regions. Expression profiling revealed that AktOSC genes exhibited distinct expression patterns across tissues, developmental stages, and disease-susceptibility groups. Finally, AktOSC8, which was specifically and highly expressed in the pericarp, was identified as a highest-priority candidate gene. Collectively, these findings provide essential foundational insights for further elucidating the mechanisms underlying triterpenoid biosynthesis and accumulation in A. trifoliata. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 4th Edition)

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15 pages, 2679 KB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the WOX Gene Family in Pepino (Solanum muricatum), Followed by Cloning and Subcellular Localization of SmWOX5 and SmWOX15

by Xuebing Zhu, Yunhe Cao, Xuemei Sun, Shipeng Yang and Lihui Wang

Curr. Issues Mol. Biol. 2026, 48(8), 782; https://doi.org/10.3390/cimb48080782 - 31 Jul 2026

Viewed by 150

Abstract

WOX transcription factors play conserved roles in plant adventitious root development, but the WOX family in pepino (Solanum muricatum) has not been systematically characterized. To investigate this family, genome-wide identification and expression analysis were performed. A total of 15 SmWOX genes were identified, unevenly distributed across 12 chromosomes and phylogenetically divided into three clades: WUS (11), Intermediate (3), and Ancient (1). RT-qPCR revealed that most SmWOX genes showed the highest expression in apical buds and the lowest in leaves; among them, SmWOX5 and SmWOX15 exhibited significantly higher expression in roots. These two genes were subsequently cloned and subjected to subcellular localization analysis. SmWOX5 (492 bp, 163 amino acids) and SmWOX15 (2514 bp, 837 amino acids) were both predicted as non-transmembrane, non-secretory proteins, with differences in phosphorylation site distribution and structural conformations. Subcellular localization showed that SmWOX5 is exclusively nuclear, whereas SmWOX15 is predominantly nuclear with partial plasma membrane distribution. The WOX family in pepino exhibits evolutionary conservation with signs of functional divergence. The high root expression and differential localization of SmWOX5 and SmWOX15 suggest their distinct regulatory roles in root development and adventitious root formation, providing candidate genes for improving cutting propagation efficiency in pepino (Solanum muricatum). Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 4th Edition)

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26 pages, 8022 KB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the Thaumatin-like Protein Genes in Filipendula ulmaria under Bipolaris sorokiniana Infection

by Ekaterina A. Istomina, Marina P. Slezina and Tatyana I. Odintsova

Curr. Issues Mol. Biol. 2026, 48(6), 640; https://doi.org/10.3390/cimb48060640 - 20 Jun 2026

Viewed by 418

Abstract

Pathogenesis-related (PR) proteins are crucial for plant defense against pathogen infection. However, the specific role of thaumatin-like proteins (TLPs), which comprise the PR-5 family, in plant immune responses has not been thoroughly investigated. Filipendula ulmaria is a medicinal plant with valuable pharmacological properties, including antimicrobial, anti-inflammatory, gastroprotective, immunomodulatory, and anticancer activities. The structure of the TLP family and its role in the immune system of meadowsweet have not been studied so far. The goal of this study was to analyze in detail the TLP gene family in meadowsweet and explore its response to fungal infection. In the meadowsweet genome, we identified 27 putative TLP genes, examined their structure and location on chromosomes, analyzed cis-regulatory elements in the promoter regions, predicted the structure and physicochemical characteristics of the encoded proteins, and performed a phylogenetic analysis. We also studied the differential expression of TLP genes under Bipolaris sorokiniana infection. Of six differentially expressed genes, three genes were up-regulated 48 h post-infection, suggesting their involvement in defense response to the fungus. The results obtained shed light on the role of the TLP gene family in the immune system of F. ulmaria and form the foundation for the creation of disease-resistant crops in agriculture and the development of bio-based antimicrobials in medicine. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 4th Edition)

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16 pages, 7872 KB

Open AccessArticle

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Corydalis ophiocarpa (Papaveraceae)

by Ming Lei, Cui Li, Jing Wang, Mei Qin, Li-Rong Huang, Xia-Lian Ou, Liang Kang, Han Liu and Zhan-Jiang Zhang

Curr. Issues Mol. Biol. 2026, 48(6), 614; https://doi.org/10.3390/cimb48060614 - 12 Jun 2026

Cited by 1 | Viewed by 608

Abstract

Corydalis ophiocarpa is a medicinally valuable plant, noted for its abundant alkaloid content. Despite its significance, the mitochondrial (mt) genome of this plant has not been characterized, which impedes both the phylogenetic understanding within the Corydalis genus and the comprehension of its full genetic potential. In this research, we successfully assembled the complete mitogenome of C. ophiocarpa by employing a hybrid method that integrates Oxford Nanopore long reads with Illumina short reads. The assembled genome forms a circular structure of 600,064 bp, with a GC content of 46.49%, and includes 63 genes, comprising 40 unique protein-coding genes (PCGs), 20 tRNAs, and three rRNAs. Through assembly and coverage analysis, we identified a 6383 bp forward repeat associated with a contig having approximately double the depth, indicating a repeat-mediated multipartite structure where the main circle may coexist with two smaller subgenomic forms. We discovered 775 C-to-U RNA editing sites across the 40 PCGs, with 95.4% being non-synonymous and favoring hydrophobic amino acid substitutions, particularly in Complex I subunits. Furthermore, we identified sixteen mt plastid DNA fragments constituting 2.43% of the mitogenome, a proportion more than double that found in the closely related C. saxicola. Phylogenetic analysis confirms that C. ophiocarpa is most closely related to C. saxicola, with C. pauciovulata as another close relative. This study presents the first complete mitogenome of C. ophiocarpa, providing a genomic basis for investigating the relationships between mt genome structure, post-transcriptional regulation, and specialized metabolism in the Corydalis genus. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 4th Edition)

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18 pages, 11871 KB

Open AccessArticle

Genome-Wide Analysis of bZIP Transcription Factors and Expression Patterns in Response to Shading Treatment in Taxus yunnanensis

by Jiangtao Fan, Pengpeng Gong, Yujia Liu, Mengke Dou, Qing Li, Qiuhong Hu, Yong Wang, Gang Wang and Xiong Huang

Curr. Issues Mol. Biol. 2026, 48(5), 521; https://doi.org/10.3390/cimb48050521 - 17 May 2026

Cited by 1 | Viewed by 449

Abstract

Basic leucine zipper (bZIP) transcription factors are widely involved in plant growth, development, environmental adaptation, and secondary metabolism. However, the bZIP gene family in Taxus yunnanensis has not been systematically characterized, and its potential involvement in shading-responsive regulation of paclitaxel biosynthesis remains unclear. In this study, a genome-wide analysis was performed to identify and characterize the bZIP family in T. yunnanensis. Phylogenetic analysis, conserved motif and domain identification, promoter cis-element analysis, chromosomal localization, and expression profiling were conducted to investigate their structural features and regulatory potential. A total of 18 TyubZIP genes were identified and classified into 10 subfamilies. These genes exhibited variation in physicochemical properties but showed conserved structural features and nuclear localization. Promoter analysis revealed abundant light-responsive, hormone-related, and stress-related cis-elements. Expression profiling indicated tissue-specific expression patterns and diverse responses to shading treatment. WGCNA further identified candidate TyubZIP genes potentially associated with paclitaxel biosynthesis. Among them, TyuHY5 was selected for functional analysis. Subcellular localization and transcriptional assays demonstrated that TyuHY5 can bind to the promoter of TyuDBTNBT and positively regulate its activity. These findings provide the first genome-wide characterization of the bZIP family in T. yunnanensis and identify TyuHY5 as a shading-responsive candidate regulator of paclitaxel biosynthesis, providing insights that may inform the genetic improvement and cultivation strategies of Taxus for enhanced paclitaxel production. Full article

(This article belongs to the Special Issue Functional Genomics and Comparative Genomics Analysis in Plants, 4th Edition)

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