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Functional Genomics and Comparative Genomics Analysis in Plants, 4th 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 October 2026 | Viewed by 1256

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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
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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 (3 papers)

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Research

26 pages, 8022 KB  
Article
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 218
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, [...] Read more.
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
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16 pages, 7872 KB  
Article
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
Viewed by 287
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 [...] Read more.
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
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18 pages, 11871 KB  
Article
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 363
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. [...] Read more.
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
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