A comprehensive pan-genomic view of structural variation, evolutionary patterns, and expression regulation in the ZmCYP450 family is provided, offering a foundation for future functional studies and maize trait improvement.
Abstract
The plant cytochrome P450 (CYP450) superfamily plays a key role in metabolic diversity and environmental adaptation; however, systematic analyses of its intraspecific structural variation, copy number dynamics, and evolutionary mechanisms remain limited. Using 27 high-quality maize reference genomes, we performed a pan-genomic analysis of the ZmCYP450 family, identifying 282 orthogroups (OGs) and 7,282 genes. The family exhibits a pattern of predominantly conserved genes with localized expansions and open pan-genome properties. PAV and CNV analyses revealed extensive gene deletions and copy number fluctuations outside core OGs, reflecting substantial intraspecific structural diversity. Analysis of duplication types and local colinearity suggested that proximal and dispersed duplications are the primary contributors to drive family expansion. Ka/Ks analysis indicated that most OGs are under purifying selection, while a subset shows evidence of positive selection. Further integration of structural variation and transcriptomic data suggested that SVs may affect gene function through mechanisms such as gene deletion, protein truncation, and remodeling of regulatory elements, suggesting a dual role of potential loss of function and expression modulation. Despite a relatively stable overall copy number, structural variant categories (‘Typical’, ‘Atypical’, and ‘Missing’) are widespread, and expression levels do not always correlate with copy number, suggesting a complex regulatory patterns. Tissue-specificity analysis revealed a large number of highly specific ZmCYP450 genes involved in secondary metabolism and environmental responses, with distinct expression profiles across different genetic backgrounds. This study provides a comprehensive pan-genomic view of structural variation, evolutionary patterns, and expression regulation in the ZmCYP450 family, offering a foundation for future functional studies and maize trait improvement.
Protein phosphatase 2C (PP2C) proteins are central regulators of plant signaling and stress responses, yet their macroevolutionary origin and diversification across the plant kingdom remain incompletely resolved. In this study, we performed a large-scale genome-wide analysis of the PP2C gene family using 402 representative plant genomes and integrated phylogenetic, duplication type, motif, expression, pangenome and selection-pressure analyses. A total of 36 960 PP2C genes were identified, showing substantial lineage-specific copy-number variation and marked expansion in angiosperms. Phylogenetic reconstruction classified plant PP2Cs into 12 subfamilies within three major clades and indicated that most subfamilies originated before the establishment of land plants, whereas angiosperm diversification mainly involved quantitative expansion rather than the emergence of new subfamilies. Duplication analysis revealed that dispersed and WGD/segmental duplication were the principal forces driving PP2C expansion, while phylogenetic tree reconciliation suggested extensive lineage-specific retention and loss after ancestral duplication events. Conserved motif analysis showed strong preservation of the catalytic scaffold, especially Motif1–Motif3 and Motif5, together with flexible remodeling of peripheral motifs. Cross-species transcriptome profiling in seven angiosperms revealed phylogenetically structured expression divergence: Clade II retained broad hormone, tissue and stress responsiveness, whereas Clades I and III displayed more condition- and organ-specific specialization. In 18 Brassica rapa accessions, 2478 PP2C genes were identified, most of which belonged to core orthogroups and syntenic regions. Ka/Ks analysis further indicated predominant purifying selection, with relaxed constraints in non-core genes. Collectively, these results provide a comprehensive evolutionary framework for PP2C functional diversification and candidate resources for stress-resistance improvement in horticultural crops.
Quanlong Liu, Jianbin Quan, Yuhua Cui et al.· Horticulture Research· 0 citations
Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded our ability to identify and interpret SVs across plant species. In this review, we summarize recent progress in understanding the formation mechanisms, classification, and functional consequences of plant SVs. We discuss major sources of SV generation, including transposable element activity, non-allelic homologous recombination (NAHR), horizontal gene transfer (HGT), and genome restructuring following polyploidization. We further highlight how LRS and graph-based pan-genomes overcome limitations of traditional linear reference genomes and enable more comprehensive characterization of genetic diversity. Beyond variant discovery, we emphasize the importance of integrating genomic, transcriptomic, epigenomic, proteomic, metabolomic, and spatial omics datasets to decipher how SVs influence gene regulation and complex agronomic traits. We also discuss current challenges, including repetitive genomes, polyploidy, computational complexity, and translation of SV knowledge into practical breeding applications. Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement.
Ru-Yi Liu, Letong Huang, Jing-Ru Mu et al.· Plants· 0 citations
This study elucidates the evolutionary trajectory and functional landscape of the wheat FIG superfamily, laying a theoretical foundation for the potential genetic improvement of photosynthetic efficiency and stress resilience in wheat.
Hui Wang, Jingjing Liang, Xiao Li et al.· BMC Plant Biology· 0 citations
The PR10 gene family plays a critical role in plant stress responses. Phylogenetic analysis across species indicated that the PR10 gene first appeared during plant terrestrialization and underwent significant expansion. And, PR10 is conserved in leguminous plants, yet its genomic architecture and functional mechanisms in alfalfa (Medicago sativa L.) remains unclear. In this study, a pan-genomic analysis of 28 alfalfa accessions identified a total of 1657 MsPR10 genes, with tandem duplication accounting for the majority of gene expansion (61.19%). These MsPR10 genes were clustered into 81 Orthologous Gene Groups (OGGs) based on conservative levels, ranging from core to cloud genes. Significant expansion of PR10 genes in Zhongmu No.1 alfalfa (ZMNO) was associated with elevated transposon activity and selective pressure. Transcriptomic analysis indicated MsPR10.SC10 may be a key gene in alfalfa salt-tolerance. Transgenic alfalfa plants overexpressing MsPR10.SC10 were generated by Agrobacterium-mediated transformation. Detailed physiological tests suggested overexpression of MsPR10.SC10 enhanced salt tolerance of alfalfa by maintaining ion homeostasis (reducing Na+/K+ ratio), boosting antioxidant capacity by increasing SOD/ POD activity and reducing H2O2/ MDA accumulation, and regulates the expression of salt stress responsive genes. This study reveals the pan-genomic architecture of the PR10 gene family members in alfalfa, and provides valuable candidate gene for breeding of salt tolerant alfalfa cultivar and may also other crops.
The NSUN family is essential for RNA 5-methylcytosine modification (m5C) in eukar-yotes. However, no NSUN genes have been identified in maize, and the characteristics of ZmNSUN genes remain unexplored. Here, we performed a comprehensive in-vestigation of NSUN genes across seven Poaceae species. Our analysis identified a total of 63 Poaceae NSUN genes, including eight ZmNSUN genes in maize. Phylogenetic and feature analyses classified the Poaceae NSUNs into six subgroups (SGs), suggest-ing that the divergence of these SGs may have occurred prior to the divergence between plants and animals. Expression profiling indicated that ZmNSUN genes are generally repressed by heat stress. Co-expression network analysis suggested potential roles of ZmNSUN genes in maize development, and expression quantitative trait locus (eQTL) analysis results demonstrated that expression levels of multiple ZmNSUN genes are significantly associated with maize agronomic traits. Collectively, these findings provide novel insights into the evolutionary dynamics of the NSUN family and highlight specific ZmNSUN genes as promising candidates for molecular breeding to improve maize yield and stress adaptability.
Background/Objectives: Whole-genome duplication (WGD) and transposed duplication (TRD) are two principal evolutionary drivers of plant genome expansion, yet the molecular mechanisms underlying their divergent co-expression patterns remain poorly characterized. Methods: In this study, based on the reference genome of tea plant (Camellia sinensis ‘Yunkang 10’, YK10), we integrated publicly available transcriptomic, ATAC-seq, H3K27ac ChIP-seq, whole-genome bisulfite sequencing (WGBS), and SNP data from eight tissues and performed a multi-layered analysis of co-expression divergence across 4071 WGD and 10,174 TRD gene pairs. Results: WGD gene pairs exhibited significantly higher co-expression rates (44.3%) than TRD pairs (33.0%), with gene length and sequence similarity jointly promoting co-expression. Chromatin accessibility and H3K27ac modification were each positively correlated with expression and co-expression; however, under equivalent chromatin accessibility conditions, TRD gene expression remained systematically attenuated, and this reduced expression state was significantly associated with elevated levels of CG, CHG, and CHH methylation, suggesting that these epigenetic marks may collectively participate in the transcriptional repression of TRD genes. Promoter-proximal SNPs exerted disproportionately deleterious effects on TRD co-expression, demonstrating that the combined effects of genetic variation and epigenetic modifications are associated with enhanced transcriptional divergence. Weighted gene co-expression network analysis (WGCNA) revealed that WGD modules showed significant associations with EC, GC, and EGC accumulation, whereas WRKY and bHLH transcription factors in the TRD MEblue module exhibited strong associations with EGCG and ECG. Conclusions: This study systematically characterizes multi-omics association patterns related to duplicate gene co-expression divergence, providing insights into potential hierarchical regulation. It offers mechanistic clues for catechin metabolic regulation and provides candidate targets for metabolite-directed breeding.