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.
Abstract
Background
As a major global food crop, wheat faces dual pressures from population growth and deteriorating agricultural environments in efforts to increase its yield. The members of the FIG superfamily are associated with photosynthetic carbon metabolism and stress-responsive pathways in plants.
Results
In this study, we conducted the first systematic pan-genomic analysis to investigate the evolution and function of the FIG superfamily in wheat. The results revealed that this family underwent significant expansion during plant evolution from aquatic to terrestrial habitats and from lower to higher forms, with functional divergence apparently predating the green algal stage as inferred from phylogenetic patterns. The members of this family were primarily derived from three ancestral species, and their expansion was largely driven by whole-genome duplication. Most members were found to be under purifying selection, whereas the TaVTC4-4B was subjected to positive selection. This gene is constitutively highly expressed in green tissues, and its promoter is enriched with cis-regulatory elements associated with light responsiveness, JA/ABA signaling, and stress responses. Expression analysis indicated its strong responsiveness to salt stresses.
Conclusions
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.
New methodologies were examined, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
Shaima Mahfood Ebrahim Abdulrahman, M. Karaismailoğlu· Bartın University Internatio...· 0 citations
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
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.
Weijian Qi, Jingcheng Wang, Jianzhong Chang et al.· Frontiers in Plant Science· 0 citations
The basic leucine zipper (bZIP) transcription factor family plays crucial roles in plant development and stress responses, yet its evolutionary dynamics and functional diversification across green plants remain poorly understood. Here, we conducted a comprehensive analysis of the bZIP family across 114 green plant taxa, from algae to angiosperms, with emphasis on Rosaceae species and Malus accessions. Phylogenetic analysis showed that most bZIP subfamilies formed stable monophyletic clades across green plants, except for two atypical evolutionary patterns. An intertwined E-M-E-I complex suggested that the core domain of subfamily M originated from the group E lineage, whereas the highly divergent subclades, S1 and I1, highlighted the uneven evolutionary rates within the family. In Rosaceae, lineage-specific whole genome duplication (WGD) events, especially in Malinae subtribe and Potentilla, markedly expanded bZIP repertoires with asymmetric retention among subfamilies. Furthermore, lineage-specific pangenome in Malus identified 1251 core and 18 unique bZIP members across diverse accessions. Pan-transcriptome identified tissue-specific expression and stress-responsive co-expression modules. And functional characterization of MP_bZIP77, a gene derived from wild apple, provides a concrete example of this regulatory mechanism by demonstrating that its overexpression enhances salt tolerance through the activation of antioxidant enzyme activities. This study provides novel insights into the evolutionary origin, expansion pattern, and functional divergence of the bZIP family in green plants and Rosaceae, while laying a theoretical and genetic foundation for future molecular breeding aimed at improving stress resistance in fruit trees.
Xuejing Cao, Cheng Chen, Weifeng Ma et al.· Horticulture Research· 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.
