Evolutionary analysis of the bZIP gene family across green plants and its lineage-specific pangenomic landscape in apple ( Malus )

Origin, Conservation and Functional Diversification of the BES1/BZR1 Gene Family During Early Land Plant Terrestrialization in Bryophytes

BRI1-EMS-SUPPRESSOR 1 (BES1)/BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factors serve as core regulators of brassinosteroid (BR) signal in seed plants, where they control diverse developmental processes, including cell elongation, vascular development, and environmental responses; however, their evolutionary trajectory and functional diversification in early-diverging land plants remain poorly characterized. In this study, we systematically characterized the BES1/BZR1 gene family across 12 representative bryophyte species covering hornworts, liverworts and mosses, with Arabidopsis thaliana included as a vascular plant outgroup. In total, 19 non-redundant BES1/BZR1 homologs were identified within bryophyte genomes. Phylogenetic reconstruction, synteny analysis and Ka/Ks selection pressure analyses collectively revealed that this gene family is evolutionarily conserved throughout bryophytes, with moss-specific lineage expansion; most paralogous gene pairs have experienced strong purifying selection during evolution. Further analyses of gene structural organization, conserved protein motifs and cis-acting promoter elements uncovered universally conserved core domains alongside lineage-specific structural and regulatory variations. Subcellular localization assays demonstrated that the majority of tested bryophyte BES1/BZR1 proteins primarily accumulate in the nucleus, and autoluminescent reporter assays verified that multiple homologs modulate E-box-driven transcriptional activity. Transcriptional expression profiling indicated that BES1/BZR1 genes from Marchantia polymorpha and Sphagnum fallax are transcriptionally responsive to exogenous BR treatment, while several paralogs in S. fallax additionally exhibit altered expression under drought stress. Collectively, our results demonstrate that the BES1/BZR1 family originated at an early stage of land plant evolution, followed by lineage-specific gene expansion and divergent transcriptional regulation in bryophytes. This work advances our understanding of ancestral BR signaling and stress response modules in the early terrestrial plant lineages.

Genome-wide identification and evolutionary analysis of the ERF-VII gene family in the tea plant (Camellia sinensis) and functional characterization of CsRAP2.2 in response to cold stress

Evolutionary trajectories of the PP2C gene family across 402 plant genomes and pan-genomic diversification in Brassica rapa

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 provides a comprehensive evolutionary framework for PP2C functional diversification and candidate resources for stress-resistance improvement in horticultural crops.

Genomic Expansion and Subgenome Expression Divergence of Sugar Transporters During Polyploid Evolution of Bamboos

Sugar transporters play a pivotal role in photoassimilate partitioning and biomass accumulation in plants. However, how whole-genome duplication (WGD) has reshaped the evolutionary trajectory of the sugar transport system in Bambusoideae remains elusive. Here, we systematically identified and characterized the SUT (Sucrose Transporters) and MST (Monosaccharide Transporters) gene families across 14 bamboo genomes representing four major lineages: herbaceous, temperate woody, neotropical woody and paleotropical woody bamboos. Our results suggest that WGD acted as the primary driving force behind the expansion of these gene families, with woody bamboos possessing significantly higher gene counts than herbaceous bamboos. Notably, extensive gene loss was observed in hexaploid lineages, aligning with the gene dosage balance hypothesis. Phylogenetic and sequence analyses demonstrated that core genes were subjected to purifying selection. Intriguingly, 21 groups of identical protein sequences across species were identified in paleotropical woody bamboos, suggesting high sequence conservation. Transcriptomic and syntenic analyses further unveiled the mechanisms of post-polyploidization expression divergence: homeologs exhibited marked expression asymmetry across subgenomes. Distinct from the broad expression pattern in herbaceous bamboos, which rely on SUT5 and a few STP (Sugar Transporter Protein) genes, woody bamboos have achieved fine-tuned expression partitioning and tissue-specific specialization during different culm developmental stages through significantly expanded SUT and STP family members. This study reveals an evolutionary pattern characterized by “WGD-driven expansion, post-polyploid fractionation, and subgenome expression divergence.” This pattern suggests a potential link to the enhanced sugar allocation efficiency required for the explosive growth of woody bamboos, offering valuable gene resources and a foundation for future functional studies in Poaceae crops.

The Evolution of Type II MIKCc MADS-Box Genes in Legumes: An Overview of Their Developmental Functions

Fabaceae (Leguminosae) is one of the most species-rich and ecologically important angiosperm families, encompassing extraordinary diversity in growth form, floral architecture, fruit morphology, and symbiotic nitrogen fixation. Despite the central role of MADS-box transcription factors in controlling key developmental processes underlying these traits, their evolutionary history in legumes remains poorly understood. Here, we present a comprehensive phylogenetic and comparative genomic analysis of MIKCc MADS-box genes across Fabaceae, sampling representatives from three of the six subfamilies and spanning major evolutionary lineages using genomic and transcriptomic data. Our analyses reveal that all type II MIKCc MADS-box gene lineages known from angiosperms are represented in Fabaceae, except for TDR8 homologs. However, several clades, including MAF/FLC , AGL16/17/ANR1 , ABS , and XAL1 , are consistently poorly represented, suggesting lineage-specific constraints or gene loss. While numerous MADS-box genes remain single copy across most legumes, others show duplications prior to the diversification of Fabaceae, including AGL6 , AGL24b , PI , SEP , and SOC1 . Subfamily-specific expansions were detected in key developmental regulators, with duplications of AGL14/19 - like , FUL , TM6 , and SOC1 in Caesalpinioideae, and AG , AGL6 , AGL79 , AP1 , FUL , and SEP lineages in Papilionoideae. These patterns coincide with documented whole-genome duplication events in both subfamilies. In addition, pervasive gene duplication in Glycine reflects a genus-specific polyploidization history. Together, these results suggest that differential retention and loss of duplicated MADS-box genes have played a central role in shaping floral and inflorescence diversity, phenological variation, and ecological adaptation in legumes. By integrating phylogenetic patterns with existing functional data, this study provides an evolutionary framework for understanding how MADS-box gene diversification has contributed to the remarkable developmental and adaptive radiation of Fabaceae.

Genome-Wide Identification and Stress Response Analysis of the GATA Gene Family in Eggplant (Solanum melongena L.)

This study elucidates the evolutionary conservation and functional diversity of the eggplant GATA family, providing valuable candidate genes for future functional research and stress-tolerant molecular breeding in eggplant.