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

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.

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

Novel insights are provided 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.

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

Pangenome and Pan‐Transcriptome Analysis of the WOX Gene Family Reveals Evolutionary Conservation and Diversification in Alfalfa

ABSTRACT The WUSCHEL‐related homeobox (WOX) gene family encodes plant‐specific transcription factors that play pivotal roles in meristem maintenance, organogenesis, regeneration, and developmental phase transitions. Despite their importance, the pangenome‐scale composition, expansion dynamics, and evolutionary constraints of WOX genes in alfalfa ( Medicago sativa ) remain poorly understood. Here, we performed an integrated pangenome and pan‐transcriptome analysis of the WOX gene family using 24 high‐quality alfalfa genomes. A total of 432 WOX genes were identified and clustered into 24 orthologous gene groups (OGGs). Pangenome profiling revealed that the WOX family is highly conserved across alfalfa accessions, with members of the Ancient clade showing greater conservation than those of the Intermediate and WUS clades. Duplication pattern analysis indicated that dispersed duplication was the primary force driving WOX family expansion, whereas whole‐genome duplication (WGD) events predominantly contributed to the long‐term retention of core and softcore members. Pairwise Ka/Ks analysis indicated strong purifying selection on most WOX gene pairs, whereas wild‐germplasm genes and Intermediate‐clade members showed elevated selective pressures. Notably, MsWOX9‐related homologs had exceptionally high Ka/Ks values, suggesting potential functional divergence linked to agronomically relevant traits. Furthermore, pan‐transcriptome analysis revealed that WOX genes could be classified into three distinct expression patterns during leaf senescence. Collectively, this study presents the first comprehensive pangenome‐ and pan‐transcriptome‐based characterization of the WOX family in alfalfa, providing new insights into its evolutionary dynamics and expression divergence.

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.

Genome-Wide Identification and Light-Induced Expression Analysis of the BPC Gene Family in Peucedanum praeruptorum Dunn

The BASIC PENTACYSTEINE (BPC) family represents a group of plant-specific transcription factors with established functions in developmental regulation and environmental adaptation. Although BPC genes have been catalogued in diverse plant species, their genome-wide characterization and light-dependent expression dynamics remain unexplored in the medicinal herb Peucedanum praeruptorum Dunn. Here, we report the systematic identification of eight PpBPC loci from the P. praeruptorum genome assembly through comprehensive bioinformatic screening. Evolutionary reconstruction grouped these eight members into three distinct clades (designated A, B, and C). Comparative genomic analyses revealed pronounced syntenic conservation between PpBPCs and their counterparts in Arabidopsis thaliana, Angelica sinensis, and Daucus carota. Members clustered within the same phylogenetic group displayed analogous exon-intron architectures and conserved motif repertoires, and all possessed the characteristic GAGA-binding domain. Examination of transcript abundance across organs demonstrated that clade A and C members shared broadly overlapping expression signatures in root, stem, and leaf tissues, whereas clade B genes exhibited organ-prevalent patterns. When seedlings were treated with three monochromatic light regimes, the PpBPC family displayed heterogeneous transcriptional responses, with individual clades showing distinct wavelength sensitivities. In particular, PpBPC6 and PpBPC8 were strongly activated by blue light. Collectively, these data delineate the foundational landscape of the PpBPC family and highlight candidate members likely involved in light signal transduction, thereby establishing a framework for future mechanistic dissection of light-responsive gene regulation in P. praeruptorum.