Genome-Wide Identification of the WOX Gene Family in Three Populus Species and Expression Profiling of Populus euphratica and Populus pruinosa Under Abiotic Stresses
Jul 2026· International Journal of Molecular Sciences· Vol 27, pp. 5999· 0 citations· 59 references
Medicine
TL;DR
Analysis of WOX genes in Populus provides comprehensive insights into the evolutionary conservation and divergence of WOX genes in Populus, establishing a theoretical foundation for the molecular breeding of stress-tolerant woody plants.
Abstract
The WUSCHEL-related homeobox (WOX) gene family plays crucial roles in plant growth, development, and stress responses. In this study, a comprehensive genome-wide analysis of WOX genes was conducted in three Populus species, P. euphratica, P. pruinosa, and P. deltoides. A total of 16, 16, and 21 WOX genes were identified, respectively, and classified into three clades (ancient, intermediate, and WUS/modern) based on phylogenetic relationships. Structural analyses revealed highly conserved homeodomain motifs and similar exon–intron organizations, indicating strong evolutionary conservation. Furthermore, synteny analyses demonstrated that whole-genome duplication or segmental duplication events were the primary drivers of WOX gene family expansion, with most duplicated gene pairs undergoing purifying selection. Promoter analysis identified abundant cis-acting elements related to light responsiveness, hormone signaling, and stress responses. Notably, transcriptomic profiling during seed germination under drought and salt stress revealed distinct interspecific expression patterns and temporal dynamics between the two desert poplars. Specifically, members such as PeWox11 and PpWox2 were significantly induced, suggesting their potential involvement in abiotic stress adaptation. These findings provide comprehensive insights into the evolutionary conservation and divergence of WOX genes in Populus, establishing a theoretical foundation for the molecular breeding of stress-tolerant woody plants.
The TIFY gene family comprises plant-specific transcriptional regulators central to jasmonic acid (JA) signaling and responses to biotic and abiotic stresses. Despite the economic importance of the banana (Musa spp.), the TIFY family remains largely uncharacterized in this crop. Here, we conducted a genome-wide identification and comprehensive analysis of the MaTIFY gene family in Musa acuminata. A total of 47 MaTIFY genes were identified, distributed across all 11 chromosomes. Phylogenetic analysis classified these into four subfamilies (TIFY, ZIZ/ZML, PPD, and JAZ), and conserved motif and domain analyses revealed a core TIFY domain architecture with subfamily-specific structural features. Gene Ontology (GO) enrichment and cis-acting regulatory element analyses suggested potential involvement in JA-mediated signaling, defense response, and hormone cross-talk. Expression profiling under drought, Fusarium oxysporum f. sp. cubense race 4 (Foc 4), and cold stress revealed distinct transcriptional responses, with MaTIFY5, MaTIFY16, MaTIFY20, MaTIFY26, and MaTIFY30 exhibiting enhanced induction in resistant cultivars compared to their susceptible counterparts. Functional characterization of MaTIFY20 confirmed its significant upregulation under drought stress and its ability to confer enhanced osmotic tolerance when heterologously expressed in yeast. These findings provide novel insights into the evolutionary dynamics and stress-responsive functions of banana TIFY genes and identify candidate targets for molecular breeding to improve abiotic and biotic stress resilience in banana.
Sheraz Ahmad, Huimin Song, Hangbo Cao et al.· International Journal of Mol...· 0 citations
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.
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.
Yang Huang, Li Jia, Kunyu Ma et al.· Horticulturae· 0 citations
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.
Hao Wen, Yiwei Bai, Zhao Guo et al.· Ecology and Evolution· 0 citations
Auxin is a central phytohormone involved in regulating plant growth, development, and stress responses, with the
Aux/IAA
gene family functioning as an essential component of the auxin signaling pathway. To elucidate the genomic features and potential functions of the
Aux/IAA
gene family in pumpkin (
Cucurbita moschata
), we performed a genome-wide identification and systematic characterization.
A total of 72
CmIAA
genes were identified, encoding proteins ranging from 158 to 1275 amino acids with predicted isoelectric points of 4.57–9.81. These genes were unevenly distributed across 20 chromosomes, with Chr17 harboring the highest number, while no
CmIAA
genes were detected on Chr3. Phylogenetic analysis classified the genes into nine subgroups (Groups Ⅰ–Ⅸ), with Groups Ⅰ, Ⅵ, and Ⅸ exhibiting relative expansion. Gene structure and conserved motif analyses revealed subgroup-specific motif compositions, with motif 1 representing the core conserved domain. Intraspecific collinearity analysis identified 54 segmentally duplicated gene pairs but no tandem duplication events, whereas interspecific synteny revealed extensive orthologous relationships between pumpkin and
Cucurbita pepo
and
Cucurbita maxima
. Promoter analysis showed that
CmIAA
genes contain multiple cis-elements associated with hormone responses and abiotic stress responses, including ABRE, MBS, and DRE. Tissue expression analysis demonstrated that many
CmIAA
genes exhibited tissue-preferential expression patterns. Under abiotic stress conditions,
CmIAA
69 showed a salt-specific expression pattern, whereas
CmIAA
39 and
CmIAA
58 responded to both salt and drought treatments, indicating that these
CmIAA
genes play distinct roles in pumpkin responses to different abiotic stresses.
This study systematically characterized the
Aux/IAA
gene family in pumpkin, highlighting its evolutionary diversity, structural conservation, and distinct regulatory features. These findings provide valuable genetic resources for further functional studies and inform the potential roles of
CmIAA
genes in abiotic stress responses.
Cold stress is a major abiotic threat to apple production.
Malus baccata
has exceptional cold hardiness and is widely used as a superior cold-resistant rootstock. The WUSCHEL-related homeobox (WOX) transcription factor family regulates plant growth, development and stress adaptation, whereas the functions of WOX genes in cold tolerance of
M. baccata
remain elusive.
In the present work, 19 MbWOX family members were identified and characterized at the genome-wide level. Evolutionary analysis, cis-element prediction, transcriptome profiling and real-time quantitative PCR (RT-qPCR) were performed to screen core cold-responsive genes. Overexpression vectors were constructed and transformed into Arabidopsis seedlings for functional verification.
Evolutionary analysis revealed that segmental duplication drove the expansion of the MbWOX family, and these genes contained a variety of stress-responsive cis-elements. Combined transcriptome and RT-qPCR analyses confirmed that
MbWOX4
and
MbWOX13
were core cold-responsive genes with distinct expression patterns. The two genes participated in cold signal transduction by interacting with different transcription factor networks. Functional tests revealed that
MbWOX4
and
MbWOX13
isoforms differentially modulated seedling cold tolerance under low-temperature stress.
Yan-Ting Tian, Hao Liu, Fei Wang et al.· Frontiers in Genetics· 0 citations
