Search Results (162)

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are pivotal upstream regulators of MAPK cascades, integrating signals that coordinate plant development and stress responses. However, the specific functions of MAPKKKs, particularly within the MEKK subfamily, in mediating cotton resistance to Verticillium wilt and Fusarium wilt remain poorly characterized. To address this, we conducted a systematic, cross-species analysis of the MAPKKK family in four key cotton species: Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii. Genome-wide identification and phylogenetic analysis revealed 660 MAPKKK genes, classifying them into the MEKK, Raf, and ZIK subfamilies. Evolutionary analysis indicated that Whole-Genome Duplication (WGD) events were the primary driver of family expansion. Promoter cis-element and Gene Ontology (GO) enrichment analyses implicated these genes in hormone signaling and stress adaptation. Expression profiling demonstrated functional modularity, with distinct members responding specifically to cold stress or cooperatively to drought and salt stresses. Upon pathogen infection, members diverged into regulatory modules associated with immune homeostasis, tissue-specific defense, and core signaling potentially governing systemic acquired resistance (SAR). The temporal expression patterns of core candidate genes were validated by qRT-PCR. This study provides, for the first time, a comprehensive evolutionary and functional framework for the MEKK subfamily within the cotton MAPKKK family. It reveals the conserved and divergent roles of this subfamily in stress adaptation and identifies key candidate genes for breeding disease-resistant cotton varieties. Full article

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus Notopterygium is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai–Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the SBP family genes in Notopterygium species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of SBPs of N. franchetii to the drought and high-temperature stresses. The 21, 18, and 18 SBP family genes of three Notopterygium species, N. incisum, N. franchetii, and N. forrestii, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same SBP subfamily had similar structures and conserved motif composition. Cis-element analysis suggested that those SBP genes may have been essential to the growth and environmental adaptation of Notopterygium. The expansion of the SBP gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the SBP gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on SBPs variations suggested that the genus Notopterygium species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of SBPs genes in Notopterygium were not species-specific, but tissue-specific. NinSBP08 and NinSBP10/12 may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the SBP gene family in the endangered herb Notopterygium species in the high-altitude Qinghai–Tibet Plateau and adjacent areas. Full article

Ormosia henryi, a rare and endemic timber tree in China, possesses exceptional economic and ecological value, but it has experienced a critical decline in wild populations. We integrated PacBio HiFi and Hi-C technologies to generate a superior, chromosome-level genome assembly, establishing a more robust genetic foundation than existing draft sequences. The resulting assembly (2.64 Gb; Contig N50 = 39.17 Mb; and Scaffold N50 = 338.40 Mb) exhibits high continuity and completeness, effectively overcoming the assembly challenges associated with high heterozygosity (1.37%) and repetitive sequence content (83.89%). Comparative genomic analysis revealed that O. henryi diverged from Lupinus albus approximately 53.82 million years ago and underwent two independent whole-genome duplication events. The historical accumulation of evolutionary resilience is reflected in the significant expansion of 276 gene families enriched in photosynthesis and phenylpropanoid biosynthesis, alongside 122 genes under positive selection involved in DNA repair and proteostasis. These genomic signatures elucidate a stable genetic foundation. While wild populations have sharply declined in recent decades, this suggests that this status underscores the overwhelming impact of intense external anthropogenic pressures, such as overexploitation and habitat fragmentation, which may have overridden the species’ inherent adaptive capacity and slow life-history strategy. This high-quality genomic resource identifies key candidate loci, such as the PIF1 helicase for growth regulation, and provides a critical framework for screening elite germplasm for population restoration. Consequently, this study establishes a theoretical and molecular basis for transitioning from fundamental research to the precision conservation and sustainable industrial application of this high-value woody species. Full article

The global aquaculture industry produces 91 million tons annually, yet achieving sustainable growth optimization remains constrained by incomplete understanding of regulatory system integration, polyploid genomic complexity, and disconnected molecular-environmental approaches. This systematic review synthesizes 180 peer-reviewed articles (1992–2025) from four databases, revealing that growth regulation operates through integrated multi-level networks: the GH-IGF axis, TGF-β/myostatin signaling, and epigenetic mechanisms responding dynamically to environmental inputs. Research acceleration is evident, with 52.2% of studies published during 2020–2025. Whole-genome duplication events created expanded gene repertoires enabling sophisticated regulatory control while presenting breeding challenges in polyploid species. CRISPR-Cas9 myostatin knockout achieves 15–30% growth enhancement, though practical implementation faces regulatory and economic barriers. DNA methylation and microRNAs enable environmental adaptation and transgenerational trait inheritance, offering complementary approaches to conventional breeding. Climate-resilient strain development requires integrating polyploid breeding methodologies, multi-omics phenotyping platforms, and validated epigenetic markers. Sustainable aquaculture intensification through precision genetics demands coordinated infrastructure development, harmonized regulatory frameworks, and international collaboration to address food security while adapting to climate change. This synthesis establishes research priorities bridging molecular mechanisms with practical applications for sustainable production enhancement. Full article

Matrix metalloproteases (MMPs) are zinc-dependent endopeptidases that are critical for extracellular matrix (ECM) remodeling, with key roles in tissue development and repair, and immune responses. Despite their evolutionary and functional importance, the diversification and regulatory dynamics of MMPs genes in teleosts remain poorly understood. This study investigates the evolutionary history of MMPs with collagenolytic activity in the vertebrates with an emphasis on teleosts. Using comparative genomics and phylogenetics we identified conserved single-copy mmp2 and mmp9 genes and duplicated mmp11 and mmp13 paralogs in all non-salmonid teleosts. Phylogenetic and synteny analyses suggest that mmp11 paralogs originated from the teleost-specific genome duplication (TSGD), whereas the origin of mmp13 paralogs originated from a more complex evolutionary scenario. Protein domain analysis confirmed conserved catalytic motifs across species, supporting functional retention. The expression patterns of paralog genes were studied in two model marine teleosts, the Sparus aurata (gilthead sea bream) and Dicentrarchus labrax (European sea bass). Developmental and adult tissue transcriptome analyses revealed three major expression patterns among the paralogs: similar expression, stage-specific or tissue-specific expression. The overall data point to varied evolutionary dynamics of MMP genes in the teleosts, tracing their origin to different whole-genome duplication events. Expression profiles on paralog genes in model teleosts suggest regulatory sub-functionalization as the most possible fate of retained MMPs paralogs in teleosts following whole-genome duplication. Full article

Sugars function as essential signaling molecules and metabolic substrates in plant growth, development, yield formation, and fruit quality. The aril of litchi (Litchi chinensis Sonn.) accumulates high levels of hexoses, primarily glucose and fructose; however, the molecular mechanisms underlying this process remain poorly characterized. This study aimed to systematically identify the monosaccharide transporter (MST) gene family in litchi and elucidate its role in aril sugar accumulation. Through a comprehensive analysis of the litchi genome, we identified a total of 45 LcMST genes, which were classified into seven distinct subfamilies: STP, ERD6L, PLT, INT, pGlcT, TMT, and VGT. Analysis of gene structure and conserved motifs revealed notable conservation among members within the same subfamily. Collinearity and gene duplication analyses suggested that the LcMST family expanded through both tandem and whole-genome duplication events, a process primarily governed by purifying selection. Expression profiling across diverse tissues demonstrated that LcMST genes exhibit distinct tissue-specific expression patterns. During fruit development in the hexose-dominant cultivar ‘Tianshuili’, the expression of the tonoplast monosaccharide transporter gene LcTMT1 exhibited a significant positive correlation with the accumulation of fructose, glucose, and total sugars. Heterologous functional complementation assays in yeast confirmed the ability of LcTMT1 to transport both glucose and fructose. In conclusion, this study presents the first genome-wide identification and characterization of the MST gene family in litchi, and identifies LcTMT1 as a key contributor of hexose accumulation in the aril. These findings establish a foundation for elucidating the molecular mechanisms of sugar accumulation in litchi fruit and for guiding future genetic improvement of fruit quality. Full article

Magnoliids represent one of the most basal lineages within angiosperms, and their ancestral floral morphology provides crucial insights into the evolution of flowers in angiosperms. MCM1-AGAMOUS-DEFICIENS-SRF (MADS)-box transcription factors play crucial roles in specifying floral organs. To understand their evolutionary history and functional divergence in magnoliids, we identified MADS-box genes, and conducted phylogenetic and expression analysis in 33 magnoliids and 8 other angiosperm plants. A total of 1310 MADS-box genes were identified and classified into Type I and Type II. The expansion of MADS-box genes in magnoliids mainly arose from whole-genome duplication events. In Liriodendron chinensis and Chimonanthus praecox, we identified floral homeotic MADS-box genes that are orthologous to the ABCDE model genes of floral organ identity determination. The broad expression pattern of A and B genes in floral organs and overlapping activity of ABCDE-model genes are consistent with the “shifting−fading borders” scheme proposed in basally diverging angiosperm lineages. Our results not only elucidate the driving forces underlying the diversification of MADS-box genes in magnoliids, but also shed light on the evolutionary models of floral development in angiosperms. Full article

Background: Transcription factors (TFs) critically regulate gene expression, orchestrating plant growth, development, and stress responses. The conserved IDD (INDETERMINATE DOMAIN) TF family modulates key developmental processes, including root, stem, and seed morphogenesis. Dendrocalamus latiflorus Munro, an economically vital sympodial bamboo in southern China, suffers significant yield losses due to prevalent bamboo shoot abortion, impacting both edible shoot production and timber output. Despite the documented roles of IDD TFs in shoot apical meristem expression and lateral organ regulation, their genome-wide characterization in D. latiflorus remains unstudied. Methods: Using IDD members from Arabidopsis thaliana, Oryza sativa, and Phyllostachys edulis as references, we identified 45 DlIDD genes in D. latiflorus. Comprehensive bioinformatics analyses included gene characterization, protein physicochemical assessment, phylogenetic reconstruction, and examination of gene structures/conserved domains. Differential expression of DlIDD genes was profiled between dormant and sprouting bamboo shoots to infer putative functions. Results: The 45 DlIDD genes were phylogenetically classified into three subfamilies and unevenly distributed across 34 chromosomes. Whole-genome duplication (WGD) events drove the expansion of this gene family. Promoter analyses revealed enriched cis-regulatory elements associated with hormone response and developmental regulation. Functional analyses suggested potential roles for DlIDD genes in bamboo shoot development. Conclusions: This study provides a foundation for future research to elucidate the functions of IDD TFs and their regulatory mechanisms in bamboo shoot morphogenesis and lateral bud development within woody monocots. Full article

RNA-directed DNA methylation (RdDM) is an epigenetic mechanism involved in several biological processes in plants, requiring complex machinery including the chromatin remodeling protein CLASSY (CLSY). The CLSY family regulates global and locus-specific DNA methylation and was initially identified in Arabidopsis thaliana. Despite reports in other plants, detailed knowledge about CLSY proteins in soybean is scarce. In this work, we used profile hidden Markov models (profile HMMs) specifically constructed for CLSY detection to identify new members in soybean and to analyze their phylogenetic relationships across bryophyte, basal angiosperm, basal eudicot, monocots, and eudicots. We identified two new candidates for CLSY1-2 and one for DRD1 in soybean and, for the first time, detected CLSY and DRD1 genes in Aquilegia coerulea. Phylogenetic analysis indicated two main CLSY groups: one similar to Arabidopsis CLSY1-2 and another to CLSY3-4. Gene duplication analysis demonstrated that whole-genome duplication/segmental duplication events contributed to CLSY family expansion in soybean. RT-qPCR analysis showed that CLSY and five other epigenetic regulator genes had stress-modulated expression during soybean germination under salt and osmotic stress, with variation among cultivars. Our findings enhance comprehension of the evolutionary dynamics of the CLSY family and furnish insights into their response to abiotic stress in soybean. Full article

GATA transcription factors are crucial for plant development and environmental responses, yet their roles in plant evolution and root nodule symbiosis are still not well understood. This study identified GATA genes across the genomes of 77 representative plant species, revealing that this gene family originated in Charophyta and significantly expanded in both gymnosperms and angiosperms. Phylogenetic analyses, along with examinations of conserved motifs and cis-regulatory elements in Glycine max and Arabidopsis, clearly demonstrated structural and functional divergence within the GATA family. Chromosomal mapping and synteny analysis indicated that GATA gene expansion in soybean primarily resulted from whole-genome duplication events. These genes also exhibit high conservation and signs of purifying selection in Glycine max, Lotus japonicus, and Medicago truncatula. Furthermore, by integrating phylogenetic and transcriptomic data from eight nitrogen-fixing legume species, several GATA genes were identified as strongly co-expressed with NIN1, suggesting their potential co-regulatory roles in nodule development and symbiosis. Collectively, this study offers a comprehensive overview of the evolutionary dynamics of the GATA gene family and highlights their potential involvement in root nodule symbiosis in legumes, thus providing a theoretical foundation for future mechanistic studies. Full article

Peanut (Arachis hypogaea L.) is a globally important oilseed cash crop, yet its limited genetic diversity and unique reproductive biology present persistent challenges for conventional crossbreeding. Traditional breeding approaches are often time-consuming and inadequate, mitigating the pace of cultivar development. Essential for double fertilization and programmed cell death (PCD), DUF679 membrane proteins (DMPs) represent a membrane protein family unique to plants. In the present study, a comprehensive analysis of the DMP gene family in peanuts was conducted, which included the identification of 21 family members. Based on phylogenetic analysis, these genes were segregated into five distinct clades (I–V), with AhDMP8A, AhDMP8B, AhDMP9A, and AhDMP9B in clade IV exhibiting high homology with known haploid induction genes. These four candidates also displayed significantly elevated expression in floral tissues compared to other organs, supporting their candidacy for haploid induction in peanuts. Subcellular localization prediction, confirmed through co-localization assays, demonstrated that AhDMPs primarily localize to the plasma membrane, consistent with their proposed roles in the reproductive signaling process. Furthermore, chromosomal mapping and synteny analyses revealed that the expansion of the AhDMP gene family is largely driven by whole-genome duplication (WGD) and segmental duplication events, reflecting the evolutionary dynamics of the tetraploid peanut genome. Collectively, these findings establish a foundational understanding of the AhDMP gene family and highlight promising targets for future applications in haploid induction-based breeding strategies in peanuts. Full article

Salt stress severely limits the growth and ornamental value of pecan (Carya illinoinensis) in salinized regions, yet the transcriptional mechanisms underlying its stress adaptation remain unclear. In this study, a comprehensive genomic analysis of the GRAS transcription factor family identified 58 CiGRAS genes in pecan. These genes were classified into 11 subfamilies and showed conserved motifs and gene structures, with variation in promoter cis-elements suggesting diverse regulatory functions. Chromosomal distribution and duplication analysis indicated that whole-genome and dispersed duplication events were the main drivers of CiGRAS expansion. Transcriptome data revealed tissue-specific expression and strong responsiveness to salt and other stresses. Under 0.6% NaCl treatment, several CiGRAS genes were significantly upregulated, especially at 48 h. Gene co-expression analysis further highlighted GRAS-enriched modules associated with redox regulation and stress signaling. qRT-PCR validation confirmed time-specific induction of seven CiGRAS genes under salt stress. These findings provide insights into the evolutionary dynamics and stress-related roles of CiGRAS genes and offer candidate regulators for improving pecan salt tolerance in ecological greening and landscape applications. Full article

Capsicum (pepper) is an economically vital genus in the Solanaceae family, with most species possessing about 3 Gb genomes. However, the recently sequenced Capsicum rhomboideum (~1.7 Gb) represents the first reported case of an extremely compact genome in Capsicum, providing a unique and ideal model for studying genome size evolution. To elucidate the mechanisms driving this variation, we performed comparative genomic analyses between the compact Capsicum rhomboideum and the reference Capsicum annuum cv. CM334 (~2.9 Gb). Although their genome size differences initially suggested whole-genome duplication (WGD) as a potential driver, both species shared two ancient WGD events with identical timing, predating their divergence and thus ruling out WGD as a direct contributor to their size difference. Instead, transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), emerged as the dominant force shaping genome size variation. Genome size strongly correlated with LTR-RT abundance, and multiple LTR-RT burst events aligned with major phases of genome expansion. Notably, the integrity and transcriptional activity of LTR-RTs decline over evolutionary time; older insertions exhibit greater structural degradation and reduced activity, reflecting their dynamic nature. This study systematically delineated the evolutionary trajectory of LTR-RTs—from insertion and proliferation to decay–uncovering their pivotal role in driving Capsicum genome size evolution. Our findings advance the understanding of plant genome dynamics and provide a framework for studying genome size variation across diverse plant lineages. Full article

Background: N6-methyladenosine (m6A) is the most prevalent chemical modification of eukaryotic RNA, playing a crucial role in regulating plant growth and development, stress responses, and other essential biological processes. The enzymes involved in m6A modification—methyltransferases (writers), demethylases (erasers), and recognition proteins (readers)—have been identified in various plant species; however, their roles in the economically significant tree species Populus deltoides × P. euramericana (NL895) remain underexplored. Results: In this study, we identified 39 m6A-related genes in the NL895 genome, comprising 8 writers, 13 erasers, and 18 readers. Evolutionary analysis indicated that the expansion of writers and readers primarily resulted from whole-genome duplication events. Purifying selection pressures were observed on all duplicated gene pairs, suggesting their essential roles in functional differentiation. Phylogenetic analysis revealed that writers, erasers, and readers are categorized into six, four, and two groups, respectively, with these genes being more conserved among dicotyledonous plants. Gene structure, protein domains, and motifs exhibited greater conservation within the same group. Promoter analysis of m6A-related genes showed enrichment of cis-acting elements associated with responses to light, phytohormones, and stress, indicating their potential involvement in gene expression regulation. Under cadmium treatment, the expression of all writers was significantly upregulated in both the aboveground and root tissues of NL895. Conclusions: This study systematically identified m6A-related gene families in Populus deltoides × P. euramericana (NL895), elucidating their evolutionary patterns and expression regulation characteristics. These findings provide a theoretical foundation for analyzing the molecular mechanisms of m6A modification in poplar growth, development, and stress adaptation, and offered candidate genes for molecular breeding in forest trees. Full article

The root system is vital for Brassica napus water/nutrient uptake and anchorage, highlighting the importance of identifying root development genes (RDGs). In this study, we identified 218 RDGs in B. napus through homology-based retrieval. Phylogenetic analysis of 22 representative species revealed that the RDGs are widely present in plants ranging from aquatic algae to angiosperms. RDGs in B. napus expanded through whole-genome duplication (WGD) events between Brassica rapa and Brassica oleracea ancestors and smaller duplications specific to B. napus. Promoter analysis identified 115 cis-elements, mainly abiotic stress-related and light-responsive. Transcription factor networks showed regulation by BBR-BPC, MIKC_MADS, AP2, and GRAS families. Transcriptome analysis under multiple stresses revealed that low nitrogen (LN) induced the most pronounced changes, with >50% (109/218) of RDGs differentially expressed in roots. Furthermore, we screened the BnaSHR-6 gene, which is co-localized in both primary roots (PR) and lateral roots (LR), and responds strongly to LN. Phenotypic analysis revealed that the BnaSHR-6 gene regulates the growth and development of both PR and LR under LN conditions, and confers a degree of resistance. These findings advance our understanding of RDGs in B. napus and provide valuable gene resources for subsequent molecular breeding. Full article