Search Results (119)

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

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

Auxin/induced-3-acetic acid (Aux/IAA) serves as a key regulator in the auxin signaling pathway of plants, which exhibits crucial functions in the development of plants. However, the Aux/IAA gene family has not yet been characterized in the genome of Castanea mollissima, an important food source in the Northern Hemisphere. During this research, 23 Aux/IAA genes were identified in the C. mollissima genome, which were unevenly distributed across seven chromosomes. CmAux/IAA genes were assigned to four subfamilies by phylogenetic analysis, and members of the same subfamily exhibited similar molecular characteristics. Collinear analysis revealed that the expansion of CmAux/IAA genes was primarily driven by whole-genome duplication (WGD) and purifying selection. The promoter regions of CmAux/IAA genes were enriched with development-related and hormone-related cis-acting elements, suggesting their crucial functions in the growth and hormonal regulation of C. mollissima. Upon the maturation of the seed kernels, the size and starch content exhibited a significant increasing trend, alongside notable changes in hormone levels. Given the connections between expression levels and physiological indicators, as well as weighted gene co-expression network analysis (WGCNA) analysis, CmIAA27a, CmIAA27b, and CmIAA27c were identified as potential regulators involved in the development of C. mollissima seed kernels. Furthermore, the reliability of the transcriptomic data was further confirmed by RT-qPCR experiments. Overall, this study provides a theoretical basis for the evolutionary expansion of the Aux/IAA gene family in C. mollissima, alongside its potential functions in seed kernel development. Full article

DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in multiple important biological processes in fish, such as gonadal development. The cellular DNA methylation level is tightly regulated by DNA methyltransferases (Dnmt). However, detailed investigations of this family in fish are very scarce. In this study, our results confirmed that teleost genomes contain 4 to 16 Dnmt genes, with diversity likely resulting from a combination of whole-genome duplication (WGD), tandem duplication, and gene loss. Differences were observed in tissue distribution, transcription abundance, and protein structure of Dnmt duplicates, supporting their subfunctionalization or neofunctionalization after duplication. Interestingly, we found that fish Dnmt3b duplicates likely have acquired the functions of mammalian Dnmt3l, which may compensate for the absence of fish Dnmt3l. Furthermore, transcriptome analysis and qPCR results indicated that DNA methyltransferase genes (Dnmt1, Dnmt3aa, Dnmt3ab, Dnmt3ba, and Dnmt3bb.1) possibly play important roles in the natural sex change of protandrous hermaphrodite blackhead seabream (Acanthopagrus schlegelii) and inferred that global remodeling of gonadal DNA methylation, regulated by DNA methyltransferase genes, was closely associated with sex change in sequentially hermaphroditic fishes. Overall, our results may help provide a better understanding of the evolution and function of DNA methyltransferases in fish. Full article

The transcription factor known as TALE (three-amino acid loop extension) is essential for plant growth, cell differentiation and responses to environmental stresses. Although the TALE gene family has been identified in various plants, there has been a lack of comprehensive whole-genome identification and analysis in Gramineae species. In this study, 123 TALE family genes were identified in five Gramineae species, which can be categorized into two main subgroups: KONX and BELL. Most of the TALE genes in the same subgroup displayed analogous gene structures and conserved motifs. Furthermore, whole genome duplication (WGD) significantly contributes to the expansion of the TALE gene family in Gramineae. The promoter region of TALE genes in Gramineae contains a large number of cis-elements associated with abiotic stress and hormone response. Tissue-specific expression analysis indicated that most OsTALE, ZmTALE and AtTALE genes were highly expressed in stems and leaves. Additionally, RNA-seq data revealed that OsTALE, ZmTALE and AtTALE genes were found to respond to abiotic stress treatments. Furthermore, we found that the expression levels of SbTALE11/19 were up-regulated in response to PEG and NaCl treatment, respectively. This study provides a significant reference for further research on the biological function of TALE transcription factors in Gramineae plants. 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

Wolfberry (Lycium barbarum L.) is a valued traditional medicinal plant and dietary supplement in China. The basic leucine zipper (bZIP) transcription factor (TF) family is a multifunctional group of regulatory proteins critical to plant biology, orchestrating processes such as growth and development, secondary metabolite biosynthesis, and stress responses to abiotic conditions. Despite its significance, limited information about this gene family in wolfberry is available. In this study, a total of 66 LbabZIP genes were identified, exhibiting a non-uniform distribution across all 12 chromosomes. Phylogenetic analysis divided these genes into 13 subgroups based on comparison with Arabidopsis bZIP proteins. Analysis of gene structures and conserved motifs revealed high similarities within individual subgroups. Gene duplication analysis indicated that dispersed duplication (DSD) and whole-genome duplication (WGD) events were the primary drivers of LbabZIP gene family expansion, with all duplicated genes subject to purifying selection. Cis-regulatory element (CRE) analysis of LbabZIP promoter regions identified numerous elements associated with plant growth and development, hormone signaling, and abiotic stress responses. Gene Ontology (GO) annotation further indicated that the LbabZIP genes are involved in transcriptional regulation, metabolism, and other biological processes. Transcriptome data and quantitative real-time PCR (qRT-PCR) analysis demonstrated tissue-specific expression patterns for several LbabZIP genes. Notably, LbaZIP21/40/49/65 showed significant involvement in wolfberry fruit development. Subcellular localization assays confirmed that these four proteins are nucleus-localized. This comprehensive analysis provides a theoretical foundation for future studies investigating the biological functions of LbabZIP genes, especially their role in wolfberry fruit development. Full article

The valine glutamine (VQ) proteins are transcription cofactors involved in various aspects of plant biology, including growth, development, and stress resistance, making them an attractive target for genetic engineering aimed at enhancing plant resilience and productivity. However, comprehensive reports or systematic studies on VQ cofactors in Salix suchowensis remain lacking. In this study, we analyzed SsVQ genes using bioinformatics methods based on the Salix suchowensis genome database. Expression profiles were further investigated through qRT-PCR under six treatments: PEG, NaCl, 40 °C, ABA, SA, and MeJA. A total of 39 SsVQ genes were identified, with phylogenetic analysis classifying them into seven groups. Collinearity analysis suggested that SsVQ gene amplification primarily resulted from whole genome duplication (WGD) or segmental duplication events. Ka/Ks ratios indicated that willow VQ genes have undergone predominantly purifying selection. Gene structure analysis revealed that SsVQ genes are intronless. Multiple sequence alignment showed that SsVQ19 shares similarity with PtVQ27, containing a hydrophilic threonine (T) residue preceding the VQ amino acid residues. Furthermore, genes within each group exhibited conserved structures and VQ motifs. Promoter and expression analyses suggested the potential roles of SsVQ genes in regulating willow responses to environmental stresses and hormonal signals. Most SsVQ genes displayed differential expression at specific time points, with six members (SsVQ2, SsVQ9, SsVQ12, SsVQ23, SsVQ32, and SsVQ34) showing sustained high-amplitude expression profiles across treatments. Notably, SsVQ34 demonstrated pronounced transcriptional induction under PEG stress, with expression levels upregulated by 62.29-fold (1 h), 49.21-fold (6 h), 99.9-fold (12 h), and 201.50-fold (24 h). Certain SsVQ genes showed co-expression under abiotic/hormonal stresses, implying synergistic functions. Paralogous gene pairs exhibited stronger co-expression than non-paralogous pairs. This study provides novel insights into the structural and functional characteristics of the VQ gene family in Salix suchowensis, establishing a foundation for future research on the stress-resistance mechanisms of willow VQ genes. Full article

Plant U-box E3 ubiquitin ligases (PUBs) serve as crucial regulators of protein degradation and are fundamentally involved in plant developmental processes and stress response mechanisms. Despite their well-characterized roles in model plant species, the PUB gene family in the hybrid poplar (Populus alba × P. tremula var. glandulosa) remains poorly understood. By conducting a comprehensive genome-wide analysis, we identified 152 PUB genes in poplar and phylogenetically classified them into five distinct clades based on a comparative analysis with Arabidopsis thaliana and tomato PUB homologs. The structural characterization revealed that numerous PagPUB proteins possess additional functional domains, including ARM and WD40 repeats, which are indicative of potential functional diversification. Genomic distribution and synteny analyses demonstrated that the expansion of the PUB gene family predominantly resulted from whole-genome duplication (WGD) events, with evolutionary constraint analyses (Ka/Ks ratios < 1) suggesting strong purifying selection. An examination of the promoter region uncovered an abundance of stress-responsive cis-elements, particularly ABRE and MYB binding sites associated with abiotic stress and hormonal regulation. Transcriptome profiling demonstrated both tissue-specific expression patterns and dynamic regulation under diverse stress conditions, including drought, salinity, temperature extremes, and pathogen infection. Our findings provide the first systematic characterization of the PUB gene family in poplar and establish a valuable framework for elucidating their evolutionary history and functional significance in environmental stress adaptation. Full article

Transcription factors play an important regulatory role in tomato fruit ripening. We identified and analyzed eight transcription factor families (TF families) associated with fruit ripening in the genomes of seven tomato species and two outgroup species, revealing the impact of whole-genome duplication (WGD) events on the structure and functional characteristics of these TF families. The results indicate that the Solanaceae Common Hexaploidization (SCH) event is the primary driver for the increase in the number of members within these TF families, leading to a more concentrated chromosomal distribution of family members. Compared with the two outgroup species, the tomato fruit-ripening-related TF families exhibit stronger codon usage bias, which may have been enhanced by WGD. Phylogenetic analysis found that family members generated by SCH show faster evolutionary rates, suggesting that SCH events significantly contribute to the evolution of these families. Additionally, our research uncovered that WGD events might maintain expression activity during fruit ripening by generating duplicate TF family members. Our study not only deepens our understanding of the mechanisms underlying tomato fruit ripening but also provides a theoretical foundation for future breeding improvements. Full article

Background/Objectives: GDSL lipase is crucial for plant growth and the response to environmental stress. While GDSL gene families have been identified in some plants, a comprehensive genome-wide identification and analysis in M. domestica is lacking. Methods: In this study, we identified 131 MdGDSLs belonging to four subfamilies, distributed across 17 chromosomes in the M. domestica genome. Results: The molecular weights (MWs) of these MdGDSLs range from 14.44 to 83.26 kDa, with isoelectric points (PI) spanning from 4.32 to 10.09. Members within the same subgroup exhibit similar gene structures and conserved motifs. Furthermore, whole genome duplication (WGD) significantly contributes to the evolution of the MdGDSL gene family. The promoter regions of MdGDSL genes contain numerous cis-elements associated with abiotic stress and hormone responses. Additionally, RNA-seq data indicate that MdGDSL genes respond to high concentrations of CaCl₂ and cold stress treatments. Conclusions: This study provides a theoretical foundation for further investigation into the mechanisms underlying growth, development, and lipid metabolism in response to stress in M. domestica. Full article

Gene duplication, as a prevalent phenomenon in the tree of life, provides a potential substrate for evolution. However, its role in the Aurantioideae remains unclear. In this study, we systematically identified, for the first time, a comprehensive landscape of five types of gene duplication in the genomes of 26 species within Aurantioideae, focusing on dissecting the duplication patterns, their potential evolutionary significance, and their impact on gene function and expression. Our results showed that the tandem duplication (TD) was a predominant duplication type and confirmed a shared ancient whole-genome duplication (γWGD) event within Aurantioideae. Ka/Ks indicated that all duplication types are under purifying selection pressure, with TD and proximal duplication (PD) undergoing rapid functional divergence. Gene Ontology (GO) enrichment analysis revealed functional specialization among different duplication types, collectively contributing to genome evolution. In addition, comparing the gene expression differentiation of the five gene duplication types between the outer and inner pericarps of Citrus maxima ‘Huazhouyou’, it was found that the proportion of gene expression differentiation in the exocarp was generally higher, suggesting tissue-specific functional roles for duplicated genes in the peel. Furthermore, gene conversion events revealed that Citrus sinensis and Citrus maxima ‘Huazhouyou’ experienced more gene conversion events, supporting that C. sinensis originated through hybridization with C. maxima as the maternal parent. Finally, the comparative analysis of gene families among 26 species in Aurantioideae revealed that small gene families (1–3 members) accounted for a substantial proportion in all species, indicating a lack of recent large-scale genome duplication events in this subfamily. These findings fill a gap in the understanding of gene duplication in Aurantioideae and provide a theoretical foundation for exploring the evolutionary mechanisms and breeding improvements within this group. Additionally, our study offers new insights into the contribution of gene duplication to functional diversification and ecological adaptation in other plants. Full article

The walnut (Juglans regia) is a woody oilseed crop with high economic and food value as its kernels are edible and its hulls can be widely used in oil extraction and plugging, chemical raw materials, and water purification. Currently, red walnut varieties have emerged, attracting consumer interest due to their high nutritional values as they are rich in anthocyanins. WD40 is a widespread superfamily in eukaryotes that play roles in plant color regulation and resistance to stresses. In order to screen for JrWD40 associated with walnut color, we identified 265 JrWD40s in walnuts by genome-wide identification, which were unevenly distributed on 16 chromosomes. According to the phylogenetic tree, all JrWD40s were classified into six clades. WGD (Whole genome duplication) is the main reason for the expansion of the JrWD40 gene family. JrWD40s were relatively conserved during evolution, but their gene structures were highly varied; lower sequence similarity may be the main reason for the functional diversity of JrWD40s. Some JrWD40s were highly expressed only in red or green walnuts. In addition, we screened 16 unique JrWD40s to walnuts based on collinearity analysis. By qRT-PCR, we found that JrWD40-133, JrWD40-150, JrWD40-155, and JrWD40-206 may regulate anthocyanin synthesis through positive regulation, whereas JrWD40-65, JrWD40-172, JrWD40-191, JrWD40-224, and JrWD40-254 may inhibit anthocyanin synthesis, suggesting that these JrWD40s are key genes affecting walnut color variation. Full article

As a subfamily of the PD-(D/E)XK nuclease superfamily, DUF506 family shows great potential in abiotic stress responding of higher plant, yet its clues of structure, evolution and functions remain largely unexplored due to their distant phylogenetic relationship with other nuclease families, especially in Triticum aestivum. In this study, 26 T. aestivum DUF506 genes (TaDUF506) were identified from genome-wide level through bioinformatic techniques. Phylogenetic and structural analyses revealed that TaDUF506 genes exhibit conserved motif and gene structure patterns intra-phylogenetic clusters but display significant divergence inter-clusters. Gene duplication identification showed that whole-genome duplication event (WGD) was the primary driver of TaDUF506 family expansion, while Ka/Ks analysis indicated that whole TaDUF506 family experienced purifying selection generally. Gene ontology analysis and protein-protein interaction prediction suggested that DUF506 plays a potential role in transcription regulation and nucleotide-excision generally. Promoter analyses highlighted an enrichment of hormone-responsive elements linked to salt stress in TaDUF1.3-3D TaDUF5.1-3A, with expression analysis demonstrated their significant upregulation under salt stress, suggesting the potential roles in stress responses. Altogether, our study advances the understanding of DUF506 gene family in higher plant from structural, evolutional and functional aspects, and thereby provides a foundation for the development of salt-tolerant wheat varieties. Full article

Background: The BBR-BPC gene family is a relatively conservative group of transcription factors, playing a key role in plant morphogenesis, organ development, and responses to abiotic stress. Brassica napus L. (B. napus), commonly known as oilseed rape, is an allopolyploid plant formed by the hybridization and polyploidization of Brassica rapa L. (B. rapa) and Brassica oleracea L. (B. oleracea), and is one of the most important oil crops. However, little is known about the characteristics, conservation, and expression patterns of this gene family in B. napus, especially under abiotic stress. Methods: To explore the characteristics and potential biological roles of the BBR-BPC gene family members in B. napus, we conducted identification based on bioinformatics and comparative genomics methods. We further analyzed the expression patterns through RNA-seq and qRT-PCR. Results: We identified 25 BBR-BPC members, which were classified into three subfamilies based on phylogenetic analysis, and found them to be highly conserved in both monocots and dicots. The conserved motifs revealed that most members contained Motif 1, Motif 2, Motif 4, and Motif 8. After whole-genome duplication (WGD), collinearity analysis showed that BBR-BPC genes underwent significant purifying selection. The promoters of most BBR-BPC genes contained cis-acting elements related to light response, hormone induction, and stress response. RNA-seq and qRT-PCR further indicated that BnBBR-BPC7, BnBBR-BPC15, BnBBR-BPC20, and BnBBR-BPC25 might be key members of this family. Conclusions: This study provides a theoretical foundation for understanding the potential biological functions and roles of the BBR-BPC gene family, laying the groundwork for resistance breeding in B. napus. Full article