Search Results (40)

Haploid breeding technology offers a promising means of significantly shortening the breeding cycle by rapidly generating homozygous inbred lines. Previous studies have shown that DMP8 is involved in haploid induction across various plant species. In this study, we performed whole-genome identification and bioinformatics analyses to investigate the evolutionary relationships, gene structures, conserved domains, and expression patterns of DMP gene family members in tomato (Solanum lycopersicum), pepper (Capsicum annuum) and eggplant (S. melongena). A total of seven, six, and eight DMP genes were identified in the genomes of tomato, pepper, and eggplant, respectively. All encoded proteins contained the DUF679 domain, and the DMP family members were clustered into three distinct groups. Collinearity analysis revealed species-specific expansions of DMP genes in the Solanaceae family. Phylogenetic analysis indicated that CaDMP8 and SmDMP8 are homologous to SlDMP8, with conserved gene and protein structures, suggesting that CaDMP8 and SmDMP8 are potential targets for developing haploid induction lines. Expression pattern analysis demonstrated that SlDMP4 and SlDMP8 are highly expressed in tomato flower tissues, suggesting their potential functional synergy. This study provides the first comprehensive insight into the evolutionary characteristics and functional diversification of the DMP gene family in Solanaceous vegetables. The findings offer a theoretical foundation for the targeted editing of DMP8 homologs to create haploid induction lines, which is critical for accelerating the genetic improvement of Solanaceous crops. 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

Proteins of the PF10950 family feature the DUF2775 domain of unknown function. The most studied are specific tissue (ST) proteins with tandem repeats, which are putative precursors of cyclopeptide alkaloids. Here, we study uncharacterised short ST (SST) proteins with the DUFF2775 domain by analysing 194 sequences from 120 species of 39 taxonomic families in silico. SST proteins have a signal peptide and their size and several other characteristics depend on their individual taxonomic family. Sequence analyses revealed that SST proteins contain two well-conserved regions, one resembling the ST repeat, which could constitute the core of cyclopeptide alkaloids. We studied the unique SST1 gene of Arabidopsis thaliana, which is adjacent to and co-expressed with a gene encoding a protein with a BURP domain, associated with cyclopeptide production. The empirical analysis indicated that the SST1 promoter is mainly activated in the roots, where most of the transcripts accumulate, and that the SST1 protein accumulates in the root vascular cambium. At the cellular level, SST fused to GFP appears in vesicles that co-localise with the endoplasmic reticulum and the vacuole. Thus, SSTs are a new type of PF10950 protein found in core eudicots with two conserved regions that could be involved in root biology. Full article

Background and Objectives: The imminent threat of antibiotic resistance has spurred studies of nonconventional antimicrobial approaches. Gallium utilization is a promising and emerging approach to treating a variety of resistant bacteria using “Trojan horse” strategies to disrupt iron-dependent processes and biofilms. This study utilized experimental evolution to test the evolvability of gallium resistance in Staphylococcus aureus and resistance traits potentially correlated with metals, antibiotics and polyfluorinated compounds, as well as its genomics foundations. Methods: Whole-genome sequencing was utilized to reveal functional networks of mutations associated with gallium resistance. Additionally, scanning electron microscopy (SEM) observation was utilized to visualize distinct morphological changes on the surface of gallium-resistant populations and compare with the control populations. Results: As demonstrated by these studies, S. aureus evolved resistance to gallium after 20 days of selection. Furthermore, these populations displayed resistance traits correlated with heavy metals and polyfluorinated compounds. In contrast, the gallium-resistant populations were very sensitive to antibiotics. Whole-genome analysis revealed significant polymorphisms in the gallium (III)-resistant populations for example, polymorphisms in staphyloferrinA export MFS transporter/D ornithine citrate ligase (sfaA/sfaD), teichoic acid D Ala esterase (fmtA), DUF3169 family protein (KQ76_RS01520) and adenine phosphoribosyltransferase (KQ76_RS08360), while polymorphisms in the ABC transporter permease subunit (pstC) and acyltransferase family protein (KQ76_RS04365) were unique to the control populations. The polymorphisms directly affected the cells’ morphology. SEM images showed significant external ultrastructural changes in the gallium-selected bacterial cells compared to the control cells. Conclusions: Our study confirmed that using gallium as an antimicrobial can have significant health and environmental implications. Full article

Background/Objectives: The Suppressor of Female Function (SOFF) and Shy Girl (SyGI) gene families play vital roles in sex determination in dioecious plants. However, their evolutionary dynamics and functional characteristics remain largely unexplored. Methods: Through this study, a systematic bioinformatics analysis of SOFF and SyGI families was performed in plants to explore their evolutionary relationships, gene structures, motif synteny and functional predictions. Results: Phylogenetic analysis showed that the SOFF family expanded over time and was divided into two subfamilies and seven groups, while SyGI was a smaller family made of compact molecules with three groups. Synteny analysis revealed that 125 duplicated gene pairs were identified in Kiwifruit where WGD/segmental duplication played a major role in duplicating these events. Structural analysis predicted that SOFF genes have a DUF 247 domain with a transmembrane region, while SyGI sequences have an REC-like conserved domain, with a “barrel-shaped” structure consisting of five α-helices and five β-strands. Promoter region analysis highlighted their probable regulatory roles in plant development, hormone signaling and stress responses. Protein interaction analysis exhibited only four SOFF genes with a close interaction with other genes, while SyGI genes had extensive interactions, particularly with cytokinin signal transduction pathways. Conclusions: The current study offers a crucial understanding of the molecular evolution and functional characteristics of SOFF and SyGI gene families, providing a foundation for future functional validation and genetic studies on developmental regulation and sex determination in dioecious plants. Also, this research enhances our insight into plant reproductive biology and offers possible targets for breeding and genetic engineering approaches. 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

Alfin-like proteins (ALs) form a plant-specific transcription factor (TF) gene family involved in the regulation of plant growth and development, and abiotic stress response. In this study, 30 ALs were identified in Brassica napus ecotype ‘Zhongshuang 11’ genome (BnaALs), and unevenly distributed on 15 chromosomes. Structural characteristic analysis showed that all of the BnaALs contained two highly conserved domains: the N terminal DUF3594 domain and the C-terminal PHD-finger domain. The BnaALs were classified into four groups (Group I-IV), supported by conserved intron–exon and protein motif structures in each group. The allopolyploid event between B. oleracea and B. rapa ancestors and the small-scale duplication events in B. napus both contributed to the large BnaALs expansion. The promoter regions of BnaALs contained multiple abiotic stress cis-elements. The BnaALs in I-IV groups were mainly expressed in cotyledon, petal, root, silique, and seed tissues, and the duplicated gene pairs shared highly similar expression patterns. RNA-seq and RT-qPCR analysis showed that BnaALs were obviously induced by low nitrogen (LN) and low phosphorus (LP) treatments in roots. Overexpressing BnaAL02 and BnaAL28 in Arabidopsis demonstrated their functions in response to LN and LP stresses. BnaAL28 enhanced primary roots’ (PRs) length and lateral roots’ (LRs) number under LP and LN conditions, where BnaAL02 can inhibit LR numbers under the two conditions. They can promote root hair (RH) elongation under LP conditions; however, they suppressed RH elongation under LN conditions. Our result provides new insight into the functional dissection of this family in response to nutrient stresses in plants. Full article

Plant cell walls are largely composed of polysaccharide polymers, including cellulose, hemicelluloses (xyloglucan, xylan, mannan, and mixed-linkage β-1,3/1,4-glucan), and pectins. Among these cell wall polysaccharides, xyloglucan, xylan, mannan, and pectins are often O-acetylated, and polysaccharide O-acetylation plays important roles in cell wall assembly and disease resistance. Genetic and biochemical analyses have implicated the involvement of three groups of proteins in plant cell wall polysaccharide O-acetylation: trichome birefringence-like (TBL)/domain of unknown function 231 (DUF231), reduced wall acetylation (RWA), and altered xyloglucan 9 (AXY9). Although the exact roles of RWAs and AXY9 are yet to be identified, members of the TBL/DUF231 family have been found to be O-acetyltransferases responsible for the O-acetylation of xyloglucan, xylan, mannan, and pectins. Here, we provide a comprehensive overview of the occurrence of O-acetylated cell wall polysaccharides, the biochemical properties, structural features, and evolution of cell wall polysaccharide O-acetyltransferases, and the potential biotechnological applications of manipulations of cell wall polysaccharide acetylation. Further in-depth studies of the biochemical mechanisms of cell wall polysaccharide O-acetylation will not only enrich our understanding of cell wall biology, but also have important implications in engineering plants with increased disease resistance and reduced recalcitrance for biofuel production. Full article

Alfin-like (AL) is a small plant-specific gene family characterized by a PHD-finger-like structural domain at the C-terminus and a DUF3594 structural domain at the N-terminus, and these genes play prominent roles in plant development and abiotic stress response. In this study, we conducted genome-wide identification and analyzed the AL protein family in Gossypium hirsutum cv. NDM8 to assess their response to various abiotic stresses for the first time. A total of 26 AL genes were identified in NDM8 and classified into four groups based on a phylogenetic tree. Moreover, cis-acting element analysis revealed that multiple phytohormone response and abiotic stress response elements were highly prevalent in AL gene promoters. Further, we discovered that the GhAL19 gene could negatively regulate drought and salt stresses via physiological and biochemical changes, gene expression, and the VIGS assay. The study found there was a significant increase in POD and SOD activity, as well as a significant change in MDA in VIGS-NaCl and VIGS-PEG plants. Transcriptome analysis demonstrated that the expression levels of the ABA biosynthesis gene (GhNCED1), signaling genes (GhABI1, GhABI2, and GhABI5), responsive genes (GhCOR47, GhRD22, and GhERFs), and the stress-related marker gene GhLEA14 were regulated in VIGS lines under drought and NaCl treatment. In summary, GhAL19 as an AL TF may negatively regulate tolerance to drought and salt by regulating the antioxidant capacity and ABA-mediated pathway. Full article

Members of DOMAIN OF UNKNOWN FUNCTION 679 membrane proteins (DMPs) have the DUF679 domain, which plays an important role in the process of plant fertilization. In this study, bioinformatics methods were used to identify and analyze the DMP gene family in pepper. The location of the expression of the DMP gene family was explored according to the transient expression of Nicotiana benthamiana, and its expression patterns in different tissues and abiotic stress treatments were analyzed by qRT-PCR. A total of 17 CaDMP genes were identified from the three capsicum varieties, and sub-cellular localization prediction showed that CaDMPs were located on the cell membrane. Phylogenetic analysis showed that CaDMP5 in subgroup Ⅳ was highly homologous with haploid induction genes in Arabidopsis and maize, and its expression level in reproductive organs was significantly higher than that in other tissues, suggesting that CaDMP5 could be a candidate gene for haploid induction in pepper. The expression of CaDMPs increased to varying degrees after different stress treatments, indicating that the DMP gene plays an important role in plant growth and development. The CaDMP gene family was systematically analyzed in this study, which provided preliminary insights for the further research of Capsicum haploid breeding. Full article

Resistance to clarithromycin, a macrolide antibiotic used in the first-line treatment of Helicobacter pylori infection, is the most important cause of treatment failure. Although most cases of clarithromycin resistance in H. pylori are associated with point mutations in 23S ribosomal RNA (rRNA), the relationships of other mutations with resistance remain unclear. We examined possible new macrolide resistance mechanisms in resistant strains using next-generation sequencing. Two resistant strains were obtained from clarithromycin-susceptible H. pylori following exposure to low clarithromycin concentrations using the agar dilution method. Sanger sequencing and whole-genome sequencing were performed to detect resistance-related mutations. Both strains carried the A2142G mutation in 23S rRNA. Candidate mutations (T1495A, T1494A, T1490A, T1476A, and G1472T) for clarithromycin resistance were detected in the Mutant-1 strain. Furthermore, a novel mutation in the gene encoding for the sulfite exporter TauE/SafE family protein was considered to be linked to clarithromycin resistance or cross-resistance, being identified as a target for further investigations. In the Mutant-2 strain, a novel mutation in the gene that encodes DUF874 family protein that can be considered as relevant with antibiotic resistance was detected. These mutations were revealed in the H. pylori genome for the first time, emphasizing their potential as targets for advanced studies. Full article

Sweetpotato (Ipomoea batatas L.) is a strategic crop with both economic and energy value. However, improving sweetpotato varieties through traditional breeding approaches can be a time-consuming and labor-intensive process due to the complex genetic nature of sweetpotato as a hexaploid species (2n = 6x = 90). Double haploid (DH) breeding, based on in vivo haploid induction, provides a new approach for rapid breeding of crops. The success of haploid induction can be achieved by manipulating specific genes. Two of the most critical genes, DMP (DUF679 membrane proteins) and MTL (MATRILINEAL), have been shown to induce haploid production in several species. Here, we identified and characterized DMP and MTL genes in sweetpotato using gene family analysis. In this study, we identified 5 IbDMPs and 25 IbpPLAs. IbDMP5 and IbPLAIIs (IbPLAIIκ, IbPLAIIλ, and IbPLAIIμ) were identified as potential haploid induction (HI) genes in sweetpotato. These results provide valuable information for the identification and potential function of HI genes in sweetpotato and provide ideas for the breeding of DH lines. Full article

Vitellogenin (Vtg) is a precursor of yolk proteins in egg-laying vertebrates and invertebrates and plays an important role in vitellogenesis and embryonic development. However, the Vtg family remains poorly characterized in Exopalaemon carinicauda, a major commercial mariculture species found along the coasts of the Yellow and Bohai Seas. In this study, 10 Vtg genes from the genomes of E. carinicauda were identified and characterized. Phylogenetic analyses showed that the Vtg genes in crustaceans could be classified into four groups: Astacidea, Brachyra, Penaeidae, and Palaemonidae. EcVtg genes were unevenly distributed on the chromosomes of E. carinicauda, and a molecular evolutionary analysis showed that the EcVtg genes were primarily constrained by purifying selection during evolution. All putative EcVtg proteins were characterized by the presence of three conserved functional domains: a lipoprotein N-terminal domain (LPD_N), a domain of unknown function (DUF1943), and a von Willebrand factor type D domain (vWD). All EcVtg genes exhibited higher expression in the female hepatopancreas than in other tissues, and EcVtg gene expression during ovarian development suggested that the hepatopancreas is the main synthesis site in E. carinicauda. EcVtg1a, EcVtg2, and EcVtg3 play major roles in exogenous vitellogenesis, and EcVtg3 also plays a major role in endogenous vitellogenesis. Bilateral ablation of the eyestalk significantly upregulates EcVtg mRNA expression in the female hepatopancreas, indicating that the X-organ/sinus gland complex plays an important role in ovarian development, mostly by inducing Vtg synthesis. These results could improve our understanding of the function of multiple Vtg genes in crustaceans and aid future studies on the function of EcVtg genes during ovarian development in E. carinicauda. Full article

The ubiquitin-specific protease (UBP) family represents a type of deubiquitinase (DUB) that plays a significant role in plant abiotic stress responses, growth, and development. Although UBP genes have been characterized in many species, a genome-wide systematic analysis and the potential functions under abiotic stresses have not yet been reported in rice (Oryza sativa L.). In this study, we identified 21 UBP gene family members in the genome of rice, all of which had UCH domains containing short but highly conserved Cys-box and His-box. The DUF4220 and DUF594 domains, which are found in monocotyledonous plants, were unique. Phylogenetic analysis suggested that OsUBP7 and OsUBP12 genes had the closest genetic relationships with AtUBP12 and AtUBP13, implying that OsUBP7 and OsUBP12 might have similar biological functions to AtUBP12 and AtUBP13. Synteny analysis revealed that OsUBP genes were expanded through segmental duplication under purifying selection. Meanwhile, they had closer evolutionary relationships with monocotyledonous plants. Additionally, all OsUBP genes had an ABRE cis-element, which was related to abscisic acid (ABA) stress hormone response. Protein interaction analysis suggested that OsUBP22 might modulate gene regulation through OsGCN5- and OsADA2-mediated chromatin modification, and OsUBP10 might regulate salt stress through modulating OsDNA2_4 stability. Specifically, the expression profiles and the transcriptional levels of 11 representative OsUBPs suggested the potential important functions of OsUBP9 and OsUBP17 under drought and cold stresses. Taken together, our study provided a systematic analysis of OsUBPs and preliminarily explored their potential roles under abiotic stresses. Our results lay a foundation for further research on the functions of the OsUBP gene family under abiotic stresses. Full article

Unknown functional domain (DUF) proteins constitute a large number of functionally uncharacterized protein families in eukaryotes. DUF724s play crucial roles in plants. However, the insight understanding of wheat TaDUF724s is currently lacking. To explore the possible function of TaDUF724s in wheat growth and development and stress response, the family members were systematically identified and characterized. In total, 14 TaDUF724s were detected from a wheat reference genome; they are unevenly distributed across the 11 chromosomes, and, according to chromosome location, they were named TaDUF724-1 to TaDUF724-14. Evolution analysis revealed that TaDUF724s were under negative selection, and fragment replication was the main reason for family expansion. All TaDUF724s are unstable proteins; most TaDUF724s are acidic and hydrophilic. They were predicted to be located in the nucleus and chloroplast. The promoter regions of TaDUF724s were enriched with the cis-elements functionally associated with growth and development, as well as being hormone-responsive. Expression profiling showed that TaDUF724-9 was highly expressed in seedings, roots, leaves, stems, spikes and grains, and strongly expressed throughout the whole growth period. The 12 TaDUF724 were post-transcription regulated by 12 wheat MicroRNA (miRNA) through cleavage and translation. RT-qPCR showed that six TaDUF724s were regulated by biological and abiotic stresses. Conclusively, TaDUF724s were systematically analyzed using bioinformatics methods, which laid a theoretical foundation for clarifying the function of TaDUF724s in wheat. Full article