BMC Genomics最新文献

{"title":"Comprehensive genomic epidemiology and antimicrobial resistance profiles of clinical Klebsiella pneumoniae species complex isolates from a tertiary hospital in Wenzhou, China (2019-2021).","authors":"Weiyan Jiang, Yanhui Chen, Meimei Lai, Yongan Ji, Suzhen Lin, Jiao Shao, Xiaojian Chen","doi":"10.1186/s12864-025-11509-w","DOIUrl":"10.1186/s12864-025-11509-w","url":null,"abstract":"<p><strong>Background: </strong>The main issue of the Klebsiella pneumoniae species complex (KpSC) research in clinical settings is the accurate identification and differentiation of the closely related species within this complex. Moreover, the emergence and spread of carbapenem-resistant K. pneumoniae (CRKP) represent a significant public health threat due to limited treatment options and high mortality rates. Understanding the genetic basis of resistance and virulence is crucial for developing effective infection control strategies. In this work, the genomic epidemiology and antimicrobial resistance profile of KpSC isolates from Wenzhou, China, was investigated to fully understand the implications of the KpSC in clinical settings.</p><p><strong>Methods: </strong>We conducted a comprehensive analysis of 156 clinical KpSC isolates collected from a tertiary hospital in China over a three-year period (2019-2021). Antimicrobial susceptibility testing was performed according to CLSI standards. Whole-genome sequencing (WGS) and subsequent bioinformatic analyses were conducted to identify resistance genes, plasmid types, and virulence factors. Phylogenetic relationships were determined using maximum-likelihood analysis.</p><p><strong>Results: </strong>All CRKP isolates exhibited high levels of resistance to carbapenems, cephalosporins, and aminoglycosides. The most prevalent carbapenemase genes were bla_KPC-2 (100%), with significant associations between bla_KPC-2 and ST11. Phylogenetic analysis revealed considerable genetic diversity, with over 50 sequence types (STs) present. A subset of isolates harbored both resistance and hypervirulence genes, including rmpA, rmpA2, and siderophore systems, which were associated with potential higher pathogenesis.</p><p><strong>Conclusion: </strong>This study provides novel insights into the molecular epidemiology of KpSC in Wenzhou, China, highlighting the coexistence of antimicrobial resistance and virulence factors in clinical isolates. The findings underscore the importance of continuous genomic surveillance and targeted therapeutic strategies to combat KpSC infections. Our research fills critical gaps in the current understanding of KpSC epidemiology in China and offers valuable data for global comparative studies, contributing to the development of effective infection control measures. Genomic surveillance in China thus provides crucial insights for local risk mapping and informs necessary adaptions for implementation of control strategies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"318"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and expression pattern analysis of the cinnamoyl-CoA reductase gene family in flax (Linum usitatissimum L.).","authors":"Xixia Song, Dandan Liu, Yubo Yao, Lili Tang, Lili Cheng, Lie Yang, Zhongjuan Jiang, Qinghua Kang, Si Chen, Jiarong Ru, Lili Zhang, Guangwen Wu, Hongmei Yuan","doi":"10.1186/s12864-025-11481-5","DOIUrl":"10.1186/s12864-025-11481-5","url":null,"abstract":"<p><strong>Background: </strong>Cinnamoyl-CoA reductase (CCR) is the first important and committed enzyme in the monolignol synthesis branch of the lignin biosynthesis (LB) pathway, catalyzing the conversion of cinnamoyl-CoAs to cinnamaldehydes and is crucial for the growth of Linum usitatissimum (flax), an important fiber crop. However, little information is available about CCR in flax (Linum usitatissimum L.).</p><p><strong>Results: </strong>In this study, we conducted a genome-wide analysis of the CCR gene family and identified a total of 22 CCR genes. The 22 CCR genes were distributed across 9 chromosomes, designated LuCCR1-LuCCR22. Multiple sequence alignment and conserved motif analyses revealed that LuCCR7/13/15/20 harbor completely conserved NADP-specific, NAD(P)-binding, and CCR signature motifs. Furthermore, each of these LuCCRs is encoded by 5 exons separated by 4 introns, a characteristic feature of functional CCRs. Phylogenetic analysis grouped LuCCRs into two clades, with LuCCR7/13/15/20 clustering with functional CCRs involved in LB in dicotyledonous plants. RNA-seq analysis indicated that LuCCR13/20 genes are highly expressed throughout all flax developmental stages, particularly in lignified tissues such as roots and stems, with increased expression during stem maturation. These findings suggest that LuCCR13/20 play crucial roles in the biosynthesis process of flax lignin. Additionally, LuCCR2/5/10/18 were upregulated under various types of abiotic stress, highlighting their potential roles in flax defense-related processes.</p><p><strong>Conclusions: </strong>This study systematically analyzes the CCR gene family (CCRGF) of flax (Linum usitatissimum L.) at the genomic level for the first time, so as to select the whole members of the CCRGF of flax and to ascertain their potential roles in lignin synthesis. Therefore, in future work, we can target genetic modification of LuCCR13/20 to optimize the content of flax lignin. As such, this research establishes a theoretical foundation for studying LuCCR gene functions and offers a new perspective for cultivating low-lignin flax varieties.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"315"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome-sequence analysis of Bacillus subtilis strain KC14-1 with broad-spectrum antifungal activity.","authors":"Xiaowei Li, Yahan Chen, Shunyi Yang, Yi Zhou, Chengde Yang","doi":"10.1186/s12864-025-11227-3","DOIUrl":"10.1186/s12864-025-11227-3","url":null,"abstract":"<p><strong>Background: </strong>Bacillus is used as a biological control agent in agricultural production. The main mechanisms responsible for its biocontrol activity encompass the generation of various antifungal active substances during life activities, competition, antagonism with pathogens, promotion of growth, and induction of plant resistance, enhancing the inhibition of pathogenic fungi. Bacillus has high biological control potential and has become a research hotspot.</p><p><strong>Results: </strong>It was found that strain KC14-1 had significant inhibitory effects on Fusarium fujikuroi, Rhizoclonia solani, Alternaria solani, Fusarium oxysporum, and Valsa mali. Based on morphological observations, physiological and biochemical determinations, and 16 S rRNA, gyrA, and gyrB gene sequencing, strain KC14-1 was identified as Bacillus subtilis. Whole genome sequencing results showed that the genome of strain KC14-1 was composed of a ring chromosome 3,908,079 bp in size, with a GC content of 43.82% and 3,895 coding genes. Anti-SMASH predicted that the genome of strain KC14-1 contained nine gene clusters that synthesised antibacterial substances. The homology between fengycin, bacillibactin, pulcherriminic acid, subtilosin A, and bacilysin was 100%.</p><p><strong>Conclusion: </strong>The biocontrol potential of Bacillus subtilis KC14-1 was determined through whole-genome analysis. Our study provides a solid foundation for developing and utilising this strain.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"319"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956405/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-34-5p mediates 20E-induced autophagy in the fat body of Bombyx mori by targeting Atg1.","authors":"Huili Qiao, Ziqian Tong, Yuanzhuo Wang, Juanjuan Yang, Yanyan Sun, Huixuan Shi, Zhuo Liu, Jianping Duan, Dandan Li, Yunchao Kan","doi":"10.1186/s12864-025-11499-9","DOIUrl":"10.1186/s12864-025-11499-9","url":null,"abstract":"<p><strong>Background: </strong>20-Hydroxyecdysone (20E) is an important hormone that regulates insect development and metamorphosis. The fat body of insects plays a crucial role in nutrient storage and energy metabolism and is considered the exchange center for regulating insect development. The fat body undergoes remarkable transformation during insect metamorphosis and is primarily regulated by 20E. microRNAs (miRNAs) have been identified in different insects and have multiple functions in various physiological processes. However, the interaction of 20E and miRNAs in fat body regulation remains unclear.</p><p><strong>Results: </strong>We constructed six small RNA libraries using Bombyx mori fat body treated with 20E. Expression and functional analyses were conducted to identify 20E-responsive miRNAs. In total, 431 miRNAs were identified, including 389 known and 42 novel miRNAs. Differential expression analysis revealed significant expression changes in the expression of 40, 9, and 18 miRNAs at 2 h, 6 h, and 12 h after 20E treatment, respectively. The expression of 10 miRNAs was validated using quantitative real-time PCR. miR-34-5p is a highly conserved miRNA among the 10 validated miRNAs, and autophagy-related gene 1 (Atg1) was considered a target gene of miR-34-5p. The expression analysis of miR-34-5p and Atg1 exhibited an opposite expression pattern in the fat body after the 20E treatment. Dual-luciferase assay indicated that miR-34-5p could inhibit Atg1 expression by targeting a binding site in CDS region of Atg1. In larval fat body, overexpressing miR-34-5p by injecting miR-34-5p agomir suppressed the expression of Atg1 and autophagy, whereas knocking down miR-34-5p by injecting miR-34-5p antagomir induced the expression of Atg1 and autophagy. Meanwhile, Atg1 silencing by RNAi also inhibited autophagy. These results indicate that miR-34-5p participates in 20E-induced autophagy in B. mori fat body by interacting with Atg1.</p><p><strong>Conclusions: </strong>We systematically identified and functionally characterized miRNAs associated with 20E regulation in the fat body of B. mori. miR-34-5p is involved in 20E-induced autophagy in B. mori by regulating its target gene Atg1. These results provide insight into the role of sophisticated interactions between miRNAs, 20E regulation, and autophagy in fat body remodeling and insect metamorphosis.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"317"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis of corpora lutea in domestic cats (Felis catus) reveals strong differences in gene expression of various hormones, hormone receptors and regulators across different developmental stages.","authors":"Beate C Braun, Michał M Hryciuk, Dorina Meneghini","doi":"10.1186/s12864-025-11510-3","DOIUrl":"10.1186/s12864-025-11510-3","url":null,"abstract":"<p><p>In the domestic cat (Felis catus), the corpus luteum (CL) is the main source of progestogen during pregnancy. Here, we studied gene expression changes in different life cycle stages of the CL of pseudopregnant cats to identify potential regulatory factors. Results revealed no support for different regression substages, which were previously defined on the basis of morphological examination analysis and intraluteal hormone content, as only a very low number of differentially expressed genes and no subclusters in PCA plot were detected. By comparing the regression stage with the developmental/maintenance stage, we detected a total of 6174 differentially expressed genes in the sample set, of which 2882 were upregulated and 3292 were downregulated. The large changes in the expression levels of some genes indicate that the endocrine function of the CL may not be restricted to progesterone (P4) secretion. The findings suggest that domestic cat CLs could also be a source of adipokines such as adiponectin or APELA. The expression of these genes is highly variable and reversed between stages. The life cycle and activity of CLs seem to be regulated by different factors, as genes encoding for the hormone receptors LHCGR and PAQR5 were more highly expressed in the development/maintenance stage, in contrast to this encoding for LEPR, which is higher expressed in regression stage. For regression stage, we identified different potential ways to modulate the cholesterol level and/or P4 concentration. Furthermore, we found differences from previous studies in other species for many genes that were studied in more detail, as well as when analysing functions and pathways. Our findings support the hypothesis that different stages of the CL life cycle in domestic cats can be characterized by changes in gene regulation and that CL life cycles are partly differentially regulated between species.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"325"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete mitochondrial genomes of the hemiparasitic genus Cymbaria (Orobanchaceae): insights into repeat-mediated recombination, phylogenetic relationships, and horizontal gene transfer.","authors":"Yang Ma, Jordi López-Pujol, Dongqing Yan, Zekun Deng, Zhen Zhou, Jianming Niu","doi":"10.1186/s12864-025-11474-4","DOIUrl":"10.1186/s12864-025-11474-4","url":null,"abstract":"<p><strong>Background: </strong>The Orobanchaceae family is widely recognized as an exemplary model system for examining the evolutionary dynamics of parasitic plants. However, reports on the mitochondrial genome (mitogenome) of the hemiparasitic tribe Cymbarieae are currently lacking. Here, we sequenced, assembled and characterized the complete mitogenome of the genus Cymbaria L. sensu stricto (C. mongolica and C. daurica).</p><p><strong>Results: </strong>A total of 51 unique mitochondrial genes, including 33 protein-coding genes, three rRNA genes, and 15 tRNA genes, are shared by the mitogenomes of the two hemiparasitic plants, exhibiting the gene content characteristic of autotrophic plants. The mitogenomes of C. mongolica and C. daurica are characterized by a pentacyclic chromosome structure (their major conformation), with lengths of 1,576,465 bp and 1,539,836 bp, respectively. Moreover, we identified and validated the presence of four minor conformations mediated by four pairs of large repeats (> 1000 bp in size) in C. mongolica and eight minor conformations mediated by six large repeats in C. daurica. We further explored codon usage, RNA editing sites, selective pressure, and nucleotide diversity in two Cymbaria mitogenomes. Phylogenetic analyses of 26 species of Lamiales revealed that the two Cymbaria species form a sister clade to the other lineages of Orobanchaceae. Extensive mitogenomic rearrangements are also observed between Cymbaria and five closely related species. Although we identified mitochondrial plastid sequences in the Cymbaria mitogenomes, The mitochondrial plastid sequences (MTPTs) in their mitogenomes represent only 2.37% and 1.74%, respectively. Additionally, there is minimal evidence of intracellular and horizontal gene transfer, with only a few genes (rpl22, rps3, and ycf2) showing low bootstrap support (BS ≤ 70%) for the relationships with the potential host plants Allium mongolicum, Leymus chinensis, and Saposhnikovia divaricata, respectively.</p><p><strong>Conclusions: </strong>We reported the mitochondrial genome in hemiparasitic Cymbaria species for the first time, which are characterized by multiple repeat-mediated recombination and little to no intracellular and horizontal gene transfer. Our findings provide valuable genetic insights for further studies on the mitogenome evolution of hemiparasitic plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"314"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of epigenomic and genomic data to predict residual feed intake and the feed conversion ratio in dairy sheep via machine learning algorithms.","authors":"Pablo Augusto de Souza Fonseca, Aroa Suarez-Vega, Cristina Esteban-Blanco, Héctor Marina, Rocío Pelayo, Beatriz Gutiérrez-Gil, Juan-José Arranz","doi":"10.1186/s12864-025-11520-1","DOIUrl":"10.1186/s12864-025-11520-1","url":null,"abstract":"<p><strong>Background: </strong>Feed efficiency (FE) is an essential trait in livestock species because of the constant demand to increase the productivity and sustainability of livestock production systems. A better understanding of the biological mechanisms associated with FEs might help improve the estimation and selection of superior animals. In this work, differentially methylated regions (DMRs) were identified via genome-wide bisulfite sequencing (GWBS) by comparing the DNA methylation profiles of milk somatic cells from dairy ewes that were divergent in terms of residual feed intake. The DMRs were identified by comparing divergent groups for residual feed intake (RFI), the feed conversion ratio (FCR), and the consensus between both metrics (Cons). Additionally, the predictive performance of these DMRs and genetic variants mapped within these regions was evaluated via three machine learning (ML) models (xgboost, random forest (RF), and multilayer feedforward artificial neural network (deeplearning)). The average performance of each model was based on the root mean squared error (RMSE) and squared Spearman correlation (rho2). Finally, the best model for each scenario was selected on the basis of the highest ratio between rho2 and RMSE.</p><p><strong>Results: </strong>In total, 12,257, 9,328, and 6,723 genes were annotated for DMRs detected in the RFI, FCR, and Cons groups, respectively. These genes are associated with important pathways for regulating FE in dairy sheep, such as protein digestion and absorption, hormone synthesis and secretion, control of energy availability, cellular signaling, and feed behavior pathways. With respect to the ML predictions, the smallest mean RMSE (0.17) was obtained using RF, which was used to predict RFI. The highest mean rho² (0.20) was obtained when the RFI was predicted via the mean methylation within the DMRs identified, the consensus groups were compared, and the genetic variants mapped within these DMRs were included. The best overall models were obtained for the prediction of RFI using the DMRs obtained in the comparison of RFI groups (RMSE = 0.10, rho² = 0.86) using xgboost and the DMRs plus the genetic variants identified via the Cons groups (RMSE = 0.07, rho² = 0.62) using RF.</p><p><strong>Conclusions: </strong>The results provide new insights into the biological mechanisms associated with FE and the control of these processes through epigenetic mechanisms. Additionally, the potential use of epigenetic information as a biomarker for the prediction of FE can be suggested based on the obtained results.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"313"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome sequencing and analysis of the symbiotic Armillaria gallica M3 with Gastrodia elata.","authors":"Cheng-Ying Luo, Yao Lu, Lei Su, Jia-Jia Liu, Jia-Yun Miao, Yi-Cen Lin, Lian-Bing Lin","doi":"10.1186/s12864-024-10897-9","DOIUrl":"10.1186/s12864-024-10897-9","url":null,"abstract":"<p><strong>Background: </strong>On the one hand, Armillaria is regarded as a plant disease that causes serious root rot of forest trees, on the other hand, Armillaria is also an important symbiotic fungi of the valuable Chinese herb Gastrodia elata. Currently, the whole genome database of Armillaria is relatively limited, and it is expected that a more comprehensive understanding of the symbiotic interactions between Armillaria and G. elata can be achieved through genome-wide comparisons and functional annotations. Whole genome sequencing of Armillaria gallica M3 strain was performed using Oxford Nanopore Technologies sequencing platform, and the sequencing data were used to perform genome assembly, gene prediction and functional annotation, carbohydrate-active enzymes, and host-pathogen interactions using bioinformatics methods.</p><p><strong>Results: </strong>In this study, we obtained an 83.33 M genome of A. gallica M3 strain, which consisted of 38 overlapping clusters with an N50 of 6,065,498 bp and a GC content of 47.43%. A total of 12,557 genes were identified in the genome of A. gallica M3, and the repetitive sequences accounted for about 44.36% of the genome. 42.26% of the genome was composed of glycoside hydrolases (GHs), 16.15% of the genome was composed of glycosyltransferases (GTs). In addition, 3412 genes in A. gallica M3 were involved in the host-pathogen interaction mechanism.</p><p><strong>Conclusions: </strong>These results have elucidated the characteristics of A. gallica M3 from a genomic perspective to a certain extent. They help to analyze the inner mechanism of A. gallica M3 being able to symbiosis with G. elata at the genomic level, which is of great significance to the next related research of A. gallica M3.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"324"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PbrBGAL6 promotes pollen tube growth by influencing apical pectin level in Pyrus bretschneideri.","authors":"Yusheng Xu, Lan Xu, Mingliang Zhang, Hao Wang, Yuqian Wang, Xueping Zhang, Kaijing Zhang, Yihu Sui, Jingjing Qian, Shuangshuang Jia, Ming Qian, Guangrong Cui","doi":"10.1186/s12864-025-11429-9","DOIUrl":"10.1186/s12864-025-11429-9","url":null,"abstract":"<p><strong>Background: </strong>β-galactosidase (BGAL), which is an important cell wall-degrading enzyme, participates in various biological processes, but its effects on pollen tube growth (PTG) remain unclear.</p><p><strong>Results: </strong>We identified 12 PbrBGAL genes (named PbrBGAL1-12) in the pear (Pyrus bretschneideri) genome. PbrBGAL members, containing three conserved domains and two enzyme active sites, were grouped into six subclasses. They were distributed in seven chromosomes, with dispersed duplication revealed as the main replication event. PbrBGAL genes contained 1 to 24 exons and 0 to 23 introns, with exon/intron structure mostly conserved within each subclass except for subclass E. Analyses of tissue-specific expression indicated that only PbrBGAL6 was highly expressed specifically in anther and pollen, with decreasing expression levels during PTG. The effective inhibition of PbrBGAL6 expression using antisense oligodeoxynucleotide technology dramatically decreased BGAL enzymatic activity, promoted PTG and increased cytoplasmic leakage and tip widths. Furthermore, suppressing PbrBGAL6 transcription decreased the apical total and methylated pectin contents in pollen tubes by significantly increasing transcription of PbrPME11, PbrPG14, PbrPG20, PbrPG21 and PbrPG24.</p><p><strong>Conclusions: </strong>We identified 12 PbrBGAL genes in the pear genome, of which PbrBGAL6 precisely modulates the apical pectin content to mediate pear PTG through its effects on PbrPME11 and PbrPGs expression. This study provides direct evidence of the involvement of BGAL in the regulation of polar PTG.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"321"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Genomic analyses revealed low genetic variation In the Intron-exon boundary of the doublesex gene within the natural populations of An. gambiae s.l. in Burkina Faso.","authors":"Mahamadi Kientega, Ioanna Morianou, Nouhoun Traoré, Nace Kranjc, Honorine Kaboré, Odette N Zongo, Abdoul-Azize Millogo, Patric Stephane Epopa, Franck A Yao, Adrien M G Belem, Austin Burt, Abdoulaye Diabaté","doi":"10.1186/s12864-025-11515-y","DOIUrl":"10.1186/s12864-025-11515-y","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"320"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}