BMC Genomics最新文献

{"title":"Integrative genomic analysis reveals shared loci for reproduction and production traits in Yorkshire pigs.","authors":"Ran Wei, Zhenyang Zhang, He Han, Jian Miao, Pengfei Yu, Hong Cheng, Wei Zhao, Xiaoliang Hou, Jianlan Wang, Yongqi He, Yan Fu, Zhen Wang, Qishan Wang, Zhe Zhang, Yuchun Pan","doi":"10.1186/s12864-025-11416-0","DOIUrl":"https://doi.org/10.1186/s12864-025-11416-0","url":null,"abstract":"<p><strong>Background: </strong>Improving reproductive performance in Yorkshire pigs, a key maternal line in three-way crossbreeding systems, remains challenging due to low heritability and historical selection pressures favoring production traits. Identifying pleiotropic genetic variants that influence both reproduction and production traits is crucial for understanding their genetic interplay and enhancing molecular breeding strategies.</p><p><strong>Results: </strong>Genome-wide association studies (GWAS) using 2,764 individuals identified 264,660 significant loci associated with reproduction traits and 12,460 loci for production traits, with 73 independent signals, including genes such as SCLT1 and CAPN9. A total of 465,047 independent loci were identified, resulting in a genome-wide significance threshold of <math><mrow><mn>2.15</mn> <mo>×</mo> <msup><mrow><mn>10</mn></mrow> <mrow><mo>-</mo> <mn>6</mn></mrow> </msup> </mrow> </math> . Genetic correlations analysis between reproduction and production traits across parities revealed varying trends, including a strengthening negative correlation between mean litter weight (MLW) and backfat thickness (BFT) with increasing parity (P1: <math><msub><mi>r</mi> <mi>g</mi></msub> </math> =-0.0376; P2: <math><msub><mi>r</mi> <mi>g</mi></msub> </math> =-0.1371; P3: <math><msub><mi>r</mi> <mi>g</mi></msub> </math> =-0.1475). Given 1062 shared significant loci between MLW and BFT, local genetic correlation was calculated within the corresponding genomic regions, resulting in a weak correlation of 0.014. Transcriptome-wide association studies (TWAS) leveraging data from the PigGTEx project, which includes 9,530 RNA-sequencing samples across 34 tissues, revealed 2,143 significant genes, with 31 linked to total number of piglets born (TNB) and 133 to number of piglets born alive (NBA). These results highlight the importance of these genes in reproductive performance, with SCLT1 being notably significant in reproductive tissues. For MLW, integrating results from multiple analyses revealed CENPE as a strong candidate gene, exhibiting significant association and colocalization. Validation in an independent population (n = 300) showed that incorporating the top 0.2% of significant single nucleotide polymorphisms (SNPs) in the GFBLUP model improved predictive accuracy, increasing from 0.0168 to 0.0242 for MLW.</p><p><strong>Conclusion: </strong>This study provides new insights into the pleiotropic genetic architecture underlying reproduction and production traits in Yorkshire pigs. Genetic correlations, shared loci, and candidate genes inform breeding program design. The increased accuracy of genomic selection using these significant loci highlights their practical utility in improving breeding efficiency. These findings suggest opportunities for refining selection strategies, although further research is warranted to fully realize their potential for enhancing breeding programs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"310"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis provides new insights into the resistance of pepper to Phytophthora capsici infection.","authors":"Fengyan Shi, Xiuxue Wang, Meijun Wei, Xi Zhang, Zhidan Wang, Xiaochun Lu, Chunlei Zou","doi":"10.1186/s12864-025-11498-w","DOIUrl":"https://doi.org/10.1186/s12864-025-11498-w","url":null,"abstract":"<p><strong>Background: </strong>Phytophthora blight is a highly destructive soil-borne disease caused by Phytophthora capsici Leonian, which threatens pepper production. The molecular mechanism of pepper resistance to phytophthora blight is unclear, and the excavation and functional analysis of resistant genes are the bases and prerequisites for phytophthora blight-resistant breeding. We aimed to analyze the expression patterns of key genes in the plant-pathogen interaction metabolic pathway and propose a working model of the pepper defense signal network against Phytophthora capsici infection.</p><p><strong>Results: </strong>The 'ZCM334' pepper material used in this study is a high-generation inbred line that is immune to Phytophthora capsici and shows no signs of infection after inoculation. Comparative transcriptome analysis of the roots of 'ZCM334' and the susceptible material 'Early Calwonder' revealed significant differences in their gene expression profiles at different stages after inoculation. Most differentially expressed genes were significantly enriched in the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, plant-pathogen interaction, and fatty acid degradation metabolic pathways. Some defense genes and transcription factors significant in pepper resistance to phytophthora blight were identified, including PR1, RPP13, FLS2, CDPK, CML, MAPK, RLP, RLK, WRYK, ERF, MYB, and bHLH, most of which were regulated after inoculation. A working model was constructed for the defense signal network of pepper against Phytophthora capsici.</p><p><strong>Conclusions: </strong>These data provide a valuable source of information for improving our understanding of the potential molecular mechanisms by which pepper plants resist infection by Phytophthora capsici. The identification of key genes and metabolic pathways provides avenues for further exploring the immune mechanism of 'ZCM334' resistance to phytophthora blight.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"311"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and comparative evolution of 14-3-3 gene family members in five Brassicaceae species.","authors":"Jingya Zhao, Shengqin Liu, Hui Ren, Owusu Edwin Afriyie, Mengzhu Zhang, Dachao Xu, Xianzhong Huang","doi":"10.1186/s12864-025-11513-0","DOIUrl":"https://doi.org/10.1186/s12864-025-11513-0","url":null,"abstract":"<p><strong>Background: </strong>The 14-3-3 proteins are highly conserved regulatory eukaryotic proteins, which are crucial in growth, development, and stress responses. However, systematic characterization of the 14-3-3 gene family in Brassicaceae species and their evolutionary relationships have not been comprehensively reported.</p><p><strong>Results: </strong>This study conducted genome-wide identification, structural characteristics, and comparative evolutionary analysis of 14-3-3 gene family members in Arabidopsis thaliana, A. lyrata, A. pumila, Camelina sativa, and Brassica oleracea using comparative genomics. Overall, a total of 108 14-3-3 genes, which were phylogenetically classified into ε and non-ε groups were identified in the five species, with the non-ε members exhibiting more similar exon-intron structures and conserved motif patterns. Collinearity analysis revealed that the Brassicaceae 14-3-3 gene family members underwent varying degrees of expansion following whole-genome duplication (WGD) events. Notably, the number of 14-3-3 gene family members between A. lyrata and A. thaliana remained similar despite the former having approximately 1.66-fold larger genome size. In contrast, the number of 14-3-3 gene family members in A. pumila and C. sativa increased in proportionately to their genome size, while gene members in the more distantly related species to A. thaliana, B. oleracea, showed irregular expansion patterns. Selection pressure analysis revealed that 14-3-3 homologs in all the five species underwent purifying selection, with the group ε members experiencing relatively weaker purifying selection. Cloning of ApGRF6-2 gene from A. pumila indicated that the ApGRF6-2 protein was localized in the cell membrane and cytoplasm, while ectopic overexpression of ApGRF6-2 in A. thaliana could promote early flowering by upregulating the expression of floral meristem identity genes.</p><p><strong>Conclusion: </strong>This study provides a comprehensive and systematic identification of the 14-3-3 gene family members in five Brassicaceae species using updated genome sequences, and the results could form a basis for further validation of functional and molecular mechanisms of 14-3-3 genes in plant growth, development, abiotic stress responses, as well as flowering regulation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"309"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742224","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":"Integrative analysis of transcriptome and metabolism reveals functional roles of redox homeostasis in low light and salt combined stress in Leymus chinensis.","authors":"Jikai Li, Suyang Fang, Hailing Zhang, Zubair Iqbal, Chen Shang, Weibo Han, Kai Huang, Xiangshen Meng, Muyuan Dai, Zhiheng Lu, Bingnan Guo, Mingnan Qu","doi":"10.1186/s12864-025-11526-9","DOIUrl":"https://doi.org/10.1186/s12864-025-11526-9","url":null,"abstract":"<p><p>Salt stress is one of the major limiting factors of Leymus chinensis (named sheepgrass) growth, which accelerates inhibitive effects that are particularly concomitant with low light regimes (LL-Salt). However, little is known about physiological and molecular mechanisms under such LL-Salt in sheepgrass. This study aims to uncover the key reprogrammed metabolic pathways induced by LL-Salt through an integrated analysis of transcriptome and metabolism. Results suggested that the growth of sheepgrass seedlings was dramatically inhibited with a ranging of 8 to 20% reduction in F_v/F_m in LL-Salt combined treatments. Catalase activities were increased by 40% in LL but significantly decreased in salt stress, ranging from 15 to 46%. Both transcriptome and metabolism analysis reveal that carbon metabolism pathways were significantly enriched in the differentially expressed genes with downregulation by both LL and salt stress treatment. Metabolites involved in the photorespiration pathway, including serine and glycolate, were downregulated in LL while upregulated in salt stress treatment, with the same pattern of expression levels of a photorespiration regulatory gene, glycolate oxidase. Collectively, we found that serval antioxidant redox pathways, including photorespiration, GSG/GSSH redox, and ABA signaling, participated in response to LL and salt combined events and highlighted the roles of cellular redox homeostasis in LL-Salt response in sheepgrass.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"312"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aromatase reduces sperm motility by down-regulating the expression of proteins related to ATP synthesis in seminal plasma extracellular vesicles.","authors":"Xuliang Luo, Yan Guo, Xuelian Li, Zi Mei, Haobo Zhou, Ping Qiu, Haoxin Wang, Yan Chen, Yanzhang Gong","doi":"10.1186/s12864-025-11500-5","DOIUrl":"https://doi.org/10.1186/s12864-025-11500-5","url":null,"abstract":"<p><strong>Background: </strong>Aromatase, encoded by Cyp19a1, is the rate limiting enzyme in biosynthesis of estrogens, and excessive aromatase can reduce the semen quality in roosters. Seminal plasma extracellular vesicles (SPEV) are nanoscale vesicles that carry and transmit signaling molecules, thereby affecting semen quality. Currently it is still unclear whether SPEV are involved in the process of that aromatase affects the quality semen in chicken. To clarify this issue, lentivirus carrying Cyp19a1 (LV-CYP19A1) for over-expression of aromatase was constructed and injected to testis of 35-week-old roosters. Semen quality and seminal plasma hormone were measured, and SPEV were also extracted and proteome sequencing was performed after treatment of LV-CYP19A1.</p><p><strong>Results: </strong>The results indicated that semen volume, fertility, sperm motility, testosterone (T) levels were significantly decreased, and estradiol (E₂) levels were significantly increased in LV-CYP19A1 group than those in control group (P < 0.05). Through proteomic analysis of SPEV, we identified 966 differentially expressed proteins (DEPs) in the comparison of LV-CYP19A1 group and control group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) items of DEPs are mainly enriched in ATP synthesis coupled electron transport, flagellated sperm motility, regulation of steroid biosynthetic process, and PI3K-Akt signaling pathway. Furthermore, 8 proteins including ENO4, APOB, SDHA, SDHB, UQCRC1, VIN, PITGB3 and FXN were identified as key proteins in SPEV involving in the process of aromatase regulated rooster semen quality.</p><p><strong>Conclusions: </strong>Our results reveal that aromatase can down-regulate the protein expression related to regulation of ATP synthesis and metabolism, and sperm motility in SPEV, thereby reducing semen quality in roosters.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"305"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742190","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":"Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.","authors":"Dingwen Su, Moritz Peters, Volker Soltys, Yingguang Frank Chan","doi":"10.1186/s12864-025-11442-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11442-y","url":null,"abstract":"<p><p>A common objective across ATAC-seq and ChIP-seq analyses is to identify differential signals across contrasted conditions. However, in differential analyses, the impact of copy number variation is often overlooked. Here, we demonstrated copy number differences among samples could drive, if not dominate, differential signals. To address this, we propose a pipeline featuring copy number normalization. By comparing the averaged signal per gene copy, it effectively segregates differential signals driven by copy number from other factors. Further applying it to Down syndrome unveiled distinct dosage-dependent and -independent changes on chromosome 21. Thus, we recommend copy number normalization as a general approach.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"306"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742194","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":"Deciphering the molecular transcriptomic mechanisms of carbon ion beams and X-ray on rice seedlings.","authors":"Jianing Ding, Chaoli Xu, Yan Du, Xiao Liu, Jingmin Chen, Zhe Li, Jing Long, Yukun Sheng, Wenjie Jin, Dan Xu, Libin Zhou","doi":"10.1186/s12864-025-11488-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11488-y","url":null,"abstract":"<p><strong>Background: </strong>Ionizing radiation (IR) is an abiotic stress factor that can be not only a means to explore plant resistance but also a potent mutagen in agricultural breeding. The diverse physical parameters of different types of IR result in varying effects on plants, which in turn leads to differences in the spectrum of genetic variations in the offspring. Investigating plant response mechanisms to different IR is crucial for enhancing plant resistance and comprehending of the differences in mutation generation from various physical mutagenic sources in mutation breeding. Nevertheless, the mechanism underlying the complex responses of plants to different IR are not yet fully comprehended.</p><p><strong>Results: </strong>we conducted transcriptome sequencing on rice seedlings that exhibited a relative root length of approximately 69% after being exposed to carbon ion beams (CIBs) and X-ray respectively. The results revealed that X-ray induced a greater number of differentially expressed genes (DEGs) than CIBs, with 5681 and 2198 DEGs were identified respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that DNA replication, damage repair, phytohormone signaling, and antioxidant pathways were implicated in the response of rice seedling to IR. These pathways demonstrated diverse response patterns following different IR. Additionally, through two IR with different linear energy transfer (LET), we found some common DEGs that contribute to the radiation response in rice seedlings, such as LOC4331062, LOC4333870.</p><p><strong>Conclusion: </strong>This study offers insights into the molecular transcriptomic mechanisms underlying the impacts of IR on rice seedlings. It provides a new perspective for further exploration of irradiation-induced damage repair factors and understanding the reasons for the differences in mutations created by different mutagenic sources in plants.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"308"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742199","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":"Multi-locus genome-wide association mapping for major agronomic and yield-related traits in sorghum (Sorghum bicolor (L.) moench) landraces.","authors":"Addisu Getahun, Admas Alemu, Habte Nida, Adugna Abdi Woldesemayat","doi":"10.1186/s12864-025-11458-4","DOIUrl":"https://doi.org/10.1186/s12864-025-11458-4","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Sorghum is a vital cereal crop for over 750 million people, ranking 5th globally. It has multiple purposes, including food, feed, and biofuels, and is essential in Ethiopia, which has a rich genetic diversity of various agroecological zones.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Objective: &lt;/strong&gt;Explore marker-trait associations (MTAs) to identify quantitative trait nucleotides (QTNs) and new candidate genes associated with agronomic and yield contributing traits in Ethiopian sorghum landraces using multi-locus GWAS models to assist the genomic-assisted breeding strategies.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Method: &lt;/strong&gt;This study investigates the genetic basis of agronomic traits in Ethiopian sorghum landraces through multi-locus Genome-Wide Association Studies (ML-GWAS). 216 landraces, improved varieties, and check cultivars were obtained from the Ethiopian Biodiversity Institute and the National Sorghum Improvement Program for this study. The experiment was conducted over two cropping seasons, employing an α-lattice design for phenotyping key traits such as days to flowering, days to maturity, plant height, seed number per plant, grain yield, and thousand seed weight. A mixed linear model (MLM) was used to analyze the phenotypic data and estimate the genetic parameters including variances and the broad sense heritability. GBS with the ApeKI restriction enzyme provided 50,165 high-quality SNP markers. The six ML-GWAS models identified significant QTNs with a LOD score threshold value of ≥ 4.0. The analysis revealed major QTNs associated with traits across multiple chromosomes, supported by a stringent filtering criterion that ensured reliability. Co-localization with known QTLs was explored using the Sorghum QTL Atlas database and candidate genes within significant QTN regions, providing the genetic architecture influencing agronomic performance were identified via the Phytozome platform using the biomaRt package.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;Pearson correlation analysis revealed significant associations among most traits, with p-values less than 0.0001, except for grain yield per plant which showed lower correlations with other traits. Genetic variability analysis indicated that days to flowering exhibited high heritability (0.7) and genetic advance (19.6%) as percent of mean, suggesting strong genetic control, while grain yield displayed extremely low h&lt;sup&gt;2&lt;/sup&gt; (0.003). A total of 351,692 SNP markers were identified across 10 sorghum chromosomes from 216 Ethiopian sorghum landraces, and we have been refining this to 50,165 filtered SNPs. Manhattan plots indicated significant marker-trait associations (MTAs) across multiple chromosomes, particularly for days to flowering and plant height. Significant QTNs were associated with key traits including flowering time, plant height, and grain yield. ML-GWAS identified 176 QTNs with varying LOD scores and phenotypic effects. Multiple genes linked to these QTNs highlight the complexity of genetic inte","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"304"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742230","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":"Metabolomics and transcriptomics analyses reveal the complex molecular mechanisms by which the hypothalamus regulates sexual development in female goats.","authors":"Qing Li, Tianle Chao, Yanyan Wang, Peipei He, Lu Zhang, Jianmin Wang","doi":"10.1186/s12864-025-11492-2","DOIUrl":"10.1186/s12864-025-11492-2","url":null,"abstract":"<p><strong>Background: </strong>The hypothalamus is a critical organ that regulates sexual development in animals. However, current research on the hypothalamic regulation of sexual maturation in female goats remains limited. In this study, we conducted metabolomic and transcriptomic analyses on the hypothalamic tissues of female Jining grey goats at different stages of sexual development (1 day old (neonatal, D1, n = 5), 2 months old (prepuberty, M2, n = 5), 4 months old (sexual maturity, M4, n = 5), and 6 months old (breeding period, M6, n = 5)).</p><p><strong>Results: </strong>A total of 418 differential metabolites (DAMs) were identified in this study, among which the abundance of metabolites such as anserine, L-histidine, carnosine, taurine, and 4-aminobutyric gradually increased with the progression of sexual development. These metabolites may regulate neuronal development and hormone secretion processes by influencing the metabolism of histidine and phenylalanine. Through combined transcriptomic and metabolomic analyses, we identified that differentially expressed genes such as mitogen-activated protein kinase kinase kinase 9 (MAP3K9), prune homolog 2 with BCH domain (PRUNE2), and potassium voltage-gated channel interacting protein 4(KCNIP4) may jointly regulate the development and energy metabolism of hypothalamic Gonadotropin-releasing hormone neurons in conjunction with DAMs, including LPC22:5, 2-Arachidonyl Glycerol ether, LPE22:5, and Lysops22:5. Additionally, we elucidated the molecular mechanism through which glutathione metabolism regulates sexual maturation in goats.</p><p><strong>Conclusions: </strong>In summary, this study illustrates the dynamic changes in metabolites and mRNA within hypothalamic tissue during postnatal sexual maturation in female Jining grey goats. This research may provide significant scientific insights for future animal breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"303"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728394","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 of the invasive North American Haemaphysalis longicornis tick as a template for bovine anti-tick vaccine discovery.","authors":"Mohamed Abdallah Mohamed Moustafa, Miranda M Barnes, Nicole E Wagner, Deanna Bodine, Kylie Bendele, Pete D Teel, Perot Saelao, Dana C Price","doi":"10.1186/s12864-025-11477-1","DOIUrl":"https://doi.org/10.1186/s12864-025-11477-1","url":null,"abstract":"<p><strong>Background: </strong>The ixodid tick Haemaphysalis longicornis Neumann, commonly referred to as the Asian longhorned tick, has expanded its range outside of East Asia into countries such as Australia, New Zealand, and the United States. Since the first U.S. detection in 2017, H. longicornis has spread to 21 states and the District of Columbia and has been implicated as a vector of various human and animal pathogens including Theileria orientalis Ikeda genotype, a causal agent of bovine theileriosis. Facilitated in part by the parthenogenetic nature of invasive populations, this tick has become a paramount threat to agricultural rangelands and U.S. livestock production. Reliance on traditional acaricides for vector control selects for resistant individuals, reducing the effectiveness of many chemical tools over time. Thus, focus has shifted to alternative control mechanisms including anti-tick vaccine development. To further such research, here we sequence and assemble a high-quality H. longicornis genome and robust gene catalog from invasive North American ticks while also providing an organ-specific transcriptomic expression catalog and in-depth informatic screening of the tick proteome for potential bovine antigenic molecules with potential utility as vaccine candidates.</p><p><strong>Results: </strong>Using a combination of PacBio HiFi single-molecule sequencing and Hi-C chromosome conformation capture data, our genome assembly contains 270 scaffolds and spans a haploid genome size of 3.09 Gbp with an N50 of 213.4 Mbp. Gene prediction identified 21,947 high-confidence gene structures containing 96.2% of the core Arthropoda odb10 orthologs. Our organ-specific transcriptome library comprising salivary glands, midgut, ovaries, foreleg and hindleg additionally highlights potential anti-tick vaccine candidates and metabolic pathways to target for future in vitro trials.</p><p><strong>Conclusions: </strong>Single-molecule sequencing of a triploid, parthenogenetic North American Haemaphysalis longicornis tick allowed for the generation of a highly contiguous genome assembly that, when coupled with extensive transcriptome profiling, resulted in a robust gene catalog containing multiple candidates for further study as anti-tick vaccine antigens.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"307"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742223","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}