BMC Genomics最新文献

{"title":"Whole transcriptome analysis in oviduct provides insight into microRNAs and ceRNA regulative networks that targeted reproduction of goat (Capra hircus).","authors":"Qingqing Liu, Zhipeng Sun, Yufang Liu, Xiaoyun He, Chunhuan Ren, Xiangyu Wang, Ran Di, Yongju Zhao, Zijun Zhang, Mingxing Chu","doi":"10.1186/s12864-025-11438-8","DOIUrl":"10.1186/s12864-025-11438-8","url":null,"abstract":"<p><strong>Background: </strong>Reproduction traits are crucial for livestock breeding and represent key economic indicators in the domestic goat (Capra hircus) industry. The oviduct, a critical organ in female mammals, plays a pivotal role in several reproductive processes; however, its molecular mechanisms remain largely unknown. Non-coding RNA and mRNAs are essential regulatory elements in reproductive processes; yet their specific roles and regulatory networks in goat oviducts remain unclear.</p><p><strong>Results: </strong>In this study, we conducted small RNA sequencing of the oviduct in high- and low-fecundity goats during the follicular (FH and FL groups, n = 10) and luteal (LH and LL groups, n = 10) phase, profiling 20 tissue samples. Combinatorial whole-transcriptome expression profiles were applied to the same samples to uncover the competitive endogenous RNA (ceRNA) regulation network associated with goat fecundity. RT-qPCR was employed to validate the miRNA profiling results, and ceRNA regulatory networks were analyzed through luciferase assay. Gene set enrichment analysis (GSEA) confirmed that the cytokine-cytokine receptor interaction and TGF-β signaling pathway, both related to embryonic development, were enriched in DEM target genes. Additionally, miR-328-3p, a core miRNA, targets SMAD3 and BOP1, which are involved in the negative regulation of cell growth and embryonic development. TOB1 and TOB2, targeted by miR-204-3p, regulate cell proliferation via the protein kinase C-activating G-protein coupled receptor signaling pathway. Analyses of ceRNA regulatory networks revealed that LNC_005981 - miR-328-3p - SMAD3 and circ_0021923 - miR-204-3p - DOT1L may affect goats' reproduction, findings that were validated using luciferase assay.</p><p><strong>Conclusion: </strong>Analysis of whole-transcriptome profiling of goat oviducts identified several key miRNAs and ceRNAs that may regulate oocyte maturation, embryo development, and the interactions between the oviduct and gametes/early embryos, providing insights into the molecular mechanisms of reproductive regulatory networks.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"250"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633467","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":"Comparative genomics reveals the high diversity and adaptation strategies of Polaromonas from polar environments.","authors":"Yuntong Du, Changhua He, Karen G Lloyd, Tatiana A Vishnivetskaya, Hongpeng Cui, Bing Li, Da Gong, Xiaopeng Fan, Dayi Zhang, Hongchen Jiang, Renxing Liang","doi":"10.1186/s12864-025-11410-6","DOIUrl":"10.1186/s12864-025-11410-6","url":null,"abstract":"<p><strong>Background: </strong>Bacteria from the genus Polaromonas are dominant phylotypes found in a variety of low-temperature environments in polar regions. The diversity and biogeographic distribution of Polaromonas have been largely expanded on the basis of 16 S rRNA gene amplicon sequencing. However, the evolution and cold adaptation mechanisms of Polaromonas from polar regions are poorly understood at the genomic level.</p><p><strong>Results: </strong>A total of 202 genomes of the genus Polaromonas were analyzed, and 121 different species were delineated on the basis of average nucleotide identity (ANI) and phylogenomic placements. Remarkably, 8 genomes recovered from polar environments clustered into a separate clade ('polar group' hereafter). The genome size, coding density and coding sequences (CDSs) of the polar group were significantly different from those of other nonpolar Polaromonas. Furthermore, the enrichment of genes involved in carbohydrate and peptide metabolism was evident in the polar group. In addition, genes encoding proteins related to betaine synthesis and transport were increased in the genomes from the polar group. Phylogenomic analysis revealed that two different evolutionary scenarios may explain the adaptation of Polaromonas to cold environments in polar regions.</p><p><strong>Conclusions: </strong>The global distribution of the genus Polaromonas highlights its strong adaptability in both polar and nonpolar environments. Species delineation significantly expands our understanding of the diversity of the Polaromonas genus on a global scale. In this study, a polar-specific clade was found, which may represent a specific ecotype well adapted to polar environments. Collectively, genomic insight into the metabolic diversity, evolution and adaptation of the genus Polaromonas at the genome level provides a genetic basis for understanding the potential response mechanisms of Polaromonas to global warming in polar regions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"248"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907789/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633423","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":"Identification of the Valine-Glutamine gene family in Chenopodium quinoa Willd and analysis of its expression pattern and subcellular localization under drought stress.","authors":"Dongfang Zhang, Xiaolin Zhu, Xuefen Du, Xian Wang, Baoqiang Wang, Xiaohong Wei","doi":"10.1186/s12864-025-11313-6","DOIUrl":"10.1186/s12864-025-11313-6","url":null,"abstract":"<p><strong>Background: </strong>Chenopodium quinoa Willd (Quinoa) is highly tolerant to drought, cold, and salt stress. Gene editing technology development, and research on quinoa's drought resistance have attracted much attention. The transcriptional cofactor VQ plays an important role in the drought response in plants, but its role in quinoa has not been reported.</p><p><strong>Results: </strong>Bioinformatics identified 23 members of the quinoa VQ gene family, mainly located in the nucleus and unevenly distributed on 10 chromosomes. Gene structure and phylogenetic analysis indicated that the VQ genes were closely related and highly conserved, forming three subfamilies. The cis-acting elements of the promoter reveal its involvement in the response to light and hormonal stress. qRT-PCR analysis showed that all VQ genes were differentially expressed under drought stress, among which CqVQ13 was significantly up-regulated, and subcellular localization indicated that it was localized to the nucleus.</p><p><strong>Conclusion: </strong>This study conducted a systematic bioinformatics analysis of the basic physicochemical properties and chromosome localization of 23 members of the CqVQ gene family. Combined with transcriptome gene expression profiling and qRT-PCR, we found that CqVQ13 was significantly up-regulated under drought stress and localized in the nucleus. This discovery provides an important candidate gene for drought response studies in quinoa and lays the foundation for further exploration of the molecular mechanisms of the VQ gene family in response to drought stress.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"252"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633439","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":"Exploration of non-coding RNAs related to intramuscular fat deposition Xinjiang Brown cattle and Angus × Wagyu cattle.","authors":"Yuxin Zhou, Wanping Ren, Wei Shao, Yu Gao, Kangyu Yao, Min Yang, Xinyu Zhang, Yiran Wang, Fengming Li, Liang Yang","doi":"10.1186/s12864-025-11453-9","DOIUrl":"10.1186/s12864-025-11453-9","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Non-coding RNAs (ncRNAs) serve as crucial regulatory elements in the process of adipogenesis in animals; however, the specific roles and interrelationships of ncRNAs in bovine fat deposition remain poorly understood. This study aims to investigate the differentially expressed ncRNAs in the longissimus dorsi muscle of Xinjiang Brown cattle (XB) and Angus &lt;math&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;/math&gt; Wagyu cattle (AW), to elucidate the regulatory mechanisms underlying lipidogenesis that may involve ncRNAs. Four Xinjiang Brown cattle and four Angus &lt;math&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;/math&gt; Wagyu cattle were selected, ensuring they are subjected to identical feeding conditions, in order to evaluate the intermuscular fat (IMF) of longissimus dorsi muscles. The fat content of muscle tissue was quantified using the Soxhlet extraction method, revealing that the fat levels in the AW group were significantly elevated compared to those in the XB group. Taking muscle samples for paraffin sectioning and observing their morphology, it was found that the fat richness of the AW group was significantly higher than that of the XB group. Utilizing high-throughput RNA sequencing technology, we conducted an extensive transcriptomic analysis of longissimus dorsi muscles of XB and AW to identify significant ncRNAs implicated in fat metabolism and adipogenesis. The miRNA analysis yielded between 109,343,831 117,258,570 clean reads, whereas the lncRNA and circRNA analyses produced between 81,607,756 102,917,174 clean reads. Subsequent analysis revealed the identification of 53 differentially expressed miRNAs, 176 differentially expressed lncRNAs, and 234 differentially expressed circRNAs. KEGG enrichment analysis revealed that the target genes of differentially expressed miRNAs, lncRNAs, and circRNAs are significantly enriched in 2, 17, and 22 distinct pathways, respectively. The pathways associated with the differential enrichment of miRNA target genes involve processes such as phosphorylation and protein modification. Concurrently, the pathways linked to the varying enrichment of lncRNA target genes encompass G protein-coupled receptor signaling, regulation of cell death and apoptosis, activities related to GTPase activation, and functions governing nucleotide triphosphatases, among others. The circRNA exhibiting differential expression are significantly enriched in a variety of biological processes, including signal transduction, nucleic acid synthesis, cellular architecture, GTPase activation, and phosphatase activities, among others. The analysis of the ncRNA interaction network suggests that AGBL1, THRB, and S100A13 may play pivotal roles in the formation and adipogenic differentiation of adipocytes. In conclusion, we conducted a comprehensive analysis and discussion of the complete transcriptome of intermuscular fat tissue from the longissimus dorsi muscles in Xinjiang Brown cattle and Angus &lt;math&gt;&lt;mo&gt;×&lt;/mo&gt;&lt;/math&gt; Wagyu cattle. This study provides a theoretical foundation for enhancing our unders","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"249"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633436","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":"A near-complete genome assembly of Fragaria iinumae.","authors":"Haiyuan Du, Yiying He, Maoxian Chen, Xu Zheng, Daping Gui, Jixing Tang, Yu Fang, Yiwei Huang, Hong Wan, Jiwei Ruan, Xin Jin, Andan Zhu","doi":"10.1186/s12864-025-11440-0","DOIUrl":"10.1186/s12864-025-11440-0","url":null,"abstract":"<p><p>Fragaria iinumae, a diploid progenitor species of octoploid strawberries, likely occupies a basal position within the genus Fragaria. In this study, we report a near-complete genome assembly of F. iinumae v2.0, totaling 241.14 Mb with a contig N50 of 33.31 Mb. We identified 14 telomeric and 7 centromeric regions across its seven chromosomes. Compared to previous assemblies, F. iinumae v2.0 demonstrates substantial improvements in both genome continuity (gaps reduced from 29 to 0) and annotation completeness, including the annotation of 4,144 new genes and 395 new gene clusters. Notably, several large structural variants were identified between the F. iinumae v1.0 and F. iinumae v2.0 genomes, with most gaps in the v1.0 assembly overlapping with structural variant breakpoints. Additionally, we found a significant expansion of telomeric repeats in the B subgenome of octoploid strawberries compared to F. iinumae. Interestingly, two telomeres consistently exhibited low repeat abundance in both the diploid and octoploid B subgenomes, suggesting significant contraction early in the evolution of F. iinumae. Furthermore, through multiple lines of genomic evidence-including phylogenetic analyses, genetic distance matrices, a burst of LTR insertions, and the distribution of NLR resistance genes, we conclude that F. iinumae may represent an early-diverging lineage within the strawberry genus. This updated assembly provides a crucial genomic resource for understanding of the origin and structural dynamics of the strawberry genus and facilitates further exploration of genome-wide consequences of polyploidy.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"253"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633410","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":"Assembly and comparative analysis of the complete mitochondrial genome of Echinacanthus longipes (Acanthaceae), endemic to the Sino-Vietnamese karst flora.","authors":"Chunming Gao, Shu Wang, Yusong Huang, Yunfei Deng","doi":"10.1186/s12864-025-11448-6","DOIUrl":"10.1186/s12864-025-11448-6","url":null,"abstract":"<p><strong>Background: </strong>Echinacanthus longipes is an endemic species in the Sino-Vietnamese karst flora in the family Acanthaceae. It displays distinctive environmental adaptation characteristics in karst regions. Although it provides an important model for understanding the role of limestone karst in speciation and endemism, the mitochondrial genome (mtDNA) of E. longipes has not been fully characterized.</p><p><strong>Results: </strong>Here, the mtDNA of E. longipes was successfully assembled as a complex structure in the form of two small circular and three linear molecules with a total length of 810,200 bp. The annotated results revealed 36 protein-coding genes (PCGs), 22 tRNA genes, and three rRNA genes in this mtDNA. Notably, substantial sequence repeats and more tRNAs translocations from the chloroplast to the mtDNA were identified. Among the PCGs of E. longipes, the majority of 401 RNA editing sites were involved in amino acid transitions to hydrophobic sites. The current phylogenetic analysis based on PCGs revealed the evolution of Lamiales and a close relationship between E. longipes and Avicennia marina. However, comparative analyses, including size, structure, GC contents, and genes, reflected the variation in the mitogenomes within Acanthaceae, and the collinearity analysis confirmed the low level of conservation in the genomes of related species in Lamiales. Moreover, the Ka/Ks analysis revealed that negative selection occurred on most PCGs, with the notable exception of ccmB, which underwent positive selection. Interestingly, the ccmB gene had the most protein editing sites.</p><p><strong>Conclusions: </strong>This study will be invaluable for the mitochondrial study of Acanthaceae. It also provides extensive information for functional genetic and adaptive studies of Echinacanthus in karst regions in the future.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"251"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633417","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":"Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors.","authors":"Martin Danner, Matthias Begemann, Florian Kraft, Miriam Elbracht, Ingo Kurth, Jeremias Krause","doi":"10.1186/s12864-025-11444-w","DOIUrl":"10.1186/s12864-025-11444-w","url":null,"abstract":"<p><p>Understanding the dark genome is a priority task following the complete sequencing of the human genome. Short open reading frames (sORFs) are a group of largely unexplored elements of the dark genome with the potential for being translated into microproteins. The definitive number of coding and regulatory sORFs is not known, however they could account for up to 1-2% of the human genome. This corresponds to an order of magnitude in the range of canonical coding genes. For a few sORFs a clinical relevance has already been demonstrated, but for the majority of potential sORFs the biological function remains unclear. A major limitation in predicting their disease relevance using large-scale genomic data is the fact that no population-level constraint metrics for genetic variants in sORFs are yet available. To overcome this, we used the recently released gnomAD 4.0 dataset and analyzed the constraint of a consensus set of sORFs and their genomic neighbors. We demonstrate that sORFs are mostly embedded into a moderately constrained genomic context, but within the gencode dataset we identified a subset of highly constrained sORFs comparable to highly constrained canonical genes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"254"},"PeriodicalIF":3.5,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633443","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":"GWAS and transcriptome analyses unravel ZmGRAS15 regulates drought tolerance and root elongation in maize.","authors":"Dongmei Wang, Xuyang Liu, Guanhua He, Kailiang Wang, Yongxiang Li, Honghui Guan, Tianyu Wang, Dengfeng Zhang, Chunhui Li, Yu Li","doi":"10.1186/s12864-025-11435-x","DOIUrl":"10.1186/s12864-025-11435-x","url":null,"abstract":"<p><strong>Background: </strong>Drought is a major abiotic stress affecting maize development and growth. Unravelling the molecular mechanisms underlying maize drought tolerance and enhancing the drought tolerance of maize is of great importance. However, due to the complexity of the maize genome and the multiplicity of drought tolerance mechanisms, identifying the genetic effects of drought tolerance remains great challenging.</p><p><strong>Results: </strong>Using a mixed linear model (MLM) based on 362 maize inbred lines, we identified 40 associated loci and 150 candidate genes associated with survival rates. Concurrently, transcriptome analysis was conducted for five drought - tolerant and five drought - sensitive lines under Well-Watered (WW) and Water-Stressed (WS) conditions. Additionally, through co-expression network analysis (WGCNA), we identified five modules significantly associated with the leaf relative water content (RWC) under drought treatment. By integrating the results of GWAS, DEGs, and WGCNA, four candidate genes (Zm00001d006947, Zm00001d038753, Zm00001d003429 and Zm00001d003553) significantly associated with survival rate were successfully identified. Among them, ZmGRAS15 (Zm00001d003553), a GRAS transcription factor considered as a key hub gene, was selected for further functional validation. The overexpression of ZmGRAS15 in maize could significantly enhance drought tolerance through regulating primary root length at the seedling stage.</p><p><strong>Conclusion: </strong>This study provides valuable information for understanding the genetic basis of drought tolerance and gene resources for maize drought tolerance breeding.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"246"},"PeriodicalIF":3.5,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623424","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":"Integrated analysis of differential expression profile of miRNA in the uterus of seasonal estrus sheep.","authors":"Fan Yang, Jiannan Liu, Yongfu La, Ran Di, Xiaoyun He, Pingqing Wang, Yufang Liu, Mingxing Chu","doi":"10.1186/s12864-025-11401-7","DOIUrl":"10.1186/s12864-025-11401-7","url":null,"abstract":"<p><strong>Background: </strong>Photoperiod is one of the important factors affecting seasonal estrus of sheep. The importance of the uterus to reproduction is self-evident. However, the uterine molecular mechanisms involved in photoperiodic regulation of seasonal estrus events in sheep remain poorly understood. In recent years, the role of uterine microRNA (miRNA) in mammalian reproduction has been continuously revealed, and it is necessary to analyze and discuss their participation in the seasonal estrus of sheep.</p><p><strong>Results: </strong>We compared the miRNA expression profile in uterine tissues of Sunit sheep at 3 different photoperiods, short photoperiod (SP), short transfer to long photoperiod (SLP), and long photoperiod (LP). The results showed that 31, 29 and 21 differentially expressed miRNA (DEM) were identified between SP and LP, SP and SLP, LP and SLP, respectively. Subsequently, we constructed co-expression networks of DEM and target genes in different periods. Among all DEM, nove_320, nove_338 and nove_339 target the largest number of mRNAs. Functional annotation analysis showed that these DEM target genes can be enriched in multiple GO and KEGG signaling pathways, such as cell proliferation, apoptosis, reproductive process and biological adhesion, which are related to animal reproduction and uterine receptivity. Finally, the expression level of DEM was verified by RT-qPCR, and the binding regulation relationship between DEM and their target genes in the co-expression network was confirmed by double luciferase reporter gene experiment.</p><p><strong>Conclusions: </strong>This study revealed the changes of miRNA expression in sheep uterus under different photoperiod, providing valuable resources for understanding the molecular mechanism of sheep seasonal estrus.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"243"},"PeriodicalIF":3.5,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623426","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":"Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq.","authors":"Kaixuan Guo, Zhanming Zhong, Haonan Zeng, Changliang Zhang, Teddy Tinashe Chitotombe, Jinyan Teng, Yahui Gao, Zhe Zhang","doi":"10.1186/s12864-025-11411-5","DOIUrl":"10.1186/s12864-025-11411-5","url":null,"abstract":"<p><strong>Background: </strong>RNA sequencing (RNA-seq) is a powerful tool for transcriptome profiling, enabling integrative studies of expression quantitative trait loci (eQTL). As it identifies fewer genetic variants than DNA sequencing (DNA-seq), reference panel-based genotype imputation is often required to enhance its utility.</p><p><strong>Results: </strong>This study evaluated the accuracy of genotype imputation using SNPs called from RNA-seq data (RNA-SNPs). SNP features from 6,567 RNA-seq samples across 28 pig tissues were used to mask whole genome sequencing (WGS) data, with the Pig Genomic Reference Panel (PGRP) serving as the reference panel. Three imputation software tools (i.e., Beagle, Minimac4, and Impute5) were employed to perform the imputation. The result showed that RNA-SNPs achieved higher imputation accuracy (CR: 0.895 ~ 0.933; r²: 0.745 ~ 0.817) than SNPs from GeneSeek Genomic Profiler Porcine SNP50 BeadChip (Chip-SNPs) (CR: 0.873 ~ 0.909; r²: 0.629 ~ 0.698), and lower accuracy in \"intergenic\" regions. After imputation, quality control (QC) by minor allele frequency (MAF) and imputation quality (DR²) could improve r² but reduce SNP retention. Among software, Minimac4 takes the least runtime in single-thread setting, while Beagle performed best in multi-thread setting and phasing. Impute5 takes up minimal memory usage but requires the maximum runtime. All tools demonstrated comparable global accuracy (CR: 0.906 ~ 0.917; r²: 0.780 ~ 0.787).</p><p><strong>Conclusions: </strong>This study offers practical guidance for conducting RNA-SNP imputation strategies in genome and transcriptome research.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"245"},"PeriodicalIF":3.5,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623400","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}