BMC Genomics最新文献

{"title":"Targeted metabolomic and transcriptomic analyses provide insights into flavonoid biosynthesis in the grain of Foxtail millet.","authors":"Zhenyan Ye, Na Qin, Senjie Fu, Huifang Zhang, Cancan Zhu, Shutao Dai, Ya Jing, Xin Wei, Chunyi Wang, Le Ju, Junxia Li","doi":"10.1186/s12864-025-11780-x","DOIUrl":"10.1186/s12864-025-11780-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"610"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538419","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":"CRISPRware: a software package for contextual gRNA library design.","authors":"Eric Malekos, Christy Montano, Susan Carpenter","doi":"10.1186/s12864-025-11775-8","DOIUrl":"10.1186/s12864-025-11775-8","url":null,"abstract":"<p><p>We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and can account for genetic variation, which allows allele-specific guide design on a genome-wide scale. As a demonstration of use and to create a publicly available resource, we use CRISPRware to identify and score gRNAs against coding sequences in six model organisms for Cas9 and Cas12A and host these in a publicly available session on the UCSC Genome Browser.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"607"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538282","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":"Extending gene set variation analysis with a reference dataset to stabilize scores.","authors":"Lorin Towle-Miller, William Jordan, Alexandre Lockhart, Johannes Freudenburg, Aman Virmani, Mandy Bergquist, Jeffrey Miecznikowski, Will Powley","doi":"10.1186/s12864-025-11769-6","DOIUrl":"10.1186/s12864-025-11769-6","url":null,"abstract":"<p><strong>Background: </strong>Biological pathways are sets of genes that jointly drive biological processes. Rather than analyzing genes individually, it is common practice to summarize sets of related genes using gene set variation analysis (GSVA). In short, GSVA summarizes a set of genes into a single score bounded between -1 and 1, where negative values suggest downregulation and positive values suggest upregulation. Although this interpretation is simple in theory, it depends on unbiased estimation of individual gene distributions. In the current version of GSVA, gene distributions are estimated using the input dataset (i.e., the scores are calculated based on the gene distributions from the same dataset). This becomes a major issue when study data does not adequately represent the full distribution of the population. For example, if RNA-seq data was collected on an imbalanced sample (e.g., more disease samples than healthy controls), it would be difficult to discern abnormalities in pathway activity since the gene distributions were estimated on a biased population. Therefore, we propose reference stabilizing GSVA (rsGSVA), a solution to this commonly ignored limitation by using reference datasets to estimate the gene distributions for a more stable GSVA score.</p><p><strong>Results: </strong>rsGSVA shows comparable power to classic GSVA, singscore, and ssGSEA under ideal settings while demonstrating stable scores on sample subsets. An application on irritable bowel disease highlights interpretational advantages of rsGSVA to other methods in up/down regulation of inflammation signatures.</p><p><strong>Conclusions: </strong>The rsGSVA technique enhances the GSVA functionality by incorporating a reference dataset. This integration of a reference dataset makes the enrichment scores independent of the input distribution and ensures their stability and reproducibility, even as samples are added or removed.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"596"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538287","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":"Ancestral and recent bursts of transposition shaped the massive genomes of plant pathogenic rust fungi.","authors":"Emma Corre, Emmanuelle Morin, Sébastien Duplessis, Cecile Lorrain","doi":"10.1186/s12864-025-11726-3","DOIUrl":"10.1186/s12864-025-11726-3","url":null,"abstract":"<p><strong>Background: </strong>Transposable elements (TEs) play a crucial role in genome evolution, influencing gene regulation, diversity, and genome architecture. Rust fungi of the order Pucciniales (Subphylum Pucciniomycotina) are the largest group of obligate biotrophic plant pathogens and harbor some of the largest and most TE-rich genomes-up to 1.2 Gb-compared to other fungi. This global genomic expansion contrasts with the smaller genomes and minimal mobilome found in other Pucciniomycotina species. Despite the availability of high-quality genome assemblies, our understanding of TE dynamics in Pucciniales remains limited due to inconsistent and incomplete TE annotations.</p><p><strong>Results: </strong>We analyzed the mobilomes of 12 Pucciniomycotina species, producing a manually curated TE library for each genome. In Pucciniales, TEs occupy 47-92% of the genome, whereas 2-36% of TEs are detected in other Pucciniomycotina genomes. The comparison of gene and TE repertoires indicates that TEs, particularly LTR-retrotransposons and TIR-DNA transposons, are the primary contributors to the genome expansion of the Pucciniales. We reconstructed the proliferation histories of TEs in the Pucciniales, combining sequence similarity, clustering, and molecular clock approaches. We highlight recent and ancient TE invasions with some LTR-Gypsy elements predating the divergence of Pucciniomycotina (~ 176 Mya), while most TE accumulation in Pucciniales occurred within the last 50 Mya. However, the TE invasions in the Pucciniales genomes do not seem to result from specific deficiencies in known TE-control mechanisms.</p><p><strong>Conclusion: </strong>Our findings uncover extensive TE proliferation in Pucciniales, predominantly driven by LTR-Gypsy expansions. The retention of ancestral TEs and the consistently TE-rich genomes observed in Pucciniales highlight TE proliferation as an ancestral genomic feature in rust fungi.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"627"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538299","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":"Tick genomics through a Nanopore: a low-cost approach for tick genomics.","authors":"Christina Meiring, Monique Eygelaar, Josephus Fourie, Michel Labuschagne","doi":"10.1186/s12864-025-11733-4","DOIUrl":"10.1186/s12864-025-11733-4","url":null,"abstract":"<p><strong>Background: </strong>The assembly of large and complex genomes can be costly since it typically requires the utilization of multiple sequencing technologies and access to high-performance computing, while creating a dependency on external service providers. The aim of this study was to independently generate draft genomes for the cattle ticks Rhipicephalus microplus and R. appendiculatus using Oxford Nanopore sequencing technology.</p><p><strong>Results: </strong>Exclusively, Oxford Nanopore sequence data were assembled with Shasta and finalized on the Amazon Web Services cloud platform, capitalizing on the availability of up to 90% discounted Spot instances. The assembled and polished R. microplus and R. appendiculatus genomes from our study were comparable to published tick genomes where multiple sequencing technologies and costly bioinformatic resources were utilized that are not readily accessible to low-resource environments. We predicted 52,412 genes for R. appendiculatus, with 31,747 of them being functionally annotated. The R. microplus annotation consisted of 60,935 predicted genes, with 32,263 being functionally annotated in the final file. The sequence data were also used to assemble and annotate genetically distinct Coxiella-like endosymbiont genomes for each tick species. The results indicated that each of the endosymbionts exhibited genome reductions. The Nanopore Q20 + library kit and flow cell were used to sequence the > 80% AT-rich mitochondrial DNA of both tick species. The sequencing generated accurate mitochondrial genomes, encountering imperfect base calling only in homopolymer regions exceeding 10 bases.</p><p><strong>Conclusion: </strong>This study presents an alternative approach for smaller laboratories with limited budgets to enter the field and participate in genomics without capital intensive investments, allowing for capacity building in a field normally exclusively accessible through collaboration and large funding opportunities.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"591"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538421","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 first nuclear and mitochondrial genomic portrait of Robinson Crusoe's (Juan Fernández Island) spiny lobster Jasus frontalis (Crustacea: Decapoda: Achelata).","authors":"J Antonio Baeza, Alyssa Baker, Sadia A Kamal, Vincent P Richards","doi":"10.1186/s12864-025-11794-5","DOIUrl":"10.1186/s12864-025-11794-5","url":null,"abstract":"<p><strong>Background: </strong>The Juan Fernández rock lobster Jasus frontalis (H. Milne-Edwards, 1837) is found along the Juan Fernández archipelago and Desventuradas Islands in the southeastern Pacific Ocean where it supports a profitable but likely unsustainable artisanal fishery. Only a few genomic resources are available for this species to support efficient managing practices. In this study, we took a first look at the genome of J. frontalis profiting from recently developed bioinformatics tools that mine for biological insight from low sequencing-depth datasets. Specifically, we have (i) estimated the nuclear genome size, (ii) assembled and described in detail the mitochondrial genome, (iii) discovered, quantified, and annotated nuclear transposable elements, and (iv) examined the phylogenetic position of the genus Jasus among spiny lobsters (family Palinuridae) using a maximum likelihood phylogenetic analysis based on translated mitochondrial protein coding genes (PCG's).</p><p><strong>Results: </strong>Using an in-silico k-mer approach, the haploid nuclear genome size (GS) calculated for J. frontalis ranged between 1.42 Gbp (estimated using k-mer = 54 bp) and 1.65 Gbp (with k-mer = 18). Our GS estimates are well below the GS (= 4.56 Gbp) determined for the same species using flow cytometry. In J. frontalis, the circular mitochondrial genome is 15,514 bp in length and contains 22 transfer (tRNA) genes, 13 PCGs, and two ribosomal RNA genes (12 S and 16 S ribosomal RNA). In the nuclear genome of J. frontalis, repetitive elements content varied between 41% (with k-mer = 54) and 64% (using k-mer = 18 bp). Nearly a third (64.94%) of the transposable elements were not annotated. Among annotated transposable elements, Long Interspersed Nuclear Elements (LINEs, 12.64%), DNA transposons (7.35%), and Long Terminal Repeats (LTRs, 5.44%) were the most common. Less abundant transposable elements included Rolling Circles (1.3%), Short Interspersed Nuclear Elements (SINEs, 0.64%), Satellite DNA (0.43%), and simple repeats (0.42%), among others. A phylomitogenomic analysis based on PCGs indicated supported the monophyletic status of the infraorder Achelata and the superfamilies Paniluridae and Syllaridae. The genus Jasus together with Sagmariasus verreauxi were recovered as a monophyletic clade that also provided support for the monophyletic status of lobsters that do not produce sound (\"Silentes\").</p><p><strong>Conclusion: </strong>The genomic resources developed in this study will support conservation strategies and efficient fisheries management in this spiny lobster that is likely overexploited.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"623"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538364","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":"Unraveling the genetic diversity and adaptive traits of laboratory pig breeds within the perspective of whole - genome resequencing.","authors":"Haonan Yuan, Changwen Li, Shengguo Zhao, Yanan Yang, Zhe Chao, Changyou Xia, Jinqiang Quan, Caixia Gao","doi":"10.1186/s12864-025-11790-9","DOIUrl":"10.1186/s12864-025-11790-9","url":null,"abstract":"<p><p>As one of the most widely used animal models for human disease research, pigs play a critical role in elucidating disease pathogenesis. However, the genetic characteristics of experimental pig breeds remain underexplored. This study employed whole-genome resequencing to investigate three representative Chinese indigenous pig breeds and two commercial European breeds. Our analysis revealed that indigenous breeds harbor 16.3 million genetic variants (88.3% SNPs), with higher nucleotide diversity compared to commercial breeds. Selective sweep analysis using Fst and π identified key genes under strong selection, including immune regulators (BTK, IL2RG, RASGRP1), metabolic gene MED12, and neuro-associated SDR16C5, with five genes exhibiting significant allele frequency divergence between populations (P < 0.05). Notably, two signature selective regions on chromosome 6 (181,025-182,387 bp and 144,185,871-144,313,689 bp) were identified, containing fixed missense mutations in coat color gene MC1R (p.T305C/p.G283A) and vision-related gene RPE65 (p.G1503A), indicating strong artificial selection for phenotypic traits. This work systematically characterizes the high genetic diversity of Chinese indigenous pigs and their genomic advantages as disease models, providing critical insights for developing precision biomedical animal models.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"604"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538426","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":"Cross-tissue gene expression interactions from bulk, single cell and spatial transcriptomics with crossWGCNA.","authors":"Aurora Savino, Raffaele M Iannuzzi, Lidia Avalle, Andrea Lobascio, Francesco Iorio, Paolo Provero, Valeria Poli","doi":"10.1186/s12864-025-11747-y","DOIUrl":"10.1186/s12864-025-11747-y","url":null,"abstract":"<p><strong>Background: </strong>Understanding the molecular interactions between cells, tissues or organs is key to understanding the functioning of a biological system as a whole.</p><p><strong>Results: </strong>Here, we propose crossWGCNA: a co-expression-based method that identifies highly interacting genes unbiasedly and that we employ to study stroma-epithelium communication in breast cancer. CrossWGCNA can be applied to bulk, single cell and spatial transcriptomics data. We validate it both in silico and experimentally, and we provide a fully documented R package allowing users to employ it.</p><p><strong>Conclusions: </strong>The wide applicability and agnostic nature of our tool make it complementary to existing methods overcoming the limitations arising from strong baseline assumptions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"583"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538283","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, evolution, and expression and metabolic regulation of the maize CHS gene family under abiotic stress.","authors":"Xiaofang Wang, Jing Wu, Huangai Li, Lei Zhu, Yan Long","doi":"10.1186/s12864-025-11761-0","DOIUrl":"10.1186/s12864-025-11761-0","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"581"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538384","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 two photo-thermo-sensitive genic male-sterile lines reveal GA-mediated regulatory mechanism for rice panicle exsertion.","authors":"Pengpeng Fang, Yi Zhou, Li Zhang, Wuhan Zhang, Qiang He, Duo Lan, Jia Zeng, Huafeng Deng, Fu Shu, Pingyong Sun","doi":"10.1186/s12864-025-11809-1","DOIUrl":"10.1186/s12864-025-11809-1","url":null,"abstract":"<p><strong>Background: </strong>Hybrid rice is pivotal for ensuring food security in China, yet challenges persist in its seed production. Sterile lines commonly face issues such as necking, gibberellins (GAs) are key regulators of panicle exsertion in rice, necessitating increased application of GAs during seed production, leading to elevated costs and environmental pollution. The novel photoperiod-thermosensitive genic male sterile line Shuang 1S addresses these limitations through its unique non-necked morphology and has super high yield of seed production.</p><p><strong>Results: </strong>To elucidate the regulatory pathways governing panicle exsertion and identify novel potential genes, this study assessed endogenous GA levels and performed RNA-seq analysis on two sterile lines, Shuang 1S and Han 2S, which displayed notable differences in panicle exsertion. Among 20 sterile lines examined, Shuang 1S demonstrated the highest panicle grains exsertion rate (91.03%) and the longest inverted first internode (28.24 cm). The findings revealed a 1.5-fold increase in GA content in Shuang 1S compared to Han 2S. Additionally, 2,147 up-regulated and 2,709 down-regulated genes were identified between SP (Shuang 1S) and HP (Han 2S), including 15 genes (10 up-regulated and 5 down-regulated) involved in GA biosynthesis and metabolism. KEGG enrichment analysis of the differentially expressed genes (DEGs) revealed significant enrichment in pathways including diterpenoid biosynthesis and plant hormone signal transduction, which are associated with gibberellic acid (GA) synthesis and catabolism.</p><p><strong>Conclusions: </strong>We found that panicle exsertion was directly related to GAs content, and mainly enriched in diterpenoid biosynthesis, plant hormone signal transduction. These findings present new potential candidate genes for future investigations into the molecular mechanisms underlying the regulation of panicle exsertion in rice.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"629"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538422","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}