Pub Date : 2026-02-25DOI: 10.1186/s12864-026-12691-1
Gabriel Campos, Henrique Mulim, Henrique Ventura, Nadson Souza, Fernando Cardoso, Hinayah Rojas de Oliveira
Background: Indicine cattle (Bos taurus indicus) are found primarily in tropical and subtropical regions, with Brazil hosting one of the largest Zebu cattle populations in the world. Understanding the genetic makeup of Nellore cattle is crucial for enhancing genomic predictions, performing association studies, and maintaining genetic diversity. This study aims to characterize Brazilian Nellore cattle via genomic information. Linkage disequilibrium, effective population size (Ne), and runs of homozygosity (ROH) were used to characterize the population. The generation proxy selection method (GPSM) was used to detect alleles with changing frequencies over time.
Results: The average linkage disequilibrium across all chromosomes was 0.28, and the Ne was 225 in the most recent generation. Only one ROH island, which is related mainly to carcass quality and fertility traits, was identified in this study. In total, the GPSM method identified 77 significant SNPs and 142 quantitative trait loci (QTLs). These regions are associated with tick resistance, carcass and growth traits, maternal ability, and reproduction.
Conclusions: The level of linkage disequilibrium estimated in the Nellore population supports the successful implementation of genomic selection in the Nellore breed. Moreover, the Ne estimated via genomic information was found to be large enough to maintain desirable levels of genetic diversity within the breed. Most ROHs identified in this study were created in more ancient generations. Moreover, significant SNPs identified via the GPSM method confirmed that genetic selection was effective in Nellore cattle, and genomic changes were observed.
{"title":"A comprehensive genomic characterization of Nellore cattle.","authors":"Gabriel Campos, Henrique Mulim, Henrique Ventura, Nadson Souza, Fernando Cardoso, Hinayah Rojas de Oliveira","doi":"10.1186/s12864-026-12691-1","DOIUrl":"https://doi.org/10.1186/s12864-026-12691-1","url":null,"abstract":"<p><strong>Background: </strong>Indicine cattle (Bos taurus indicus) are found primarily in tropical and subtropical regions, with Brazil hosting one of the largest Zebu cattle populations in the world. Understanding the genetic makeup of Nellore cattle is crucial for enhancing genomic predictions, performing association studies, and maintaining genetic diversity. This study aims to characterize Brazilian Nellore cattle via genomic information. Linkage disequilibrium, effective population size (Ne), and runs of homozygosity (ROH) were used to characterize the population. The generation proxy selection method (GPSM) was used to detect alleles with changing frequencies over time.</p><p><strong>Results: </strong>The average linkage disequilibrium across all chromosomes was 0.28, and the Ne was 225 in the most recent generation. Only one ROH island, which is related mainly to carcass quality and fertility traits, was identified in this study. In total, the GPSM method identified 77 significant SNPs and 142 quantitative trait loci (QTLs). These regions are associated with tick resistance, carcass and growth traits, maternal ability, and reproduction.</p><p><strong>Conclusions: </strong>The level of linkage disequilibrium estimated in the Nellore population supports the successful implementation of genomic selection in the Nellore breed. Moreover, the Ne estimated via genomic information was found to be large enough to maintain desirable levels of genetic diversity within the breed. Most ROHs identified in this study were created in more ancient generations. Moreover, significant SNPs identified via the GPSM method confirmed that genetic selection was effective in Nellore cattle, and genomic changes were observed.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147302260","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}
Pub Date : 2026-02-25DOI: 10.1186/s12864-026-12687-x
Rooban Sivakumar, K A Arul Senghor, V M Vinodhini, K M Ramkumar
{"title":"In silico prioritisation of EDN1 missense variants identifies mature endothelin-1 substitutions with predicted receptor-binding effects.","authors":"Rooban Sivakumar, K A Arul Senghor, V M Vinodhini, K M Ramkumar","doi":"10.1186/s12864-026-12687-x","DOIUrl":"https://doi.org/10.1186/s12864-026-12687-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147282254","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}
Pub Date : 2026-02-25DOI: 10.1186/s12864-026-12684-0
Xiao-Yun Niu, Pu Yang
{"title":"Genome resequencing revealed genetic differentiation and promoter variation in wax secretion genes among geographic populations of Ericerus pela.","authors":"Xiao-Yun Niu, Pu Yang","doi":"10.1186/s12864-026-12684-0","DOIUrl":"https://doi.org/10.1186/s12864-026-12684-0","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147302262","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":"Characteristics of the mitochondrial genome of the invasive plant Tagetes minuta (Asteraceae) on the Qinghai-Tibet Plateau and its evolutionary significance.","authors":"Ngawang Bonjor, Zhefei Zeng, Rongfang Wang, Dorgon Dolma, Hui Zhang, Jiaqi He, Ciyang Bacuo, Ngawang Norbu, Xiaoyan Jia, La Qiong, Junwei Wang","doi":"10.1186/s12864-026-12679-x","DOIUrl":"https://doi.org/10.1186/s12864-026-12679-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147275584","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}
Pub Date : 2026-02-24DOI: 10.1186/s12864-026-12678-y
Ana Marín-Gordillo, Elio López-García, Verónica Romero-Gil, Virginia Martín-Arranz, Francisco Noé Arroyo-López, Francisco Rodríguez-Gómez
{"title":"Hybrid genome assembly and comprehensive genomic analysis of Lactiplantibacillus pentosus LP309 reveal its probiotic and technological potential.","authors":"Ana Marín-Gordillo, Elio López-García, Verónica Romero-Gil, Virginia Martín-Arranz, Francisco Noé Arroyo-López, Francisco Rodríguez-Gómez","doi":"10.1186/s12864-026-12678-y","DOIUrl":"https://doi.org/10.1186/s12864-026-12678-y","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147282158","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}
Pub Date : 2026-02-24DOI: 10.1186/s12864-026-12668-0
Alexander Van Uffelen, Andrea Gobbo, Marie-Alice Fraiture, Andrés Posadas, Nancy H C Roosens, Kathleen Marchal, Sigrid C J De Keersmaecker, Kevin Vanneste
{"title":"Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).","authors":"Alexander Van Uffelen, Andrea Gobbo, Marie-Alice Fraiture, Andrés Posadas, Nancy H C Roosens, Kathleen Marchal, Sigrid C J De Keersmaecker, Kevin Vanneste","doi":"10.1186/s12864-026-12668-0","DOIUrl":"https://doi.org/10.1186/s12864-026-12668-0","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147282123","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}
Pub Date : 2026-02-24DOI: 10.1186/s12864-026-12674-2
Evan Long, Grey Monroe
Recent advances in protein structure prediction have opened new avenues for understanding the potential impact of genetic mutations and how they might affect protein structure. In this study, we analyzed the distribution and structural characteristics of mutations in four plant species: Arabidopsis, rice, sugar beet, and cassava. We integrated population genotype datasets with protein structure predictions to map mutation positions to their corresponding gene protein products and structural features. Our analysis reveals that high-effect mutations are more likely to occur in unstructured, disordered regions of proteins rather than in well-folded, conserved regions. This finding suggests that natural selection exerts greater pressure to conserve sequence integrity in folded regions, which are crucial for protein function. Conversely, disordered regions may tolerate higher variability exhibiting a higher frequency of impactful mutations. By providing a comprehensive overview of mutation distribution in relation to protein structure, this study enhances our understanding of the evolutionary pressures shaping plant proteomes. The insights gained from this research could inform future studies on protein function, evolutionary biology, and plant improvement strategies.
{"title":"Protein structure and selection pressure in plants: using mutation to understand the functional importance of protein structure.","authors":"Evan Long, Grey Monroe","doi":"10.1186/s12864-026-12674-2","DOIUrl":"https://doi.org/10.1186/s12864-026-12674-2","url":null,"abstract":"<p><p>Recent advances in protein structure prediction have opened new avenues for understanding the potential impact of genetic mutations and how they might affect protein structure. In this study, we analyzed the distribution and structural characteristics of mutations in four plant species: Arabidopsis, rice, sugar beet, and cassava. We integrated population genotype datasets with protein structure predictions to map mutation positions to their corresponding gene protein products and structural features. Our analysis reveals that high-effect mutations are more likely to occur in unstructured, disordered regions of proteins rather than in well-folded, conserved regions. This finding suggests that natural selection exerts greater pressure to conserve sequence integrity in folded regions, which are crucial for protein function. Conversely, disordered regions may tolerate higher variability exhibiting a higher frequency of impactful mutations. By providing a comprehensive overview of mutation distribution in relation to protein structure, this study enhances our understanding of the evolutionary pressures shaping plant proteomes. The insights gained from this research could inform future studies on protein function, evolutionary biology, and plant improvement strategies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147282233","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}
Pub Date : 2026-02-24DOI: 10.1186/s12864-026-12672-4
Paweł Błażej, Dorota Mackiewicz, Paweł Mackiewicz
{"title":"Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.","authors":"Paweł Błażej, Dorota Mackiewicz, Paweł Mackiewicz","doi":"10.1186/s12864-026-12672-4","DOIUrl":"https://doi.org/10.1186/s12864-026-12672-4","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147282275","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}
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