Pub Date : 2026-02-27DOI: 10.1186/s12864-026-12700-3
Lina Baz
{"title":"Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.","authors":"Lina Baz","doi":"10.1186/s12864-026-12700-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12700-3","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147302217","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 : 2026-02-27DOI: 10.1186/s12864-026-12659-1
Hira Tazeen, Aftab Ahmad, Syed Sibt E Hassan, Zhumei Ren
{"title":"Gene retroposition and functional diversification of retrocopies in the Rhus gall aphid Schlechtendalia chinensis.","authors":"Hira Tazeen, Aftab Ahmad, Syed Sibt E Hassan, Zhumei Ren","doi":"10.1186/s12864-026-12659-1","DOIUrl":"https://doi.org/10.1186/s12864-026-12659-1","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147316214","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":"The molecular basis underlying the differential development of immune organs between Huaifu and Cherry Valley ducks during early growth.","authors":"Zhiyu He, Shuai Xin, Yunyi Chen, Xiaopeng Li, Jiwei Hu, Hua He, Liang Li, Hehe Liu, Jiwen Wang","doi":"10.1186/s12864-026-12696-w","DOIUrl":"https://doi.org/10.1186/s12864-026-12696-w","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147316306","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 : 2026-02-27DOI: 10.1186/s12864-025-12457-1
Electine Magoye, Marc W Schmid, Chandra Ramakrishnan, Adrian B Hehl
{"title":"Genome-wide transcriptomic analysis of Toxoplasma gondii reveals stage-specific regulatory programs and metabolic adaptations driving oocyst sporulation.","authors":"Electine Magoye, Marc W Schmid, Chandra Ramakrishnan, Adrian B Hehl","doi":"10.1186/s12864-025-12457-1","DOIUrl":"https://doi.org/10.1186/s12864-025-12457-1","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147316290","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 : 2026-02-26DOI: 10.1186/s12864-026-12681-3
Salih Kumru, Fenny Patel, Akif Er, Sevki Kayis, Jochen Blom, Larry A Hanson, Hasan C Tekedar
{"title":"Comparative genomics insights into Pseudomonas rhodesiae: environmental distribution, resistance determinants, virulence factors, and evolutionary implications.","authors":"Salih Kumru, Fenny Patel, Akif Er, Sevki Kayis, Jochen Blom, Larry A Hanson, Hasan C Tekedar","doi":"10.1186/s12864-026-12681-3","DOIUrl":"https://doi.org/10.1186/s12864-026-12681-3","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147302243","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 : 2026-02-26DOI: 10.1186/s12864-026-12635-9
Kazi Chamonara, Md Habib Ullah Masum, Mohammad Sharif Uddin, Afifa Siddiqua, Sumaia Sultana, Sajedul Islam
Background: Shrimp exports generate substantial employment opportunities and revenue in Bangladesh. Nevertheless, the occurrence of Vibrio-associated epidemics remains a significant public health concern, with broader socio-economic consequences. This study characterizes the genomic and pathogenic features of the V. cholerae strain associated with local seafood market in Bangladesh. We employed whole-genome sequencing (WGS) using Nanopore long-read sequencing technology to investigate the genetic diversity, antimicrobial resistance, and virulence determinants of V. cholerae isolated from giant freshwater shrimps in Noakhali, Bangladesh.
Results: The genome of V. cholerae strain SU109 was assembled with high completeness (97.63%) and contiguity (L50 = 1). Functional and pathway investigations revealed that the strain possesses a sophisticated network of genes and metabolic processes, demonstrating its survival capabilities across various conditions. The pathway analysis identified numerous biosynthetic gene clusters (ectoine, vibriobactin, terpene, isocyanide, and β-lactone) associated with the synthesis of secondary metabolites, suggesting environmental resilience, iron acquisition, stress adaptation, microbial competitiveness, and may contribute to the strain's virulence and ecological fitness. Pangenome studies identified 2,120 core genes, highlighting substantial genetic diversity and adaptability. A phylogenetic study indicated a close evolutionary link between shrimp and clinical strains, suggesting potential genome conservation across environmental and clinical isolates.
Conclusion: These findings indicate that V. cholerae strain SU109 may serve as a reservoir of virulence- and resistance-associated traits in seafood, highlighting the need for continued surveillance, stringent hygiene practices, and careful interpretation of genomic predictions to evaluate public health risks.
{"title":"Genomic and phenotypic characterization of Vibrio cholerae strain SU109: a genomic investigation of a shrimp-associated strain from Bangladesh.","authors":"Kazi Chamonara, Md Habib Ullah Masum, Mohammad Sharif Uddin, Afifa Siddiqua, Sumaia Sultana, Sajedul Islam","doi":"10.1186/s12864-026-12635-9","DOIUrl":"https://doi.org/10.1186/s12864-026-12635-9","url":null,"abstract":"<p><strong>Background: </strong>Shrimp exports generate substantial employment opportunities and revenue in Bangladesh. Nevertheless, the occurrence of Vibrio-associated epidemics remains a significant public health concern, with broader socio-economic consequences. This study characterizes the genomic and pathogenic features of the V. cholerae strain associated with local seafood market in Bangladesh. We employed whole-genome sequencing (WGS) using Nanopore long-read sequencing technology to investigate the genetic diversity, antimicrobial resistance, and virulence determinants of V. cholerae isolated from giant freshwater shrimps in Noakhali, Bangladesh.</p><p><strong>Results: </strong>The genome of V. cholerae strain SU109 was assembled with high completeness (97.63%) and contiguity (L50 = 1). Functional and pathway investigations revealed that the strain possesses a sophisticated network of genes and metabolic processes, demonstrating its survival capabilities across various conditions. The pathway analysis identified numerous biosynthetic gene clusters (ectoine, vibriobactin, terpene, isocyanide, and β-lactone) associated with the synthesis of secondary metabolites, suggesting environmental resilience, iron acquisition, stress adaptation, microbial competitiveness, and may contribute to the strain's virulence and ecological fitness. Pangenome studies identified 2,120 core genes, highlighting substantial genetic diversity and adaptability. A phylogenetic study indicated a close evolutionary link between shrimp and clinical strains, suggesting potential genome conservation across environmental and clinical isolates.</p><p><strong>Conclusion: </strong>These findings indicate that V. cholerae strain SU109 may serve as a reservoir of virulence- and resistance-associated traits in seafood, highlighting the need for continued surveillance, stringent hygiene practices, and careful interpretation of genomic predictions to evaluate public health risks.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147302219","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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