Pub Date : 2026-02-11DOI: 10.1186/s12864-026-12637-7
Madelein Dippenaar, Hans Jacob Maree, Rachelle Bester
{"title":"From reads to results: comparing Oxford Nanopore to Illumina sequencing for citrus virus surveillance.","authors":"Madelein Dippenaar, Hans Jacob Maree, Rachelle Bester","doi":"10.1186/s12864-026-12637-7","DOIUrl":"https://doi.org/10.1186/s12864-026-12637-7","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155989","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 : 2026-02-11DOI: 10.1186/s12864-026-12646-6
Dandan Ma, Lu Ma, Jiawen Cui, Erdong Zhang, Ting Guo, Lei Zhang
{"title":"The complete mitochondrial genome of Prinsepia Uniflora (Rosaceae): De novo assembly, characterization, and phylogenetic analysis.","authors":"Dandan Ma, Lu Ma, Jiawen Cui, Erdong Zhang, Ting Guo, Lei Zhang","doi":"10.1186/s12864-026-12646-6","DOIUrl":"https://doi.org/10.1186/s12864-026-12646-6","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146164108","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 : 2026-02-11DOI: 10.1186/s12864-026-12571-8
E Rosell-Moll, E Capilla, I Navarro, D Garcia de la Serrana
{"title":"Analyzing the transcriptomic diversity in isolated mature adipocytes from the major fat depots in rainbow trout (Oncorhynchus mykiss).","authors":"E Rosell-Moll, E Capilla, I Navarro, D Garcia de la Serrana","doi":"10.1186/s12864-026-12571-8","DOIUrl":"https://doi.org/10.1186/s12864-026-12571-8","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146164125","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 : 2026-02-11DOI: 10.1186/s12864-026-12617-x
Weizhi Shi, Xiaoming Fan, Dongdong Li, Junying Chen, Yue Tan, Xin Yu, Yuan Tian, Yang Liu, Lei Fang, Zhongming Huo, Xiwu Yan
{"title":"Energy metabolism and the transcriptome provide new insights into the response mechanism of Manila clam (Rudiatapes philippinarum) between Southern and Northern China populations under high-temperature stress.","authors":"Weizhi Shi, Xiaoming Fan, Dongdong Li, Junying Chen, Yue Tan, Xin Yu, Yuan Tian, Yang Liu, Lei Fang, Zhongming Huo, Xiwu Yan","doi":"10.1186/s12864-026-12617-x","DOIUrl":"https://doi.org/10.1186/s12864-026-12617-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146164151","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 : 2026-02-10DOI: 10.1186/s12864-026-12556-7
Nan Sun, Wenxin Zhang, Dandan Yu, Mi Zhang, Yang Zou, Ximei Dong, Yiping Wang, Nana Song, Yaya Guo, Chen Jiang, Weifeng Wang, Lingyin Kong, Bo Liang, Jia Fei, Sijia Lu, Zhiyu Peng, Ting Yu, Jiale Xiang, Shoufang Qu
Background: Preimplantation genetic testing for structural rearrangements (PGT-SR) facilitates the selection of embryos with balanced karyotype prior to implantation. Currently, there is a critical need for reference materials (RMs) to ensure PGT-SR development.
Results: This study designed a novel and comprehensive strategy to produce renewable RMs using quartet families of structural rearrangements. A panel of quartet RMs for PGT-SR was successfully developed from 13 families, including 8 reciprocal translocations, 2 Robertsonian translocations, 2 inversions, and 1 normal family. Each quartet RMs comprised 3 tubes of DNA and 1 tube of sorted cells mimicking embryonic cells, all passed stringent quality assessments. The panel of quartet RMs was characterized by three volunteer laboratories with 100% accuracy and 100% specificity, using different sequencing platforms to assess the biomimetics. Additionally, while both short-read and long-read genome sequencing could detect exact breakpoints of the reciprocal translocations and standard inversion, long-read genome sequencing outperformed short-read sequencing for complex structural rearrangements.
Conclusions: This panel of quartet RMs for PGT-SR is well-characterized, renewable, and publicly accessible, playing a crucial role in proficiency test and quality assurance for structural rearrangement detection. The methods developed in this study are adaptable for other preimplantation genetic tests, thereby enhancing the advancement of assisted reproduction techniques.
{"title":"Generation of quartet reference materials for preimplantation genetic testing for structural rearrangements.","authors":"Nan Sun, Wenxin Zhang, Dandan Yu, Mi Zhang, Yang Zou, Ximei Dong, Yiping Wang, Nana Song, Yaya Guo, Chen Jiang, Weifeng Wang, Lingyin Kong, Bo Liang, Jia Fei, Sijia Lu, Zhiyu Peng, Ting Yu, Jiale Xiang, Shoufang Qu","doi":"10.1186/s12864-026-12556-7","DOIUrl":"https://doi.org/10.1186/s12864-026-12556-7","url":null,"abstract":"<p><strong>Background: </strong>Preimplantation genetic testing for structural rearrangements (PGT-SR) facilitates the selection of embryos with balanced karyotype prior to implantation. Currently, there is a critical need for reference materials (RMs) to ensure PGT-SR development.</p><p><strong>Results: </strong>This study designed a novel and comprehensive strategy to produce renewable RMs using quartet families of structural rearrangements. A panel of quartet RMs for PGT-SR was successfully developed from 13 families, including 8 reciprocal translocations, 2 Robertsonian translocations, 2 inversions, and 1 normal family. Each quartet RMs comprised 3 tubes of DNA and 1 tube of sorted cells mimicking embryonic cells, all passed stringent quality assessments. The panel of quartet RMs was characterized by three volunteer laboratories with 100% accuracy and 100% specificity, using different sequencing platforms to assess the biomimetics. Additionally, while both short-read and long-read genome sequencing could detect exact breakpoints of the reciprocal translocations and standard inversion, long-read genome sequencing outperformed short-read sequencing for complex structural rearrangements.</p><p><strong>Conclusions: </strong>This panel of quartet RMs for PGT-SR is well-characterized, renewable, and publicly accessible, playing a crucial role in proficiency test and quality assurance for structural rearrangement detection. The methods developed in this study are adaptable for other preimplantation genetic tests, thereby enhancing the advancement of assisted reproduction techniques.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155957","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 : 2026-02-10DOI: 10.1186/s12864-026-12545-w
Caitlin Guccione, Igor Sfiligoi, Antonio Gonzalez, Justin P Shaffer, Mariya Kazachkova, Yuhan Weng, Daniel McDonald, Shailja C Shah, Samuel S Minot, Thomas G Paulson, William M Grady, Ludmil B Alexandrov, Rob Knight, Kit Curtius
{"title":"Community assembly modeling of the microbiome within Barrett's esophagus and esophageal adenocarcinoma.","authors":"Caitlin Guccione, Igor Sfiligoi, Antonio Gonzalez, Justin P Shaffer, Mariya Kazachkova, Yuhan Weng, Daniel McDonald, Shailja C Shah, Samuel S Minot, Thomas G Paulson, William M Grady, Ludmil B Alexandrov, Rob Knight, Kit Curtius","doi":"10.1186/s12864-026-12545-w","DOIUrl":"10.1186/s12864-026-12545-w","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155965","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 : 2026-02-10DOI: 10.1186/s12864-026-12598-x
Siavash Salek Ardestani, Elmira Mohandesan
{"title":"GENOVIS: a Python package for the visualization of population genetic analyses.","authors":"Siavash Salek Ardestani, Elmira Mohandesan","doi":"10.1186/s12864-026-12598-x","DOIUrl":"10.1186/s12864-026-12598-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":"190"},"PeriodicalIF":3.7,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12903657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146155955","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}
Pub Date : 2026-02-10DOI: 10.1186/s12864-026-12518-z
Hongning Wang, Hongchang Zhao, Shanyuan Zhu, Wang Jian, Daoqing Gong
{"title":"Genome-wide association analysis to identify candidate genes for growth rate traits in Chinese endemic geese.","authors":"Hongning Wang, Hongchang Zhao, Shanyuan Zhu, Wang Jian, Daoqing Gong","doi":"10.1186/s12864-026-12518-z","DOIUrl":"https://doi.org/10.1186/s12864-026-12518-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146149015","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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