Pub Date : 2026-01-07DOI: 10.1186/s12864-025-12507-8
Karol Mierzejewski, Aleksandra Kurzyńska, Monika Golubska, Robert Stryiński, Ismena Gałęcka, Jarosław Całka, Paula Borrajo, Manuel Pazos, Mónica Carrera, Iwona Bogacka
{"title":"PET microplastics induce lipotoxicity in the porcine pancreas.","authors":"Karol Mierzejewski, Aleksandra Kurzyńska, Monika Golubska, Robert Stryiński, Ismena Gałęcka, Jarosław Całka, Paula Borrajo, Manuel Pazos, Mónica Carrera, Iwona Bogacka","doi":"10.1186/s12864-025-12507-8","DOIUrl":"https://doi.org/10.1186/s12864-025-12507-8","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145910416","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 : 2026-01-07DOI: 10.1186/s12864-025-12508-7
Enock K Amoako, Kelly L Bennett, Anastasia Hernandez-Koutoucheva, Isaiah Debrah, Collins M Morang'a, Stephen Binaansim, Victor A Asoala, Cristina Ariana, Keziah L Malm, Gordon Awandare, Alistair Miles, Chris S Clarkson, Lucas N Amenga-Etego
{"title":"Genomic population structure and insecticide resistance mechanisms in the malaria vector An. coluzzii across contrasting bioclimatic zones in West Africa.","authors":"Enock K Amoako, Kelly L Bennett, Anastasia Hernandez-Koutoucheva, Isaiah Debrah, Collins M Morang'a, Stephen Binaansim, Victor A Asoala, Cristina Ariana, Keziah L Malm, Gordon Awandare, Alistair Miles, Chris S Clarkson, Lucas N Amenga-Etego","doi":"10.1186/s12864-025-12508-7","DOIUrl":"10.1186/s12864-025-12508-7","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917078","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 : 2026-01-07DOI: 10.1186/s12864-025-12455-3
Alan S Brown, Manuel Llinás, Shaun Mahony
{"title":"Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.","authors":"Alan S Brown, Manuel Llinás, Shaun Mahony","doi":"10.1186/s12864-025-12455-3","DOIUrl":"10.1186/s12864-025-12455-3","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145917128","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 : 2026-01-07DOI: 10.1186/s12864-025-12515-8
Tingting Zheng, Dehua Cheng, Yuxia Yang, Sijia Lu, Huiying Li, Liangqun Xie, Qinhua Li, Hong Ye
Objective: This study completed the karyotyping of a patient with a complex chromosomal insertion and identified the location of the breakpoint for implementing preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) to differentiate between normal and carrier embryos, aiming to assess the clinical outcome of PGT-SR in couples with complex chromosome rearrangements (CCRs).
Method: The Chromosome conformation based Karyotyping technique (C-Moka) was implemented to identify karyotypes and analyze chromosomal breakpoints, with subsequent verification of karyotype results by fluorescence in situ hybridization (FISH). Whole genome sequencing (WGS) of embryos followed by copy number variation and second-generation sequencing (NGS) based single nucleotide polymorphism (SNP) haplotyping to discriminate between normal and carrier embryos were carried out in PGT-SR cycles.
Results: Based on the precise breakpoint sequences identified by C-Moka, mapping allele with resolved carrier status (MaReCs) was used to distinguish a normal embryo from a carrier embryo among two balanced euploidy embryos, resulting in the birth of a healthy baby after transfer of the normal embryo.
Conclusion: This case demonstrates the feasibility of C-Moka technique in assisting CCRs diagnosis and directly identifying breakpoints to construct haplotypes without family lineage or reference embryo pre-tests.
{"title":"Identification of a complex chromosomal insertion using the chromosome conformation based karyotyping technique for the implementation of PGT-SR.","authors":"Tingting Zheng, Dehua Cheng, Yuxia Yang, Sijia Lu, Huiying Li, Liangqun Xie, Qinhua Li, Hong Ye","doi":"10.1186/s12864-025-12515-8","DOIUrl":"https://doi.org/10.1186/s12864-025-12515-8","url":null,"abstract":"<p><strong>Objective: </strong>This study completed the karyotyping of a patient with a complex chromosomal insertion and identified the location of the breakpoint for implementing preimplantation genetic testing for chromosomal structural rearrangements (PGT-SR) to differentiate between normal and carrier embryos, aiming to assess the clinical outcome of PGT-SR in couples with complex chromosome rearrangements (CCRs).</p><p><strong>Method: </strong>The Chromosome conformation based Karyotyping technique (C-Moka) was implemented to identify karyotypes and analyze chromosomal breakpoints, with subsequent verification of karyotype results by fluorescence in situ hybridization (FISH). Whole genome sequencing (WGS) of embryos followed by copy number variation and second-generation sequencing (NGS) based single nucleotide polymorphism (SNP) haplotyping to discriminate between normal and carrier embryos were carried out in PGT-SR cycles.</p><p><strong>Results: </strong>Based on the precise breakpoint sequences identified by C-Moka, mapping allele with resolved carrier status (MaReCs) was used to distinguish a normal embryo from a carrier embryo among two balanced euploidy embryos, resulting in the birth of a healthy baby after transfer of the normal embryo.</p><p><strong>Conclusion: </strong>This case demonstrates the feasibility of C-Moka technique in assisting CCRs diagnosis and directly identifying breakpoints to construct haplotypes without family lineage or reference embryo pre-tests.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145910466","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 : 2026-01-06DOI: 10.1186/s12864-025-12496-8
Kai Zhang, Wenbing Wang, Junrong Li, Zhen Liang, Maoteng Li
Background: Long noncoding RNAs (lncRNAs) have been shown to play important roles in plant abiotic stress response and adaptation. However, the identification and characterization of genome-wide drought-responsive lncRNAs in rapeseed (Brassica napus L.) have been limited. Therefore, this study was the first to identify the expression profile of lncRNAs in rapeseed seeds responding to prolonged drought stress and subsequent short-term rewatering.
Results: A total of 6 000 lncRNAs were identified, among which 181 were classified as differentially expressed lncRNAs (DELs) in response to either drought stress or subsequent rewatering. Comparative analysis revealed that only 14 DELs were shared between the 159 DELs identified during drought stress and the 27 DELs detected upon rewatering. GO enrichment analysis showed that the co-expressed DEGs, primarily involved in photosynthesis, central carbon metabolism, stomatal movement, and strigolactone metabolism, were significantly down-regulated under drought stress but markedly up-regulated in subsequent rewatering. Furthermore, drought‑responsive competing endogenous RNA (ceRNA) networks were constructed based on the identified DETs and DEGs. Two ceRNA modules, MSTRG.57345.1-bna-miR164a/b/c/d-HSP2 and MSTRG.57345.1-bna-miR395d/e/f-HSFA7a, which are based on the newly identified lncRNA MSTRG.57345.1, were detected for the first time in rapeseed under drought stress and subsequent rewatering.
Conclusions: The present study advances our understanding of the expression patterns and functional role of rapeseed lncRNAs in the response to drought stress and the subsequent rewatering. It provides novel insights into lncRNA-mRNA networks and lncRNA-miRNA-mRNA networks in the seeds of B. napus. These findings offer a valuable reference for further genetic research and molecular breeding programs aimed at rapeseed improvement.
{"title":"Genome-wide analysis of long noncoding RNAs in response to drought stress in the seeds of Brassica napus.","authors":"Kai Zhang, Wenbing Wang, Junrong Li, Zhen Liang, Maoteng Li","doi":"10.1186/s12864-025-12496-8","DOIUrl":"https://doi.org/10.1186/s12864-025-12496-8","url":null,"abstract":"<p><strong>Background: </strong>Long noncoding RNAs (lncRNAs) have been shown to play important roles in plant abiotic stress response and adaptation. However, the identification and characterization of genome-wide drought-responsive lncRNAs in rapeseed (Brassica napus L.) have been limited. Therefore, this study was the first to identify the expression profile of lncRNAs in rapeseed seeds responding to prolonged drought stress and subsequent short-term rewatering.</p><p><strong>Results: </strong>A total of 6 000 lncRNAs were identified, among which 181 were classified as differentially expressed lncRNAs (DELs) in response to either drought stress or subsequent rewatering. Comparative analysis revealed that only 14 DELs were shared between the 159 DELs identified during drought stress and the 27 DELs detected upon rewatering. GO enrichment analysis showed that the co-expressed DEGs, primarily involved in photosynthesis, central carbon metabolism, stomatal movement, and strigolactone metabolism, were significantly down-regulated under drought stress but markedly up-regulated in subsequent rewatering. Furthermore, drought‑responsive competing endogenous RNA (ceRNA) networks were constructed based on the identified DETs and DEGs. Two ceRNA modules, MSTRG.57345.1-bna-miR164a/b/c/d-HSP2 and MSTRG.57345.1-bna-miR395d/e/f-HSFA7a, which are based on the newly identified lncRNA MSTRG.57345.1, were detected for the first time in rapeseed under drought stress and subsequent rewatering.</p><p><strong>Conclusions: </strong>The present study advances our understanding of the expression patterns and functional role of rapeseed lncRNAs in the response to drought stress and the subsequent rewatering. It provides novel insights into lncRNA-mRNA networks and lncRNA-miRNA-mRNA networks in the seeds of B. napus. These findings offer a valuable reference for further genetic research and molecular breeding programs aimed at rapeseed improvement.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905489","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 : 2026-01-06DOI: 10.1186/s12864-025-12474-0
Burak Muhammed Öner, Ahmed Sidar Aygören, Ayşe Gül Kasapoğlu, Sümeyra Uçar, Esra Yaprak, Selman Muslu, Esma Yiğider, Emre İlhan, Abdulkadir Çiltaş, Murat Aydın, Ertan Yıldırım
{"title":"Genome-wide analysis of Phaseolus vulgaris L. miR172 gene family members under heavy metal stress.","authors":"Burak Muhammed Öner, Ahmed Sidar Aygören, Ayşe Gül Kasapoğlu, Sümeyra Uçar, Esra Yaprak, Selman Muslu, Esma Yiğider, Emre İlhan, Abdulkadir Çiltaş, Murat Aydın, Ertan Yıldırım","doi":"10.1186/s12864-025-12474-0","DOIUrl":"https://doi.org/10.1186/s12864-025-12474-0","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145910390","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 : 2026-01-06DOI: 10.1186/s12864-025-12510-z
Yuying Yuan, Min Zhong, Depeng Yan, Junying Chen, Shiqi Xu, Jie Wu, Weisheng Liu, Taili Nie, Xiaolin Zeng
{"title":"Genome-wide identification of the GT transcription factor family in alfalfa and functional characterization of MsGT16 in salt stress tolerance.","authors":"Yuying Yuan, Min Zhong, Depeng Yan, Junying Chen, Shiqi Xu, Jie Wu, Weisheng Liu, Taili Nie, Xiaolin Zeng","doi":"10.1186/s12864-025-12510-z","DOIUrl":"https://doi.org/10.1186/s12864-025-12510-z","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145910424","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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