Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations
Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268...
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The Royal Society
2025-05-01
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| Series: | Open Biology |
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| Online Access: | https://royalsocietypublishing.org/doi/10.1098/rsob.240382 |
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| author | Hancheng Bao Na Xue Boyuan Wang Han Yu Ming Huang Jinghong He Shuanglin Dong Yangen Zhou Qinfeng Gao Yuan Tian |
| author_facet | Hancheng Bao Na Xue Boyuan Wang Han Yu Ming Huang Jinghong He Shuanglin Dong Yangen Zhou Qinfeng Gao Yuan Tian |
| author_sort | Hancheng Bao |
| collection | DOAJ |
| description | Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits. |
| format | Article |
| id | doaj-art-c4faad51c9fa4a0f955a2af3f19f72fa |
| institution | DOAJ |
| issn | 2046-2441 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Open Biology |
| spelling | doaj-art-c4faad51c9fa4a0f955a2af3f19f72fa2025-08-20T03:08:13ZengThe Royal SocietyOpen Biology2046-24412025-05-0115510.1098/rsob.240382Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populationsHancheng Bao0Na Xue1Boyuan Wang2Han Yu3Ming Huang4Jinghong He5Shuanglin Dong6Yangen Zhou7Qinfeng Gao8Yuan Tian9Ocean University of China, Qingdao, Shandong, People’s Republic of ChinaOcean University of China, Qingdao, Shandong, People’s Republic of ChinaAuburn University, Auburn, AL, USAOcean University of China, Qingdao, Shandong, People’s Republic of ChinaOcean University of China, Qingdao, Shandong, People’s Republic of ChinaOcean University of China, Qingdao, Shandong, People’s Republic of ChinaOcean University of China, Qingdao, Shandong, People’s Republic of ChinaOcean University of China, Qingdao, Shandong, People’s Republic of ChinaOcean University of China, Qingdao, Shandong, People’s Republic of ChinaOcean University of China, Qingdao, Shandong, People’s Republic of ChinaGene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits.https://royalsocietypublishing.org/doi/10.1098/rsob.240382pan-genomegene presence/absence variationsrainbow troutartificial selection |
| spellingShingle | Hancheng Bao Na Xue Boyuan Wang Han Yu Ming Huang Jinghong He Shuanglin Dong Yangen Zhou Qinfeng Gao Yuan Tian Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations Open Biology pan-genome gene presence/absence variations rainbow trout artificial selection |
| title | Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations |
| title_full | Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations |
| title_fullStr | Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations |
| title_full_unstemmed | Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations |
| title_short | Exploration of gene presence/absence variations in Oncorhynchus mykiss and their differentiation between wild and selection populations |
| title_sort | exploration of gene presence absence variations in oncorhynchus mykiss and their differentiation between wild and selection populations |
| topic | pan-genome gene presence/absence variations rainbow trout artificial selection |
| url | https://royalsocietypublishing.org/doi/10.1098/rsob.240382 |
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