Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves
Summary: Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade,...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-05-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124725004681 |
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| author | Shikai Liu Chenyu Shi Chenguang Chen Ying Tan Yuan Tian Daniel J. Macqueen Qi Li |
| author_facet | Shikai Liu Chenyu Shi Chenguang Chen Ying Tan Yuan Tian Daniel J. Macqueen Qi Li |
| author_sort | Shikai Liu |
| collection | DOAJ |
| description | Summary: Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade, we show that despite genome size reduction during evolution, these bivalves maintain remarkable genetic variability. By constructing a haplotype-resolved genome for Crassostrea sikamea, we identify widespread haplotype divergent sequences (HDSs), representing genomic regions unique to each haplotype. We show that HDSs are driven by transposable elements, playing a key role in creating and maintaining genetic diversity during oyster evolution. Comparisons of haplotype-resolved genomes across four bivalve orders uncover diverse HDS origins, highlighting a role in genetic innovation and expression regulation across broad timescales. Further analyses show that, in oysters, haplotype polymorphisms drive gene expression variation, which is likely to promote phenotypic plasticity and adaptation. These findings advance our understanding of the relationships among genome structure, diversity, and adaptability in a highly successful invertebrate group. |
| format | Article |
| id | doaj-art-f764f00b51f74edd9abe065a2ab69c6f |
| institution | DOAJ |
| issn | 2211-1247 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj-art-f764f00b51f74edd9abe065a2ab69c6f2025-08-20T03:09:39ZengElsevierCell Reports2211-12472025-05-0144511569710.1016/j.celrep.2025.115697Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalvesShikai Liu0Chenyu Shi1Chenguang Chen2Ying Tan3Yuan Tian4Daniel J. Macqueen5Qi Li6Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China; Corresponding authorKey Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, ChinaKey Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, ChinaKey Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, ChinaKey Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, ChinaThe Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UKKey Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China; Corresponding authorSummary: Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade, we show that despite genome size reduction during evolution, these bivalves maintain remarkable genetic variability. By constructing a haplotype-resolved genome for Crassostrea sikamea, we identify widespread haplotype divergent sequences (HDSs), representing genomic regions unique to each haplotype. We show that HDSs are driven by transposable elements, playing a key role in creating and maintaining genetic diversity during oyster evolution. Comparisons of haplotype-resolved genomes across four bivalve orders uncover diverse HDS origins, highlighting a role in genetic innovation and expression regulation across broad timescales. Further analyses show that, in oysters, haplotype polymorphisms drive gene expression variation, which is likely to promote phenotypic plasticity and adaptation. These findings advance our understanding of the relationships among genome structure, diversity, and adaptability in a highly successful invertebrate group.http://www.sciencedirect.com/science/article/pii/S2211124725004681CP: Genomics |
| spellingShingle | Shikai Liu Chenyu Shi Chenguang Chen Ying Tan Yuan Tian Daniel J. Macqueen Qi Li Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves Cell Reports CP: Genomics |
| title | Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves |
| title_full | Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves |
| title_fullStr | Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves |
| title_full_unstemmed | Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves |
| title_short | Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves |
| title_sort | haplotype resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves |
| topic | CP: Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2211124725004681 |
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