Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams
Abstract Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam (Tridacna maxima) genome to demonstrate how symbiosis has left complex signatures...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-024-07423-8 |
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| author | Ruiqi Li Carlos Leiva Sarah Lemer Lisa Kirkendale Jingchun Li |
| author_facet | Ruiqi Li Carlos Leiva Sarah Lemer Lisa Kirkendale Jingchun Li |
| author_sort | Ruiqi Li |
| collection | DOAJ |
| description | Abstract Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam (Tridacna maxima) genome to demonstrate how symbiosis has left complex signatures in an animal’s genome. Giant clams thrive in oligotrophic waters by forming a remarkable association with photosymbiotic dinoflagellate algae. Genome-based demographic inferences uncover a tight correlation between T. maxima global population change and major paleoclimate and habitat shifts, revealing how abiotic and biotic factors may dictate T. maxima microevolution. Comparative analyses reveal genomic features that may be symbiosis-driven, including expansion and contraction of immunity-related gene families and a large proportion of lineage-specific genes. Strikingly, about 70% of the genome is composed of repetitive elements, especially transposable elements, most likely resulting from a symbiosis-adapted immune system. This work greatly enhances our understanding of genomic drivers of symbiosis that underlie metazoan evolution and diversification. |
| format | Article |
| id | doaj-art-6912eca79eca4d2ebb0fcd9132524658 |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-6912eca79eca4d2ebb0fcd91325246582025-01-05T12:43:13ZengNature PortfolioCommunications Biology2399-36422025-01-018111210.1038/s42003-024-07423-8Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clamsRuiqi Li0Carlos Leiva1Sarah Lemer2Lisa Kirkendale3Jingchun Li4Department of Ecology and Evolutionary Biology, University of Colorado BoulderUniversity of Guam Marine LaboratoryUniversity of Guam Marine LaboratoryCollections and Research, Western Australian MuseumDepartment of Ecology and Evolutionary Biology, University of Colorado BoulderAbstract Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam (Tridacna maxima) genome to demonstrate how symbiosis has left complex signatures in an animal’s genome. Giant clams thrive in oligotrophic waters by forming a remarkable association with photosymbiotic dinoflagellate algae. Genome-based demographic inferences uncover a tight correlation between T. maxima global population change and major paleoclimate and habitat shifts, revealing how abiotic and biotic factors may dictate T. maxima microevolution. Comparative analyses reveal genomic features that may be symbiosis-driven, including expansion and contraction of immunity-related gene families and a large proportion of lineage-specific genes. Strikingly, about 70% of the genome is composed of repetitive elements, especially transposable elements, most likely resulting from a symbiosis-adapted immune system. This work greatly enhances our understanding of genomic drivers of symbiosis that underlie metazoan evolution and diversification.https://doi.org/10.1038/s42003-024-07423-8 |
| spellingShingle | Ruiqi Li Carlos Leiva Sarah Lemer Lisa Kirkendale Jingchun Li Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams Communications Biology |
| title | Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams |
| title_full | Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams |
| title_fullStr | Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams |
| title_full_unstemmed | Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams |
| title_short | Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams |
| title_sort | photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams |
| url | https://doi.org/10.1038/s42003-024-07423-8 |
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