Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene
Abstract The wisent (Bison bonasus) is Europe’s largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of the highly conserved single copy mammalian genes which improves contiguity a thousand-fold over an existing assembly. Extended runs...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-11-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-024-07295-y |
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| author | Chiara Bortoluzzi Xena Marie Mapel Stefan Neuenschwander Fredi Janett Hubert Pausch Alexander S. Leonard |
| author_facet | Chiara Bortoluzzi Xena Marie Mapel Stefan Neuenschwander Fredi Janett Hubert Pausch Alexander S. Leonard |
| author_sort | Chiara Bortoluzzi |
| collection | DOAJ |
| description | Abstract The wisent (Bison bonasus) is Europe’s largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of the highly conserved single copy mammalian genes which improves contiguity a thousand-fold over an existing assembly. Extended runs of homozygosity in the wisent genome compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1580 bp deletion removing the protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 sequenced samples across the Bovinae subfamily showed that the deletion is fixed in both Bison species but absent in Bos and Bubalus. The THRSP transcript is abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus, but absent in bison. This indicates that the deletion likely inactivates THRSP in bison. We show that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also demonstrate that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing. |
| format | Article |
| id | doaj-art-0b16d3ec08914fefa1c57ca11c589daf |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Nature Portfolio |
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| series | Communications Biology |
| spelling | doaj-art-0b16d3ec08914fefa1c57ca11c589daf2024-12-01T12:40:35ZengNature PortfolioCommunications Biology2399-36422024-11-017111010.1038/s42003-024-07295-yGenome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP geneChiara Bortoluzzi0Xena Marie Mapel1Stefan Neuenschwander2Fredi Janett3Hubert Pausch4Alexander S. Leonard5Animal Genomics, ETH ZurichAnimal Genomics, ETH ZurichAnimal Genetics, ETH ZurichClinic of Reproductive Medicine, University of ZurichAnimal Genomics, ETH ZurichAnimal Genomics, ETH ZurichAbstract The wisent (Bison bonasus) is Europe’s largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of the highly conserved single copy mammalian genes which improves contiguity a thousand-fold over an existing assembly. Extended runs of homozygosity in the wisent genome compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1580 bp deletion removing the protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 sequenced samples across the Bovinae subfamily showed that the deletion is fixed in both Bison species but absent in Bos and Bubalus. The THRSP transcript is abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus, but absent in bison. This indicates that the deletion likely inactivates THRSP in bison. We show that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also demonstrate that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing.https://doi.org/10.1038/s42003-024-07295-y |
| spellingShingle | Chiara Bortoluzzi Xena Marie Mapel Stefan Neuenschwander Fredi Janett Hubert Pausch Alexander S. Leonard Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene Communications Biology |
| title | Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene |
| title_full | Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene |
| title_fullStr | Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene |
| title_full_unstemmed | Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene |
| title_short | Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene |
| title_sort | genome assembly of wisent bison bonasus uncovers a deletion that likely inactivates the thrsp gene |
| url | https://doi.org/10.1038/s42003-024-07295-y |
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