A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination
Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due...
| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2023
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| Acceso en línea: | https://hdl.handle.net/10568/138214 |
| _version_ | 1855539229699866624 |
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| author | Arick, Mark Grover, Corrinne Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma Thrash, Adam Youngblood, Ramey Ezzell, Lauren Alam, Md. Benzie, John Hamilton, Matthew Karsi, Attila Lawrence, Mark Peterson, Daniel |
| author_browse | Alam, Md. Arick, Mark Benzie, John Ezzell, Lauren Grover, Corrinne Hamilton, Matthew Hsu, Chuan-Yu Karsi, Attila Lawrence, Mark Magbanua, Zenaida Miller, Emma Pechanova, Olga Peterson, Daniel Thrash, Adam Youngblood, Ramey |
| author_facet | Arick, Mark Grover, Corrinne Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma Thrash, Adam Youngblood, Ramey Ezzell, Lauren Alam, Md. Benzie, John Hamilton, Matthew Karsi, Attila Lawrence, Mark Peterson, Daniel |
| author_sort | Arick, Mark |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs. |
| format | Journal Article |
| id | CGSpace138214 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1382142025-12-08T10:11:39Z A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination Arick, Mark Grover, Corrinne Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma Thrash, Adam Youngblood, Ramey Ezzell, Lauren Alam, Md. Benzie, John Hamilton, Matthew Karsi, Attila Lawrence, Mark Peterson, Daniel aquaculture genomes sex determination rohu fish rui ddrad-seq Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs. 2023-03-09 2024-01-21T05:16:20Z 2024-01-21T05:16:20Z Journal Article https://hdl.handle.net/10568/138214 en Open Access application/pdf Oxford University Press Mark Arick, Corrinne Grover, Chuan-Yu Hsu, Zenaida Magbanua, Olga Pechanova, Emma Miller, Adam Thrash, Ramey Youngblood, Lauren Ezzell, Md. Alam, John Benzie, Matthew Hamilton, Attila Karsi, Mark Lawrence, Daniel Peterson. (14/1/2023). A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination. G3-GENES GENOMES GENETICS. |
| spellingShingle | aquaculture genomes sex determination rohu fish rui ddrad-seq Arick, Mark Grover, Corrinne Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma Thrash, Adam Youngblood, Ramey Ezzell, Lauren Alam, Md. Benzie, John Hamilton, Matthew Karsi, Attila Lawrence, Mark Peterson, Daniel A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination |
| title | A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination |
| title_full | A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination |
| title_fullStr | A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination |
| title_full_unstemmed | A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination |
| title_short | A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination |
| title_sort | high quality chromosome level genome assembly of rohu carp labeo rohita and its utilization in snp based exploration of gene flow and sex determination |
| topic | aquaculture genomes sex determination rohu fish rui ddrad-seq |
| url | https://hdl.handle.net/10568/138214 |
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