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...
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ftpubmed:oai:pubmedcentral.nih.gov:9997561 2023-05-15T15:32:20+02:00 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 A Grover, Corrinne E Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma R Thrash, Adam Youngblood, Ramey C Ezzell, Lauren Alam, Md Samsul Benzie, John A H Hamilton, Matthew G Karsi, Attila Lawrence, Mark L Peterson, Daniel G 2023-01-14 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997561/ http://www.ncbi.nlm.nih.gov/pubmed/36639248 https://doi.org/10.1093/g3journal/jkad009 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997561/ http://www.ncbi.nlm.nih.gov/pubmed/36639248 http://dx.doi.org/10.1093/g3journal/jkad009 © The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. G3 (Bethesda) Genome Report Text 2023 ftpubmed https://doi.org/10.1093/g3journal/jkad009 2023-03-12T02:24:20Z 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. Text Atlantic salmon PubMed Central (PMC) Halda ENVELOPE(25.170,25.170,70.853,70.853) G3 Genes|Genomes|Genetics 13 3 |
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op_collection_id |
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English |
topic |
Genome Report |
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Genome Report Arick, Mark A Grover, Corrinne E Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma R Thrash, Adam Youngblood, Ramey C Ezzell, Lauren Alam, Md Samsul Benzie, John A H Hamilton, Matthew G Karsi, Attila Lawrence, Mark L Peterson, Daniel G 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 |
topic_facet |
Genome Report |
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 |
Text |
author |
Arick, Mark A Grover, Corrinne E Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma R Thrash, Adam Youngblood, Ramey C Ezzell, Lauren Alam, Md Samsul Benzie, John A H Hamilton, Matthew G Karsi, Attila Lawrence, Mark L Peterson, Daniel G |
author_facet |
Arick, Mark A Grover, Corrinne E Hsu, Chuan-Yu Magbanua, Zenaida Pechanova, Olga Miller, Emma R Thrash, Adam Youngblood, Ramey C Ezzell, Lauren Alam, Md Samsul Benzie, John A H Hamilton, Matthew G Karsi, Attila Lawrence, Mark L Peterson, Daniel G |
author_sort |
Arick, Mark A |
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_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_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_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 |
publisher |
Oxford University Press |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997561/ http://www.ncbi.nlm.nih.gov/pubmed/36639248 https://doi.org/10.1093/g3journal/jkad009 |
long_lat |
ENVELOPE(25.170,25.170,70.853,70.853) |
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Halda |
geographic_facet |
Halda |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
G3 (Bethesda) |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9997561/ http://www.ncbi.nlm.nih.gov/pubmed/36639248 http://dx.doi.org/10.1093/g3journal/jkad009 |
op_rights |
© The Author(s) 2023. Published by Oxford University Press on behalf of the Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_doi |
https://doi.org/10.1093/g3journal/jkad009 |
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G3 Genes|Genomes|Genetics |
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13 |
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3 |
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