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https://hdl.handle.net/20.500.12348/5469
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
dc.creator | Arick, M.A. | en_US |
dc.creator | Grover, C.E. | en_US |
dc.creator | Hsu, C. | en_US |
dc.creator | Magbanua, Z. | en_US |
dc.creator | Pechanova, O. | en_US |
dc.creator | Miller, E.R. | en_US |
dc.creator | Thrash, A. | en_US |
dc.creator | Youngblood, R.C. | en_US |
dc.creator | Ezzell, L. | en_US |
dc.creator | Alam, M.S. | en_US |
dc.creator | Benzie, J. | en_US |
dc.creator | Hamilton, M.G. | en_US |
dc.creator | Karsi, A. | en_US |
dc.creator | Lawrence, M.L. | en_US |
dc.creator | Peterson, D.G. | en_US |
dc.date.accessioned | 2023-02-22T10:00:34Z | |
dc.date.available | 2023-02-22T10:00:34Z | |
dc.date.issued | 2023 | en_US |
dc.identifier.citation | 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. | en_US |
dc.identifier.issn | 2160-1836 | en_US |
dc.identifier.uri | https://hdl.handle.net/20.500.12348/5469 | |
dc.description.abstract | 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. | en_US |
dc.format | en_US | |
dc.language | en | en_US |
dc.publisher | OXFORD UNIV PRESS INC | en_US |
dc.rights | CC-BY-4.0 | en_US |
dc.source | G3-GENES GENOMES GENETICS;(2023) | en_US |
dc.subject | genome | en_US |
dc.subject | rui | en_US |
dc.subject | ddrad-seq | en_US |
dc.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 | en_US |
dc.type | Journal Article | en_US |
cg.contributor.funder | United States Agency for International Development | en_US |
cg.contributor.funder | Mississippi State University, Feed the Future Innovation Lab for Fish | en_US |
cg.coverage.country | Bangladesh | en_US |
cg.coverage.region | Southern Asia | en_US |
cg.subject.agrovoc | aquaculture | en_US |
cg.subject.agrovoc | sex determination | en_US |
cg.subject.agrovoc | rohu | en_US |
cg.subject.agrovoc | fish | en_US |
cg.contributor.affiliation | WorldFish | en_US |
cg.contributor.affiliation | Bangladesh Agricultural University | en_US |
cg.contributor.affiliation | Iowa State University | en_US |
cg.contributor.affiliation | Mississippi State University | en_US |
cg.identifier.status | Open access | en_US |
cg.identifier.ISIindexed | ISI indexed | en_US |
cg.contribution.worldfishauthor | Benzie, J. | en_US |
cg.contribution.worldfishauthor | Hamilton, M.G. | en_US |
cg.description.theme | Sustainable aquaculture | en_US |
dc.identifier.doi | https://dx.doi.org/10.1093/g3journal/jkad009 | en_US |
cg.creator.id | John Benzie: 0000-0001-9599-8683 | en_US |
cg.creator.id | Matthew Gray Hamilton: 0000-0001-8098-8845 | en_US |
cg.subject.sdg | SDG 1 - No poverty | en_US |
cg.subject.sdg | SDG 2 - Zero hunger | en_US |
cg.subject.sdg | SDG 14 - Life below water | en_US |
cg.subject.actionArea | Resilient Agrifood Systems | en_US |
cg.subject.impactArea | Nutrition, health and food security | en_US |
cg.contributor.initiative | Aquatic Foods | en_US |
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Sustainable aquaculture [2702]