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De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

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Title De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita
Not Available
 
Creator Paramananda Das
Lakshman Sahoo
Sofia P. Das
Amrita Bit
Chaitanya G. Joshi
Basdeo Kushwaha
Dinesh Kumar
Tejas M. Shah
Ankit T. Hinsu
Namrata Patel
Siddhi Patnaik
Suyash Agarwal
Manmohan Pandey
Shreya Srivastava
Prem Kumar Meher
Pallipuram Jayasankar
Prakash G. Koringa
Naresh S. Nagpure
Ravindra Kumar
Mahender Singh
Mir Asif Iquebal
Sarika Jaiswal
Neeraj Kumar
Mustafa Raza
Kanta Das Mahapatra
Joykrushna Jena
 
Subject rohu carp
draft genome
de novo assembly
orthologous gene family
synteny
phylogenetics
otophysan
 
Description Not Available
Here we report for the first time the draft genome of Indian major carp, rohu widely cultured in Indian subcontinent. The scaffold N50 was found to be 1.95 Mb and there were 26,400 protein coding genes and 40.63% repeats.

Resequencing of 10 riverine rohu populations identified ~5 million SNPs which will provide a valuable resource for undertaking genome wide association studies, genomic selection, population genomics and fine-mapping of QTLs in this species.

Phylogenetic analysis taking protein sequences of 335 single copy genes of 14 Otophysans revealed that rohu carp (Labeoninae) was at a position equidistant to the other species in the Otophysi clade, forming a sister group.

All the six families and four subfamilies under the four otophysan lineages were monophyletic.
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Date 2022-03-15T06:32:48Z
2022-03-15T06:32:48Z
2020-04-21
 
Type Research Paper
 
Identifier Das P, Sahoo L, Das SP, Bit A, Joshi CG, Kushwaha B, Kumar D, Shah TM, Hinsu AT, Patel N, Patnaik S, Agarwal S, Pandey M, Srivastava S, Meher PK, Jayasankar P, Koringa PG, Nagpure NS, Kumar R, Singh M, Iquebal MA, Jaiswal S, Kumar N, Raza M, Das Mahapatra K and Jena J (2020) De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita. Front. Genet. 11:386. doi: 10.3389/fgene.2020.00386
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http://krishi.icar.gov.in/jspui/handle/123456789/70229
 
Language English
 
Relation Not Available;
 
Publisher Not Available