De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita
KRISHI: Publication and Data Inventory Repository
View Archive InfoField | Value | |
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 Singh3, 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
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 1.95Mb with annotation of 26,400 protein coding genes. 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. The draft genome of rohu and SNPs generated in the present study represent essential resource for genetic improvement of important performance traits in this species. Besides, the information generated will provide foundation for future research in evolutionary biology and comparative genomics. Department of Biotechnology, Ministry of Science and Technology, Gov. of India, New Delhi, India vide Sanction Grant No. BT/PR3688/AAQ/3/571/2011 |
|
Date |
2021-07-24T11:13:09Z
2021-07-24T11:13:09Z 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
1664-8021 http://krishi.icar.gov.in/jspui/handle/123456789/49901 |
|
Language |
English
|
|
Relation |
Not Available;
|
|
Publisher |
Frontiers
|
|