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Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita

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Title Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita
Not Available
 
Creator Sofia P Das
Amrita Bit
Siddhi Patnaik
L Sahoo
P K Meher
P Jayasankar
T M Saha
A B Patel
Namrata Patel
P Koringa
C G Joshi
Suyash Agarwal
Manmohan Pandey
Shreya Srivastava
B Kushwaha
Ravindra Kumar
N S Nagpure
M A Iquebal
Sarika Jaiswal
Dinesh Kumar
J K Jena
P Das
 
Subject CLC-Bio
Labeo rohita
Roche 454 GS FLX
mitogenome
next-generation sequencing
 
Description Not Available
Labeo rohita, popularly known as rohu, is a widely cultured species in whole Indian subcontinent. In the present study, we used in-silico approach to resolve complete mitochondrial genome of rohu. Low-depth shotgun sequencing using Roche 454 GS FLX (Branford, Connecticut, USA) followed by de novo assembly in CLC Genomics Workbench version 7.0.4 (Aarhus, Denmark) revealed the complete mitogenome of L. rohita to be 16 606 bp long (accession No. KR185963). It comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 putative control region. The gene order and organization are similar to most vertebrates. The mitogenome in the present investigation has 99% similarity with that of previously reported mitogenomes of rohu and this is also evident from the phylogenetic study using maximum-likelihood (ML) tree method. This study was done to determine the feasibility, accuracy and reliability of low-depth sequence data obtained from NGS platform as compared to the Sanger sequencing. Thus, NGS technology has proven to be competent and a rapid in-silico alternative to resolve the complete mitochondrial genome sequence, thereby reducing labors and time.
Department of Biotechnology, Govt. of India, New Delhi and Indian Council of Agricultural Research.
 
Date 2021-07-23T06:13:24Z
2021-07-23T06:13:24Z
2015-08-11
 
Type Research Paper
 
Identifier Das SP, Bit A, Patnaik S, Sahoo L, Meher PK, Jayasankar P, Saha TM, Patel AB, Patel N, Koringa P, Joshi CG, Agarwal S, Pandey M, Srivastava S, Kushwaha B, Kumar R, Nagpure NS, Iquebal MA, Jaiswal S, Kumar D, Jena JK, Das P. Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita. Mitochondrial DNA A DNA Mapp Seq Anal. 2016 Sep;27(5):3517-8. doi: 10.3109/19401736.2015.1074197. Epub 2015 Aug 11. PMID: 26260184.
2470-1394
2470-1408
http://krishi.icar.gov.in/jspui/handle/123456789/49459
 
Language English
 
Relation Not Available;
 
Publisher Taylor & Francis