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
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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 |
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Subject |
CLC-Bio
Labeo rohita Roche 454 GS FLX mitogenome next-generation sequencing |
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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. |
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Date |
2021-07-23T06:13:24Z
2021-07-23T06:13:24Z 2015-08-11 |
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Type |
Research Paper
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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 |
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Language |
English
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Relation |
Not Available;
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Publisher |
Taylor & Francis
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