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http://krishi.icar.gov.in/jspui/handle/123456789/49459| Title: | Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita |
| Other Titles: | Not Available |
| Authors: | 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 |
| ICAR Data Use Licennce: | http://krishi.icar.gov.in/PDF/ICAR_Data_Use_Licence.pdf |
| Author's Affiliated institute: | ICAR - Central Institute of Freshwater Aquaculture, Bhubaneshwar Department of Animal Biotechnology , College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand ICAR::National Bureau of Fish Genetic Resources, Lucknow ICAR-Indian Agricultural Statistics Research Institute, New Delhi |
| Published/ Complete Date: | 2015-08-11 |
| Project Code: | Not Available |
| Keywords: | CLC-Bio Labeo rohita Roche 454 GS FLX mitogenome next-generation sequencing |
| Publisher: | Taylor & Francis |
| Citation: | 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. |
| Series/Report no.: | Not Available; |
| Abstract/Description: | 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. |
| Description: | Not Available |
| ISSN: | 2470-1394 2470-1408 |
| Type(s) of content: | Research Paper |
| Sponsors: | Department of Biotechnology, Govt. of India, New Delhi and Indian Council of Agricultural Research. |
| Language: | English |
| Name of Journal: | Mitochondrial DNA Part A - DNA Mapping, Sequencing & Analysis |
| Journal Type: | Publishes original high-quality manuscripts on physical, chemical, and biochemical aspects of mtDNA and proteins involved in mtDNA metabolism, and/or interactions. Manuscripts on cytosolic and extracellular mtDNA, and on dysfunction caused by alterations in mtDNA integrity as well as methodological papers detailing novel approaches for mtDNA manipulation in vitro and in vivo are welcome |
| NAAS Rating: | 7.07 |
| Impact Factor: | 1.42 |
| Volume No.: | 27 |
| Page Number: | 3517-8 |
| Name of the Division/Regional Station: | Molecular Biology and Biotechnology |
| Source, DOI or any other URL: | 10.3109/19401736.2015.1074197 https://www.tandfonline.com/doi/abs/10.3109/19401736.2015.1074197 |
| URI: | http://krishi.icar.gov.in/jspui/handle/123456789/49459 |
| Appears in Collections: | FS-NBFGR-Publication |
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