title: Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita.
abstract: 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.
authors.affiliation: a ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Bhubaneswar , Odisha , India .
authors.forename: Sofia P
authors.initials: SP
authors.lastname: Das
authors.affiliation: a ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Bhubaneswar , Odisha , India .
authors.forename: Amrita
authors.initials: A
authors.lastname: Bit
authors.affiliation: a ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Bhubaneswar , Odisha , India .
authors.forename: Siddhi
authors.initials: S
authors.lastname: Patnaik
authors.affiliation: a ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Bhubaneswar , Odisha , India .
authors.forename: L
authors.initials: L
authors.lastname: Sahoo
authors.affiliation: a ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Bhubaneswar , Odisha , India .
authors.forename: P K
authors.initials: PK
authors.lastname: Meher
authors.affiliation: a ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Bhubaneswar , Odisha , India .
authors.forename: P
authors.initials: P
authors.lastname: Jayasankar
authors.affiliation: b Department of Animal Biotechnology , College of Veterinary Science and Animal Husbandry, Anand Agricultural University , Anand , Gujarat , India .
authors.forename: T M
authors.initials: TM
authors.lastname: Saha
authors.affiliation: b Department of Animal Biotechnology , College of Veterinary Science and Animal Husbandry, Anand Agricultural University , Anand , Gujarat , India .
authors.forename: A B
authors.initials: AB
authors.lastname: Patel
authors.affiliation: b Department of Animal Biotechnology , College of Veterinary Science and Animal Husbandry, Anand Agricultural University , Anand , Gujarat , India .
authors.forename: Namrata
authors.initials: N
authors.lastname: Patel
authors.affiliation: b Department of Animal Biotechnology , College of Veterinary Science and Animal Husbandry, Anand Agricultural University , Anand , Gujarat , India .
authors.forename: P
authors.initials: P
authors.lastname: Koringa
authors.affiliation: b Department of Animal Biotechnology , College of Veterinary Science and Animal Husbandry, Anand Agricultural University , Anand , Gujarat , India .
authors.forename: C G
authors.initials: CG
authors.lastname: Joshi
authors.affiliation: c ICAR-National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India , and.
authors.forename: Suyash
authors.initials: S
authors.lastname: Agarwal
authors.affiliation: c ICAR-National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India , and.
authors.forename: Manmohan
authors.initials: M
authors.lastname: Pandey
authors.affiliation: c ICAR-National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India , and.
authors.forename: Shreya
authors.initials: S
authors.lastname: Srivastava
authors.affiliation: c ICAR-National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India , and.
authors.forename: B
authors.initials: B
authors.lastname: Kushwaha
authors.affiliation: c ICAR-National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India , and.
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.affiliation: c ICAR-National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India , and.
authors.forename: N S
authors.initials: NS
authors.lastname: Nagpure
authors.affiliation: d ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India.
authors.forename: M A
authors.initials: MA
authors.lastname: Iquebal
authors.affiliation: d ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India.
authors.forename: Sarika
authors.initials: S
authors.lastname: Jaiswal
authors.affiliation: d ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Kumar
authors.affiliation: c ICAR-National Bureau of Fish Genetic Resources , Lucknow , Uttar Pradesh , India , and.
authors.forename: J K
authors.initials: JK
authors.lastname: Jena
authors.affiliation: a ICAR - Central Institute of Freshwater Aquaculture , Kausalyaganga , Bhubaneswar , Odisha , India .
authors.forename: P
authors.initials: P
authors.lastname: Das
mesh_terms: D000818:Animals; D001482:Base Composition; D003530:Cyprinidae / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D023061:Gene Order; D059646:Genome Size; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004275:DNA, Ribosomal; D012343:RNA, Transfer
keywords: CLC-Bio; Labeo rohita; Roche 454 GS FLX; mitogenome; next-generation sequencing