title: Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes.
abstract: Whole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequence the mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data of Clarias batrachus, generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome using both de novo and reference based approaches. Both the methods yielded almost similar results and the best assembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotation resulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order was found to be identical with other catfishes. Variation analyses between assembled and the reference (GenBank Acc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequences and tRNA supports the monophyly of catfishes. Two SSRs were identified in C. batrachus mitogenome, out of which one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrial genes were found to evolve at a much faster pace than the d-loop, which in turn are followed by the rRNAs; the tRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among the coding genes, ND2 evolves most rapidly. The variations present in the coding regions of the mitogenome and their comparative analyses with other catfish species may be useful in species conservation and management programs.
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: Basdeo
authors.initials: B
authors.lastname: Kushwaha
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: Suyash
authors.initials: S
authors.lastname: Agarwal
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: Manmohan
authors.initials: M
authors.lastname: Pandey
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: N S
authors.initials: NS
authors.lastname: Nagpure
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: Mahender
authors.initials: M
authors.lastname: Singh
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: Shreya
authors.initials: S
authors.lastname: Srivastava
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001, India.
authors.forename: C G
authors.initials: CG
authors.lastname: Joshi
authors.affiliation: Division of Fish Genetics & Biotechnology, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
authors.forename: P
authors.initials: P
authors.lastname: Das
authors.affiliation: Division of Fish Genetics & Biotechnology, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
authors.forename: L
authors.initials: L
authors.lastname: Sahoo
authors.affiliation: Division of Fish Genetics & Biotechnology, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
authors.forename: P
authors.initials: P
authors.lastname: Jayasankar
authors.affiliation: Division of Fish Genetics & Biotechnology, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
authors.forename: P K
authors.initials: PK
authors.lastname: Meher
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001, India.
authors.forename: T M
authors.initials: TM
authors.lastname: Shah
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001, India.
authors.forename: A B
authors.initials: AB
authors.lastname: Patel
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001, India.
authors.forename: Namrata
authors.initials: N
authors.lastname: Patel
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat 388001, India.
authors.forename: P
authors.initials: P
authors.lastname: Koringa
authors.affiliation: Division of Fish Genetics & Biotechnology, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
authors.forename: Sofia Priyadarsani
authors.initials: SP
authors.lastname: Das
authors.affiliation: Division of Fish Genetics & Biotechnology, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
authors.forename: Siddhi
authors.initials: S
authors.lastname: Patnaik
authors.affiliation: Division of Fish Genetics & Biotechnology, ICAR- Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
authors.forename: Amrita
authors.initials: A
authors.lastname: Bit
authors.affiliation: Centre for Agricultural Bio-informatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India.
authors.lastname: Sarika
authors.affiliation: Centre for Agricultural Bio-informatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India.
authors.forename: M A
authors.initials: MA
authors.lastname: Iquebal
authors.affiliation: Centre for Agricultural Bio-informatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Kumar
authors.affiliation: Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, India.
authors.forename: J K
authors.initials: JK
authors.lastname: Jena
keywords: Clarias batrachus; Indian catfish; Mitogenome; Phylogenetics; WGS data