L. Sahoo

Complete mitochondrial genome of Labeo rohita.

The complete mitochondrial genome of Labeo rohita, an important cultivable fish, was determined for the first time. The genome is 16,611 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region. The gene organisation and its order were similar to other vertebrates. The overall base composition on heavy strand was as follows A: 32.5%, G: 15.2%, C: 27.7%, T: 24.47%, and the A+T content 56.9%. The control region contains a microsatellite, (TA)12, a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of Indian major carps.

Preliminary genetic linkage map of Indian major carp, Labeo rohita (Hamilton 1822) based on microsatellite markers

Linkage map with wide marker coverage is an essential resource for genetic improvement study for any species. Sex-averaged genetic linkage map of Labeo rohita, popularly known as ‘rohu’, widely cultured in the Indian subcontinent, was developed by placing 68 microsatellite markers generated by a simplified method. The parents and their F 1 progeny (92 individuals) were used as segregating populations. The genetic linkage map spans a sex-averaged total length of 1462.2 cM, in 25 linkage groups. The genome length of rohu was estimated to be 3087.9 cM. This genetic linkage map may facilitate systematic searches of the genome to identify genes associated with commercially important characters and marker-assisted selection programmes of this species.

Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes

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.

DNA fingerprinting of Flavobacterium columnare using RAPD-PCR

In the present study, DNA fingerprinting of eight strains of Flavobacterium columnare was done by random amplification of polymorphic DNA (RAPD) fingerprinting method. The strains were collected from Fish Health Management Division, Central Institute of Freshwater Aquaculture, Bhubaneswar, India. A total number of 160 primers were screened for RAPD-PCR, of which 10 primers yielded amplification with all the strains. The molecular weight of amplified bands varied from 0.29–2.63 Kb. The number of bands varied from 1 to 8. Unique band was seen with primer OPY-15 with molecular weight 0.75 Kb that can be used for epidemiological study. Genetic variability was investigated using NTSYS software. Highest genetic similarity was found between MS1 and MS3 followed by MS5 and MS7. Minimum genetic similarity was found between MS2 and MS8. Phylogenetic tree was constructed using UPGMA and neighbor joining methods.

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.