Prabhati Kumari Sahoo

Complete mitochondrial genome organization of Schizothorax richardsonii (Gray, 1832)

Abstract The complete mitochondrial genome of Schizothorax richardsonii, an endemic coldwater fish of Himalayas, was determined for the first time. The genome is 16,592 bp in length and consists of 13 protein coding genes, 22 tRNAs, 2 rRNA genes and one putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was as follows: A: 29.9%, G: 17.7%, C: 26.9%, T: 25.5%, A + T content 55.4% and the G + C content 44.6%. The control region contains a microsatellite; (TA)13 exists between 16,469 and 16,494 bp. This study will provide the rationale for the management and conservation of the snow trout.

Complete mitochondrial genome organization of Tor putitora

Abstract The complete mitochondrial genome of Tor putitora, an endemic coldwater fish of Himalayas was determined for the first time. The genome is 16,576 bp in length and consists of 13 protein coding genes, 22 tRNAs, 2 rRNA genes and 1 putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was; A: 31.9%, G: 15.6%, C: 27.5%, T: 25%, A + T content 56.9% and the G + C content 43.1%. The control region was also consisted of a microsatellite locus (TA) 13 between 16, 456 to 16, 481 bp. The present study will provide the rationale for the management and conservation of T. putitora.

Transcriptome profiling and expression analysis of immune responsive genes in the liver of Golden mahseer (Tor putitora) challenged with Aeromonas hydrophila

Abstract Transcriptome profiling has been used to decipher the novel mechanisms behind immune responses of the fishes. However, the molecular mechanism underlining immune response in mahseer is not studied so far. Fishes are greatly affected by bacterial pathogens such as Aeromonas hydrophila. In this study, transcriptome response of golden mahseer (Tor putitora) infected with A. hydrophila was examined using paired end Illumina sequencing of liver tissue to understand the immune response of the fish. The de novo assembly generated 61,042 unigenes ranging from 200 to 9322 bp in length and an average length of 463 bp. The gene ontology annotations resulted a total of 131,826 term assignments to the annotated transcriptome including 60,846 (46.16%) allocations from the biological process; 21,603 (16.39%) from molecular function and 49,377 (37.46%) from cellular components. Differential gene expression analysis of the transcriptome data from challenged and control group revealed 1104 upregulated and 1304 down‐regulated unigenes. The differentially expressed genes were mainly involved in the pathways including cell surface receptor signaling, TH1 and TH2 cell differentiation, pathogen recognition, and immune system process/defense response especially complement cascade. Twelve unigenes including ankyrin, serum amyloid, hsp4b, STAT3, complement factor c3 and c7 were validated using qPCR and found differentially expressed in accordance with in silico expression analysis. The results obtained in this study will provide the first and crucial information on the molecular mechanism of mahseer fishes against bacterial infection. HighlightsFirst transcriptome profile of Golden mahseer with particular reference to bacterial stress.61042 unigenes were isolated from de novo assembly of liver transcriptome.2408 differentially expressed gene were identified under A. hydrophila challenge.Liver and spleen were found to be the major sites of immune response.Twelve differentially expressed genes were validated at different time points using qPCR.

The complete mitochondrial genome of threatened chocolate mahseer (Neolissochilus hexagonolepis) and its phylogeny

The chocolate mahseer (Neolissochilus hexagonolepis) is an important food and game fish of North Eastern India. To study the phylogenetic status we sequenced the complete mitochondrial genome of N. hexagonolepis. The mitogenome is 16,563 bp in length and composed of 13 protein coding genes, 22 tRNAs, 2 rRNAs and one putative control region. The overall base composition was A 31.8%, T 25.0%, G 15.8%, C 27.4% and A+T content 56.9%, G+C content 43.1%. The phylogenetic analysis using the complete mitochondrial genome revealed that the chocolate mahseer belonged to same clade of mahseer group of fishes but different from genera Barbus and Acrossocheilus. The present study will be helpful for the evolution and conservation genetic studies of N. hexagonolepis.

The complete mitogenome of brown trout (Salmo trutta fario) and its phylogeny

Abstract The complete mitochondrial genome of Salmo trutta fario, commonly known as brown trout, was sequenced using NGS technology. The mitochondrial genome size was determined to be 16 677 bp and composed of 13 protein-coding gene (PCG), 22 tRNAs, 2 rRNA genes, and 1 putative control region. The overall mitogenome composition of S. trutta fario is A: 28.13%, G: 16.44%, C: 29.47%, and T: 25.96% with A + T content of 54.09% and G + C content of 45.91%. The gene arrangement and the order are similar to other vertebrates. The phylogenetic tree constructed using 42 complete mitogenomes of Salmonidae fishes confirmed the position of the present species under the genus Salmo of subfamily Salmoninae. NGS platform was proved to be a rapid and time-saving technology to reveal complete mitogenomes.

De novo assembly and characterization of tissue-specific transcriptome in the endangered golden mahseer, Tor putitora.

The golden mahseer (Tor putitora) graces most of the Himalayan Rivers of India and neighboring South Asian countries. Despite its several importance as a research model, as food, and in sport fishing, knowledge on transcriptome database is nil. Therefore, it was targeted to develop reference transcriptome databases of the species using next-generation sequencing. In the present study, 100,540,130 high-quality paired-end reads were obtained from six cDNA libraries of spleen, liver, gill, kidney, muscle, and brain with 28.4 GB data using Illumina paired-end sequencing technology. Tissue-specific transcriptomes as well as complete transcriptome assembly were analyzed for concise representation of the study. In brief, the de novo assembly of individual tissue resulted in an average of 31,829 (18,512–46,348) contigs per sample, while combined transcriptome comprised 77,907 unique transcript fragments (unigenes) assembled from reads of six tissues. Approximately 75,407 (96.8%) unigenes could be annotated according to their homology matches in the nr, SwisseProt, GO, or KEGG databases. Comparative analysis showed that 84% of the unigenes have significant similarity to zebra fish RefSeq proteins. Tissue-specific-dominated genes were also identified to hypothesize their localization and expression in individual tissue. In addition, 2485 simple sequence repeats (SSRs) were detected from 77,907 transcripts in the combined transcriptome of the golden mahseer. This study has generated organ-specific transcriptome profiles, which will be helpful to understand the local adaptation, genome evolution, and also future functional studies on immune system of the golden mahseer.

Complete mitochondrial genome organization of Schizothorax plagiostomus (Heckel, 1838)

Abstract The complete mitochondrial genome of Schizothorax plagiostomus, an endemic coldwater fish of Himalayas, was determined for the first time. The genome is 16,576 bp in length and consists of 13 protein coding genes, 22 tRNAs, 2rRNA genes and 1 putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was A 30%, G 17.4%, C 26.8%, T 25.8%, A + T content 55.8% and the G + C content 44.2%. The control region consists of a microsatellite locus (TA)12 between 16,460 and 16,483 bp. The present study will provide the rationale for the management and conservation of S. plagiostomus.

Complete mitochondrial genome organization of Tor tor (Hamilton, 1822)

Abstract The complete mitochondrial genome of Tor tor, a threatened “Mahseer” was sequenced for the first time. The mitochondrial genome size determined to be 16,554 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNA genes and a control region or displacement loop (D-Loop) region, resembling the typical organizational pattern of most of the teleost. The overall base composition found was A: 31.8%, T: 25%, G: 15.7% and C: 27.4%; A + T: 56.9% and G + C: 43.1%. The phylogenetic tree constructed using 11 other cyprinids’ total mtDNA datasets confirmed the location of present species among mahseers. The total sequence data could support further study in molecular systematics, species identification, evolutionary and conservation genetics.

Complete mitochondrial genome organization of Schizothorax esocinus (Heckel, 1838)

Abstract The complete mitochondrial genome of Schizothorax esocinus, an endemic coldwater fish of Himalayas, was determined for the first time. The genome is 16,583 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2rRNA genes and 1 putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was; A 29.8%, G 17.8%, C 27%, T 25.4%, A + T content 55.2% and the G + C content 44.8%. The control region was also consisted of a microsatellite locus (TA) 13 between 16,463 to 16,488 bp. The present study will provide the rationale for the management and conservation of S. esocinus.

Molecular characterization of rainbow trout, Oncorhynchus mykiss (Walbaum, 1792) stocks in India

In India, rainbow trout was introduced by British more than 100 years ago (Agarwal 2006) for recreational purposes. The fish is being cultured in both government and private farms of different coldwater states of India, mainly in Jammu and Kashmir, Himachal Pradesh, Sikkim, Arunachal Pradesh and Uttarakhand, and also in Nilgiri hills of south India for breeding and rearing purposes. In recent past, growth and production rate of this fish in various farms has been reduced. Microsatellite markers in combination with recent statistical approaches represent a useful tool for genetic characterization which ultimately supports the management of cultured stocks. These markers have been successfully used to evaluate the wild and farm stocks of rainbow trout in western Australia (Ward et al. 2003); resident and anadromus forms in the Walla Walla river (Narum et al. 2004); domesticated strains of rainbow trout in USA (Silverstein et al. 2004); strains in northern and eastern Europe (Gross et al. 2007) and three groups of different origin in north of Iran (Yousefian et al. 2012). Hence, the present study was carried out to assess the genetic variability in different stocks of rainbow trout in India using microsatellite markers.