Muscle transcriptome resource for growth, lipid metabolism and immune system in Hilsa shad, Tenualosa ilisha.

The information on the genes involved in muscle growth, lipid metabolism and immune systems would help to understand the mechanisms during the spawning migration in Hilsa shad, which in turn would be useful in its future domestication process. The primary objective of this study was to generate the transcriptome profile of its muscle through RNA seq. The total RNA was isolated and library was prepared from muscle tissue of Tenualosa ilisha, which was collected from Padma River at Farakka, India. The prepared library was then sequenced by Illumina HiSeq platform, HiSeq 2000, using paired-end strategy. A total of 8.68 GB of pair-end reads of muscle transcriptome was generated, and 43,384,267 pair-end reads were assembled into 3,04,233 contigs, of which 23.99% of assembled contigs has length ≥ 150 bp. The total GO terms were categorised into cellular component, molecular function and biological process through PANTHER database. Fifty-three genes related to muscle growth were identified and genes in different pathways were: 75 in PI3/AKT, 46 in mTOR, 76 in MAPK signalling, 24 in Janus kinase-signal transducer and activator of transcription, 45 in AMPK and 27 in cGMP pathways. This study also mined the genes involved in lipid metabolism, in which glycerophospholipid metabolism contained highest number of genes (32) and four were found to be involved in fatty acid biosynthesis. There were 58 immune related genes found, in which 31 were under innate and 27 under adaptive immunity. The present study included a large genomic resource of T. ilisha muscle generated through RNAseq, which revealed the essential dataset for our understanding of regulatory processes, specifically during the seasonal spawning migration. As Hilsa is a slow growing fish, the genes identified for muscle growth provided the basic information to study myogenesis. In addition, genes identified for lipid metabolism and immune system would provide resources for lipid synthesis and understanding of Hilsa defense mechanisms, respectively.

Cross-priming of microsatellite loci in subfamily cyprininae (family Cyprinidae): their utility in finding markers for population genetic analysis in three Indian major carps.

This study is aimed to identify polymorphic microsatellite markers and establish their potential for population genetics studies in three carp (family cyprinidae; subfamily cyprininae) species, Labeo rohita, Catla catla and Cirrhinus mrigala through use of cyprinid primers. These species have high commercial value and knowledge of genetic variation is important for management of farmed and wild populations. We tested 108 microsatellite primers from 11 species belonging to three different cyprinid subfamilies, Cyprininae, Barbinae and Leuciscinae out of which 63 primers (58.33%) successfully amplified orthologous loci in three focal species. Forty-two loci generated from 29 primers were polymorphic in these three carp species. Sequencing of amplified product confirmed the presence of SSRs in these 42 loci and orthologous nature of the loci. To validate potential of these 42 polymorphic loci in determining the genetic variation, we analyzed 486 samples of three focal species collected from Indus, Ganges and Brahmaputra river systems. Results indicated significant genetic variation, with mean number of alleles per locus ranging from 6.80 to 14.40 and observed heterozygosity ranging from 0.50 to 0.74 in the three focal species. Highly significant (P < 0.00001) allelic homogeneity values revealed that the identified loci can be efficiently used in population genetics analysis of these carp species. Further, thirty-two loci from 19 primers were useful for genotyping in more than one species. The data from the present study was compiled with cross-species amplification data from previous results on eight species of subfamily cyprininae to compare cross-transferability of microsatellite loci. It was revealed that out of 226 heterologous loci amplified, 152 loci that originated from 77 loci exhibited polymorphism and 45 primers were of multispecies utility, common for 2-7 species.

Characterization of polymorphic microsatellite markers and genetic diversity in wild bronze featherback, Notopterus notopterus (Pallas, 1769).

Six polymorphic microsatellite DNA loci were identified in the primitive fish, bronze featherback, Notopterus notopterus for the first time and demonstrated significant population genetic structure. Out of the six primers, one primer (NN90) was specific to N. notopterus (microsatellite sequence within the RAG1 gene) and five primers were product of successful cross-species amplification. Sixty-four primers available from 3 fish species of order Osteoglossiformes and families Notopteridae and Osteoglossidae were tested to amplify homologous microsatellite loci in N. notopterus. Fifteen primer pairs exhibited successful cross-priming PCR product. However, polymorphism was detected only at five loci. To assess the significance of these six loci (including NN90) in population genetic study, 215 samples of N. notopterus from five rivers, viz Satluj, Gomti, Yamuna, Brahmaputra and Mahanadi were analyzed. The five sample sets displayed different diversity levels and observed heterozygosity ranged from 0.6036 to 0.7373. Significant genotype heterogeneity (P < 0.0001) and high FST (0.2205) over all loci indicated that the samples are not drawn from the same genepool. The identified microsatellite loci are promising for use in fine-scale population structure analysis of N. notopterus.

Genetic divergence in natural populations of bronze featherback, Notopterus notopterus (Osteoglossiformes: Notopteridae) from five Indian rivers, analyzed through mtDNA ATPase6/8 regions.

The present study characterized 842 bp fragment of mitochondrial ATP synthase 6 and 8 (ATPase6/8) genes in Notopterus notopterus. In all, 97 samples of N. notopterus were collected from five distant rivers; viz Satluj, Gomti, Yamuna, Brahmaputra and Mahanadi representing 4 river basins in India. The analysis of variation revealed presence of 23 haplotypes in ATPase6/8 gene with haplotype diversity (Hd) of 0.899 and nucleotide diversity (π) of 0.00336. The within population variation which was 41.78% of the total variation of 58.22% was found among population. The Fst value of 0.582 (P < 0.05) of the total population was found significant. The results concluded that the polymorphism in ATPase6/8 gene is a potential marker that is important for determining genetic divergence of wild N. notopterus populations. The findings reveal common ancestry of mahanadi population with the populations in rivers of Indo-Gangetic region. However, long evolutionary isolation must be responsible for the high genetic divergence between N. notopterus in Mahanadi and other regions.