EST-based identification of immune-relevant genes from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758)

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.

Identification of novel EST-SSR markers by transcriptome sequencing in ridgetail white prawn Exopalaemon carinicauda

The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of 14273 SSR loci were identified from 130,082 assembled transcripts, with 6590 pairs of PCR primers designed. A total of 12,155 sequences containing SSR were predicted; and 2764 (22.74%) transcripts had significant matches to the NCBI non redundant protein (Nr) database. 11,563 transcripts were assigned into gene ontology (GO) categories. A set of 200 primers selected randomly were synthesized, of which 152 (76.0%) were successfully amplified. Further test with 60 pairs of polymorphic SSR primers to evaluate the genetic diversity of 30 wild populations and 43 loci were polymorphic, which had a polymorphic information content between 0.204 and 0.911. The results enriched genomic resources of E. carinicauda and provided powerful information for future conservation and breeding researches.

Transcriptome assembly and identification of genes and SNPs associated with growth traits in largemouth bass (Micropterus salmoides)

Growth is one of the most crucial economic traits of all aquaculture species, but the molecular mechanisms involved in growth of largemouth bass (Micropterus salmoides) are poorly understood. The objective of this study was to screen growth-related genes of M. salmoides by RNA sequencing and identify growth-related single-nucleotide polymorphism (SNP) markers through a growth association study. The muscle transcriptomes of fast- and slow-growing largemouth bass were obtained using the RNA-Seq technique. A total of 54,058,178 and 54,742,444 qualified Illumina read pairs were obtained for the fast-growing and slow-growing groups, respectively, giving rise to 4,865,236,020 and 4,926,819,960 total clean bases, respectively. Gene expression profiling showed that 3,530 unigenes were differentially expressed between the fast-growing and slow-growing phenotypes (false discovery rate ≤0.001, the absolute value of log₂ (fold change) ≥1), including 1,441 up-regulated and 2,889 down-regulated unigenes in the fast-growing largemouth bass. Analysis of these genes revealed that several signalling pathways, including the growth hormone-insulin-like growth factor 1 axis and signalling pathway, the glycolysis pathway, and the myostatin/transforming growth factor beta signalling pathway, as well as heat shock protein, cytoskeleton, and myofibril component genes might be associated with muscle growth. From these genes, 10 genes with putative SNPs were selected, and 17 SNPs were genotyped successfully. Marker-trait analysis in 340 individuals of Youlu No. 1 largemouth bass revealed three SNPs associated with growth in key genes (phosphoenolpyruvate carboxykinase 1, FOXO3b, and heat shock protein beta-1). This research provides information about key genes and SNPs related to growth, providing new clues to understanding the molecular basis of largemouth bass growth.