Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)

Abstract

Rohu is a leading candidate species for freshwater aquaculture in South-East Asia. Unlike common carp the monsoon breeding habit of rohu restricts its seed production beyond season indicating strong genetic control over spawning. Genetic information is limited in this regard. The problem is exacerbated by the lack of genomic-resources. We identified 182 reproduction-related genes previously by Sanger-sequencing which were less to address the issue of seasonal spawning behaviour of this important carp. Therefore, the present work was taken up to generate transcriptome profile by mRNAseq. 16GB, 72bp paired end (PE) data was generated from the pooled-RNA of twelve-tissues from pre-spawning rohu using IlluminaGA-II-platform. There were 64.97 million high-quality reads producing 62,283 contigs and 88,612 numbers of transcripts using velvet and oases programs, respectively. Gene ontology annotation identified 940 reproduction-related genes consisting of 184 mainly associated with reproduction, 223 related to hormone-activity and receptor-binding, 178 receptor-activity and 355 embryonic-development related-proteins. The important reproduction-relevant pathways found in KEGG analysis were GnRH-signaling, oocyte-meiosis, steroid-biosynthesis, steroid-hormone biosynthesis, progesterone-mediated oocyte-maturation, retinol-metabolism, neuroactive-ligand-receptor interaction, neurotrophin-signaling and photo-transduction. Twenty nine simple sequence repeat containing sequences were also found out of which 12 repeat loci were polymorphic with mean expected-&-observed heterozygosity of 0.471 and 0.983 respectively. Quantitative RT-PCR analyses of 13-known and 6-unknown transcripts revealed differences in expression level between preparatory and post-spawning phase. These transcriptomic sequences have significantly increased the genetic-&-genomic resources for reproduction-research in Labeo rohita.

Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

“…In this network, we determined that the TCONS_00429684/TCONS_00309450-ssc-miR-1249-GRIK4 interaction axis was involved in the regulatory network. Concerning mRNAs, function enrichment analyses showed that GRIK4 has been involved in a reproduction-relevant pathway, such as neuroactive ligand-receptor interactions, which play important roles in reproduction processes [46]. In the present study, high levels of GRIK4 expression was noticed in the LH group compared with the LL group.…”

Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

“…In this network, we determined that the TCONS_00429684/TCONS_00309450-ssc-miR-1249-GRIK4 interaction axis was involved in the regulatory network. Concerning mRNAs, function enrichment analyses showed that GRIK4 has been involved in a reproduction-relevant pathway, such as neuroactive ligand-receptor interactions, which play important roles in reproduction processes [47]. In the present study, high levels of GRIK4 expression was noticed in the LH group compared with the LL group.…”

RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

“…,; Sahu et al . ). Among the NGS techniques, Illumina sequencing and de novo assembly has gained popularity over Roche 454 and SOLID platforms in addressing the global mRNA expression levels in non‐model species (Wang et al .…”

“…The next-generation RNA sequencing and de novo assembly of the sequences have taken precedence over whole genome sequencing in obtaining functional information on non-model organisms (Firmino et al 2013;Schunter et al 2014). This is also the preferred method for identification of simple sequence repeats (SSRs) or microsatellites that assist in genetic diversity studies (Luikart et al 2003;Sahu et al 2015). Among the NGS techniques, Illumina sequencing and de novo assembly has gained popularity over Roche 454 and SOLID platforms in addressing the global mRNA expression levels in non-model species Liu et al 2012).…”