Transcriptomics of a Giant Freshwater Prawn (Macrobrachium rosenbergii): De Novo Assembly, Annotation and Marker Discovery

Abstract

BackgroundGiant freshwater prawn (Macrobrachium rosenbergii or GFP), is the most economically important freshwater crustacean species. However, as little is known about its genome, 454 pyrosequencing of cDNA was undertaken to characterise its transcriptome and identify genes important for growth.Methodology and Principal FindingsA collection of 787,731 sequence reads (244.37 Mb) obtained from 454 pyrosequencing analysis of cDNA prepared from muscle, ovary and testis tissues taken from 18 adult prawns was assembled into 123,534 expressed sequence tags (ESTs). Of these, 46% of the 8,411 contigs and 19% of 115,123 singletons possessed high similarity to sequences in the GenBank non-redundant database, with most significant (E value < 1e–5) contig (80%) and singleton (84%) matches occurring with crustacean and insect sequences. KEGG analysis of the contig open reading frames identified putative members of several biological pathways potentially important for growth. The top InterProScan domains detected included RNA recognition motifs, serine/threonine-protein kinase-like domains, actin-like families, and zinc finger domains. Transcripts derived from genes such as actin, myosin heavy and light chain, tropomyosin and troponin with fundamental roles in muscle development and construction were abundant. Amongst the contigs, 834 single nucleotide polymorphisms, 1198 indels and 658 simple sequence repeats motifs were also identified.ConclusionsThe M. rosenbergii transcriptome data reported here should provide an invaluable resource for improving our understanding of this species' genome structure and biology. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs.

SINGLE NUCLEOTIDE POLYMORPHISMS IDENTIFIED FROM BLUNT SNOUT BREAM (Megalobrama amblycephala) TRANSCRIPTOME THROUGH NEXT GENERATION SEQUENCING

“…This is much lower than previous finding of one SNP every 302 bp reported from transcriptomic database of blunt snout bream (M. amblycephala) using 454 pyrosequencing (Gao et al, 2012). The ratio of transition over transversion plays an important role in genes identification after affected by generation selection (Jung et al, 2011;Morton et al, 2006). Interestingly, the ratio of transition over transversion (1.71) in this study is accordance with the previous report on such ratio calculated in database of human SNPs identified from EST sequences (Picoult-Newberg et al, 1999).…”

Adult male morphotype variation in giant freshwater prawn (Macrobrachium rosenbergii): Genomic and experimental analysis of factors affecting the male social dominance hierarchy

“…Top-hit species distribution matched to the non-redundant database, showed similar results to that reported in other crustacean taxa (Jung et al, 2011;Zhang et al, 2011;Li et al, 2012).…”

“…Macrobrachium nipponense, Macrobrachium rosenbergii, Eriocheir sinensis and some penaeid shrimp taxa (Jung et al, 2011;Leekitcharoenphon et al, 2010;Ma et al, 2012;Zhang et al, 2011).…”

“…Recently, comprehensive genetic data sets from adult GFP tissues were obtained using 454 pyrosequencing to characterise the GFP transcriptome and to identify genes important for growth for which only limited molecular data had been available previously (Jung et al 2011). There have also been recent attempts to identify specific gene markers linked to economically important traits in GFP using single nucleotide polymorphism markers (SNPs) (Thanh et al, 2010;Jung et al 2011).…”

“…There have also been recent attempts to identify specific gene markers linked to economically important traits in GFP using single nucleotide polymorphism markers (SNPs) (Thanh et al, 2010;Jung et al 2011).…”