In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns

Abstract

Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this technology, transcriptome sequencing of three tissue types: hepatopancreas, gill and muscle, has been undertaken to generate functional genomics data for M. rosenbergii at a massive scale. De novo assembly of 75-bp paired end Ilumina reads has generated 102,230 unigenes. Sequence homology search and in silico prediction have identified known and novel protein coding candidate genes (∼24%), non-coding RNA, and repetitive elements in the transcriptome. Potential markers consisting of simple sequence repeats associated with known protein coding genes have been successfully identified. Using KEGG pathway enrichment, differentially expressed genes in different tissues were systematically represented. The functions of gill and hepatopancreas in the context of neuroactive regulation, metabolism, reproduction, environmental stress and disease responses are described and support relevant experimental studies conducted previously in M. rosenbergii and other crustaceans. This large scale gene discovery represents the most extensive transcriptome data for freshwater prawn. Comparison with model organisms has paved the path to address the possible conserved biological entities shared between vertebrates and crustaceans. The functional genomics resources generated from this study provide the basis for constructing hypotheses for future molecular research in the freshwater shrimp.

Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics

“…For example, ~3 times more contigs were recovered from Hyas araneus than originally described (Harms et al , 2013), likely due to Illumina, rather than Roche 454, data becoming available for this species. However, contig numbers for Portunus trituberculatus (123,015 vs. 94,511) and Macrobrachium rosenbergii (95,321 vs. 102,230) were similar relative to previous transcriptome assemblies, likely because they were generated from the same sequence data with comparable assembly methods (Lv et al , 2013; Mohd-Shamsudin et al , 2013). Lastly, to the best of our knowledge, this is the first report of a gill transcriptome for Carcinus aestuarii , which possessed 48,355 contigs and a similar annotation rate to that of C. sapidus (Table 1).…”

“…Specifically, the four gill data sets were from the crabs Portunus trituberculatus (Lv et al , 2013), Hyas araneus (Harms et al , 2014; Harms et al , 2013), and Carcinus aestuarii (Romiguier et al , 2014), and the giant river prawn Macrobrachium rosenbergii (Mohd-Shamsudin et al , 2013). …”

An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods

“…However, at present the genomic data available for the Caridea are rather scarce. No Caridean genome has been sequenced and only few transcriptome datasets are available for two Palaemonidae species, M. rosenbergii (Mohd-Shamsudin et al 2013) and M. nipponense (Ma et al 2012;Jin et al 2013). The most documented type of genomic data remains b Fig.…”

Enhanced muscle regeneration in freshwater prawn Macrobrachium rosenbergii achieved through in vivo silencing of the myostatin gene

“…The T7 primers were designed by incorporating the region 5′‐TAA TAC GAC TCA CTA TAG GG‐3′ into both the forward and reverse primers of Mr MSTN and GFP. The primers for the cogene regulation study were designed using the template of respective unigenes that are identified from the transcriptome data of M. rosenbergii (Mohd‐Shamsudin et al, ). Elongation factor – 1 (EF‐1) was used as a control for quantitative polymerase chain reaction, and the primer was designed based on an expressed sequence tags similar to the EF‐1‐alpha from M. rosenbergii (GenBank accession no.…”