De Novo Transcriptome Sequencing Analysis and Comparison of Differentially Expressed Genes (DEGs) in Macrobrachium rosenbergii in China

Abstract

Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture. However the gene discovery in this species has been limited to small-scale data collection in China. We used the next generation sequencing technology for the experiment; the transcriptome was sequenced of samples of hepatopancreas organ in individuals from 4 GFP groups (A1, A2, B1 and B2). De novo transcriptome sequencing generated 66,953 isogenes. Using BLASTX to search the Non-redundant (NR), Search Tool for the Retrieval of Interacting Genes (STRING), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases; 21,224 unigenes were annotated, 9,552 matched unigenes with the Gene Ontology (GO) classification; 5,782 matched unigenes in 25 categories of Clusters of Orthologous Groups of proteins (COG) and 20,859 unigenes were consequently assigned to 312 KEGG pathways. Between the A and B groups 147 differentially expressed genes (DEGs) were identified; between the A1 and A2 groups 6,860 DEGs were identified and between the B1 and B2 groups 5,229 DEGs were identified. After enrichment, the A and B groups identified 38 DEGs, but none of them were significantly enriched. The A1 and A2 groups identified 21,856 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function and the KEGG pathway defined 2,459 genes had a KEGG Ortholog - ID (KO-ID) and could be categorized into 251 pathways, of those, 9 pathways were significantly enriched. The B1 and B2 groups identified 5,940 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function, and the KEGG pathway defined 1,543 genes had a KO-ID and could be categorized into 240 pathways, of those, 2 pathways were significantly enriched. We investigated 99 queries (GO) which related to growth of GFP in 4 groups. After enrichment we identified 23 DEGs and 1 KEGG PATHWAY ‘ko04711’ relation with GFP growth.

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

“…Mating of sex-reversed females (neo-males) with normal females (ZW) could increase a higher ratio of females, while mating of sex-reversed males (neo-females) with normal males could produce all-male (ZZ × ZZ) progeny [1,6,7]. Recently, along with the emergence of high-throughput sequencing, RNA-seq as a most powerful tool is available for illustrating the mechanisms of immune response [35], determining the expression pattern of reproduction, growth, and pheromone communication in hepatopancreas, gill, muscle, and antennal gland [36][37][38]. In the present study, we profiled to detect the transcriptomes of gonads in females, super females, and the males using RNA-seq, with the aim of interpreting the molecular mechanism involved in the sex determination, and identifying sex-related candidate genes.…”

The Single-molecule long-read sequencing of Scylla paramamosain

“…olivacea 34 , Carcinus maenas 35,36 , Gecarcinus lateralis 37–41 , P . sanguinolentus 42 , Charybdis feriatus 43 , Litopenaeus vannamei 44–48 , Macrobrachium rosenbergii 49–52 , M . nipponense 53,54 , Exopalaemon carinicauda 55–57 , Oratosquilla oratoria 58–60 , Homarus americanus 61 , and so on.…”

Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

“…As a pivotal tool to study biological/physiological mechanisms, transcriptome analyses can facilitate the identification of differentially expressed genes (DEGs) according to the different growth characteristics of GFPs, help screen key genes involved in pertinent growth pathways and help comprehensively elucidate the growth regulation mechanisms of GFPs. In GFPs, de novo transcriptome sequencing analysis has been previously used, for example, for comparison of DEGs between small‐ and big‐sized individuals (Nguyen Thanh, Zhao, & Liu, 2014), identification of genes and markers associated with reproduction (Jung et al., 2016), detection of genes involved in ovarian maturation (Jiang, Yuan, et al., 2019) and identification of genes potentially affecting social dominance hierarchy in adult males (Aziz et al., 2017).…”