Transcriptome Analysis of Androgenic Gland for Discovery of Novel Genes from the Oriental River Prawn, Macrobrachium nipponense, Using Illumina Hiseq 2000

Abstract

BackgroundThe oriental river prawn, Macrobrachium nipponense, is an important aquaculture species in China, even in whole of Asia. The androgenic gland produces hormones that play crucial roles in sexual differentiation to maleness. This study is the first de novo M. nipponense transcriptome analysis using cDNA prepared from mRNA isolated from the androgenic gland. Illumina/Solexa was used for sequencing.Methodology and Principal FindingThe total volume of RNA sample was more than 5 ug. We generated 70,853,361 high quality reads after eliminating adapter sequences and filtering out low-quality reads. A total of 78,408 isosequences were obtained by clustering and assembly of the clean reads, producing 57,619 non-redundant transcripts with an average length of 1244.19 bp. In total 70,702 isosequences were matched to the Nr database, additional analyses were performed by GO (33,203), KEGG (17,868), and COG analyses (13,817), identifying the potential genes and their functions. A total of 47 sex-determination related gene families were identified from the M. nipponense androgenic gland transcriptome based on the functional annotation of non-redundant transcripts and comparisons with the published literature. Furthermore, a total of 40 candidate novel genes were found, that may contribute to sex-determination based on their extremely high expression levels in the androgenic compared to other sex glands,. Further, 437 SSRs and 65,535 high-confidence SNPs were identified in this EST dataset from which 14 EST-SSR markers have been isolated.ConclusionOur study provides new sequence information for M. nipponense, which will be the basis for further genetic studies on decapods crustaceans. More importantly, this study dramatically improves understanding of sex-determination mechanisms, and advances sex-determination research in all crustacean species. The huge number of potential SSR and SNP markers isolated from the transcriptome may shed the lights on research in many fields, including the evolution and molecular ecology of Macrobrachium species.

Identification of androgenic gland microRNA and their target genes to discover sex-related microRNA in the oriental river prawn, Macrobrachium nipponense

“…Studies into the androgenic gland of M. nipponense have also been popular in the recent years. The androgenic gland transcriptome of M. nipponense has been previously constructed (Jin et al, 2013), and used to analyze many sex-related homologous genes and novel genes, which helped outline the basic sex-determination mechanism of M. nipponense (Zhang et al, 2013a,b,c;Jin et al, 2014;Li et al, 2015b).…”

Molecular cloning and expression pattern of oriental river prawn (Macrobrachium nipponense) nitric oxide synthase

“…The NOS expressed sequence tag obtained from the M. nipponense AG transcriptome (Jin et al, 2013) was used to design four gene-specific primers (Table 1). The cloning of M. nipponense NOS (MnNOS) cDNA was achieved by 5' and 3'-RACE using the 5'-and 3' Full RACE Kit (TaKaRa) following the manufacturer protocols.…”

“…The annual production of farmed oriental river prawn approximates 20 billion tons (Bureau of Fisheries, Ministry of Agriculture, 2014). Although previous studies have examined M. nipponense testes complementary DNA (cDNA) libraries and the AG transcriptome (Qiao et al, 2012;Jin et al, 2013), insufficient information regarding sex determination and differentiation-related genes is available for this species. It is known that males grow faster and accumulate more weight by the time of harvesting compared to females in many Macrobrachium species, including M. nipponense (Jin et al, 2013).…”

“…Although previous studies have examined M. nipponense testes complementary DNA (cDNA) libraries and the AG transcriptome (Qiao et al, 2012;Jin et al, 2013), insufficient information regarding sex determination and differentiation-related genes is available for this species. It is known that males grow faster and accumulate more weight by the time of harvesting compared to females in many Macrobrachium species, including M. nipponense (Jin et al, 2013). In addition, sexual precocity (i.e., early sexual maturity) has become problem at cultured stocks, resulting in a reduction in market value (Qiao et al, 2012).…”

“…Currently, male sexual differentiation-related genes in this organism are poorly understood and require further study to clarify the means by which M. nipponense sex is determined. Jin et al (2013) identified NOS as a novel candidate gene and significantly expressed in the AG. Moreover, these authors suggested that it may play an important role in the sex-determination mechanism of the oriental river prawn.…”