The complete mitochondrial genome of Macrobrachium nipponense

Knepper, M. A.; Feng, Jianbin; Lin, Jing-Yun; Li, Jiale

doi:10.1016/j.gene.2011.07.017

Cited by 89 publications

(47 citation statements)

References 37 publications

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“…The oriental river prawn, Macrobrachium nipponense (Crustacea; Decapoda; Palaemonidae), is an important commercial prawn species that is widely distributed in freshwater and low-salinity estuarine regions in China and other Asian countries (Cai and Shokita, 2006;Feng et al, 2008;Ma et al, 2011). It is an important fishery resource in China, with an annual aquaculture production of 205,010 tons (Bureau of Fishery, Ministry of Agriculture, 2009).…”

Section: Introductionmentioning

confidence: 99%

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

Jin¹,

Fu²,

Jiang³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The oriental river prawn, Macrobrachium nipponense, is an important aquaculture species in China. The androgenic gland produces hormones that play crucial roles in the differentiation of crustaceans to the male sex. MicroRNA (miRNA) post-transcriptionally regulates many protein-coding genes, influencing important biological and metabolic processes. However, currently, there is no published data identifying miRNA in M. nipponense. In this study, we identified novel miRNA in the androgenic gland of M. nipponense. Using the high-throughput Illumina Solexa system, 1077 miRNA were identified from small RNA libraries by aligning with the de novo androgenic gland transcriptome of M. nipponense (obtained from RNA-Seq) and the sequences in the miRBase21 database. A total of 8,248, 76,011, and 78,307 target genes were predicted in the EST and SRA sequences provided in the NCBI database, and the androgenic gland transcriptome of M. nipponense, respectively. Some potential sex-18397 Identification of androgenic gland microRNA ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 18396-18406 (2015) related miRNA were identified based on the function of the predicted target genes. The results of our study provide new information regarding the miRNA expression in M. nipponense, which could be the basis for further genetic studies on decapod crustaceans.

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Section: Introductionmentioning

confidence: 99%

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

Jin¹,

Fu²,

Jiang³

et al. 2015

Genet. Mol. Res.

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“…The oriental river prawn, Macrobrachium nipponense (Crustacea; Decapoda; Palaemonidae), is an important commercial prawn species, that is widely distributed in freshwater and low-salinity estuarine regions in China and other Asian countries [1]–[7] with an aquaculture production of 205,010 tons annually for aquaculture only [8]. As known, within many other Macrobrachium species, the males grow faster and gain more weight at harvest time than females.…”

Section: Introductionmentioning

confidence: 99%

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

Jin

Zhou

et al. 2013

PLoS ONE

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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.

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“…The oriental river prawn Macrobrachium nipponense , a member of the Palaemonidae family of decapod crustaceans, is widely distributed in freshwater and low-salinity regions of estuaries [1]. This prawn is a useful model organism for studying reproduction and development in decapod species for multiple reasons.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of the Oriental River Prawn, Macrobrachium nipponense Using 454 Pyrosequencing for Discovery of Genes and Markers

et al. 2012

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BackgroundThe oriental river prawn, Macrobrachium nipponense, is an economically and nutritionally important species of the Palaemonidae family of decapod crustaceans. To date, the sequencing of its whole genome is unavailable as a non-model organism. Transcriptomic information is also scarce for this species. In this study, we performed de novo transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for M. nipponense using high-throughput sequencing technologies.Methodology and Principal FindingsTotal RNA was isolated from eyestalk, gill, heart, ovary, testis, hepatopancreas, muscle, and embryos at the cleavage, gastrula, nauplius and zoea stages. Equal quantities of RNA from each tissue and stage were pooled to construct a cDNA library. Using 454 pyrosequencing technology, we generated a total of 984,204 high quality reads (338.59Mb) with an average length of 344 bp. Clustering and assembly of these reads produced a non-redundant set of 81,411 unique sequences, comprising 42,551 contigs and 38,860 singletons. All of the unique sequences were involved in the molecular function (30,425), cellular component (44,112) and biological process (67,679) categories by GO analysis. Potential genes and their functions were predicted by KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literature, many putative genes involved in sex determination, including DMRT1, FTZ-F1, FOXL2, FEM1 and other potentially important candidate genes, were identified for the first time in this prawn. Furthermore, 6,689 SSRs and 18,107 high-confidence SNPs were identified in this EST dataset.ConclusionsThe transcriptome provides an invaluable new data for a functional genomics resource and future biological research in M. nipponense. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will be essential for accelerating aquaculture breeding programs with this species.

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The complete mitochondrial genome of Macrobrachium nipponense

Cited by 89 publications

References 37 publications

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

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

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

Transcriptome Analysis of the Oriental River Prawn, Macrobrachium nipponense Using 454 Pyrosequencing for Discovery of Genes and Markers

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