Transcriptomics,Genomics

Dataset Information

148

Transcriptome sequencing of Macrobrachium nipponense hepatopancreas at different nitrite concentrations


ABSTRACT: Macrobrachium nipponense is one of the commonest species threatened by ambient superfluous nitrite. The mechanism of nitrite stress at the molecular level was studied using de novo RNA-Seq to explore the molecular pathways in M. nipponense exposed to the acute nitrite stress (26.05 mg/L nitrite-N) for 24h and the chronic nitrite stress (6.58 mg/L nitrite-N) for 21d. A total of 175.13 million reads were obtained and assembled into 58,871 unigenes with an average length of 1,028.7 bp and N50 of 1,294bp. 2,824 and 2,610 unigenes in the acute and chronic nitrite stress were significantly differentially expressed respectively. Based on the change in GO analysis and KEGG pathway analysis, pathways both in the acute and chronic nitrite stress were glycosphingolipid biosynthesis - ganglio series, alanine aspartate and glutamate metabolism, biotin metabolism and amino sugar and nucleotide sugar metabolism which revealed the commonly functional pathways in acute and chronic nitrite stress. The markedly altered pathways were divided into four sections of immunity, metabolism, cell and others. Immunity section contained the most pathways among the classifications as phagosome, folate biosynthesis, glycerolipid metabolism, glycine, serine and threonine metabolism, selenoamino acid metabolism, cysteine and methionine metabolism, amino sugar and nucleotide sugar metabolism and taurine and hypotaurine metabolism in the acute nitrite stress and lysosome, alanine, aspartate and glutamate metabolism, arginine and proline metabolism, glycosaminoglycan degradation and amino sugar and nucleotide sugar metabolism in the chronic nitrite stress. This is the first report of whole molecular responses of M. nipponense under acute and chronic nitrite stress through de novo transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanisms of the nitrite stress for crustacean species. Overall design: Examination of 4 different nitrite treated hepatopancreas in Macrobrachium nipponense

INSTRUMENT(S): Illumina HiSeq 2500 (Macrobrachium nipponense)

SUBMITTER: Xu Zhixin  

PROVIDER: GSE74684 | GEO | 2016-11-04

SECONDARY ACCESSION(S): PRJNA301151

REPOSITORIES: GEO

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Publications

Comparative transcriptome analysis reveals molecular strategies of oriental river prawn Macrobrachium nipponense in response to acute and chronic nitrite stress.

Xu Zhixin Z   Li Tongyu T   Li Erchao E   Chen Ke K   Ding Zhili Z   Qin Jian G JG   Chen Liqiao L   Ye Jinyun J  

Fish & shellfish immunology 20151212


Macrobrachium nipponense is an economically and nutritionally important species threatened by ambient superfluous nitrite. De novo RNA-Seq was used to explore the molecular mechanism in M. nipponense exposed to the acute nitrite stress (26.05 mg/L nitrite-N) for 24 h and the chronic nitrite stress (1.38 mg/L nitrite-N) for 28 d A total of 175.13 million reads were obtained and assembled into 58,871 unigenes with an average length of 1028.7 bp and N50 of 1294 bp. Under the acute and chronic nitri  ...[more]

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