Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)

ABSTRACT: Comparisons of gene expression profiles between testis and ovary of juvenile and wild brooders were made through a cDNA microarray in the black tiger shrimp (Penaeus monodon). Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR. Selected genes were further characterized. A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,568 features. RNA samples were extracted from both testes and ovaries of pooled juveniles (4 month-old, pooled from n=114 ), individual juvenile and broodstocks from West sides of Thailand. The RNA from ovaries were labeled with Cy3 dye as a reference and those of testes were labeled with Cy5 dye.

ORGANISM(S): Penaeus monodon

SUBMITTER: nitsara karoonuthaisiri

PROVIDER: E-GEOD-22090 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon).

Wongsurawat Thidathip T Leelatanawit Rungnapa R Thamniemdee Natechanok N Uawisetwathana Umaporn U Karoonuthaisiri Nitsara N Menasveta Piamsak P Klinbunga Sirawut S

BMC molecular biology 20100809

<h4>Background</h4>Poor reproductive maturation of the black tiger shrimp (Penaeus monodon) in captivity is one of the serious threats to sustainability of the shrimp farming industry. Understanding molecular mechanisms governing reproductive maturation processes requires the fundamental knowledge of integrated expression profiles in gonads of this economically important species. In P. monodon, a non-model species for which the genome sequence is not available, expressed sequence tag (EST) and c ...[more]

PMID: 20696033

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Project description:Background: Aquaculture of the black tiger prawn Penaeus monodon remains severely constrained by an almost total dependence on wild-caught broodstock. Reliance on wild-caught broodstock stems, for the most part, from reduced reproductive potential of captive-reared females. Reproductive performance of captive-reared females is usually characterised by longer latency period, lower egg production, egg hatch rates and post-larval survivorship compared with their wild-caught counterparts. Improved understanding of the cellular and associated molecular events occurring during peneaid ovarian maturation could therefore be fundamental to improving reproductive success of captive-reared animals. Methodology/Principle Findings: In support of other studies, our histological analyses of developing oocytes revealed differences between wild-caught and captive-reared P. monodon, including reduced lipid accumulation in oocytes of captive-reared animals. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Custom oligonucleotide microarrays were constructed and screened with transcripts derived from the ovary, cephalothorax and eyestalk from animals of all ovarian maturation stages. Ovarian maturation-related differential expression patterns were observed for 111 transcripts, with 53 transcripts displaying differential expression between wild-caught and captive-reared animals. Notably transcripts encoding vitellogenin - the major egg yolk protein precursor, and a lipid storage droplet protein (which we named pmLSD) which is involved in lipid accumulation, were found to be more highly expressed in wild-caught animals. pmLSD transcripts localise to pre-vitellogenic oocytes of wild-caught animals and the pmLSD protein is exclusively localised to the surface of lipid droplets of oocytes at vitellogenic and cortical rod stages. We have employed oligonucleotide microarray analysis to compare expression profiles of genes involved in ovarian maturation among wild-caught and captive-reared animals. Target preparation and microarray hybridisation. Ovarian RNA samples from nine wild-caught animals representing six ovarian maturation stages (P, 2, 24, V, R, E) were used in microarray hybridisations. Similarly, RNA samples from three captive-reared animals representing four maturation stages (P, 24, V, E) were used in microarray hybridisations. For wild-caught animals, samples from each ovarian maturation stage were pooled into groups of four and five, enabling two hybridisations. For captive-reared animals, samples from each ovarian maturation stage from all three animals were pooled enabling one hybridisation for each stage. Importantly, as the four stages for captive-reared animals were (1) pre-ablation pre-vitellogenic, (2) post-ablation pre-vitellogenic, (3) post-ablation vitellogenic, (4) post-ablation vitellogenic with cortical rods, this arrangement allowed for 2 samples of captive-reared pre-vitellogenic and 2 samples of captive-reared vitellogenic, thereby enabling t-tests between samples, while also allowing analysis across the whole 4 stages via cluster analysis. All hybridisations were single channel hybridisations conducted using equal amounts of RNA pooled from each individual.

Dataset Information

Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)

Publications

Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon).

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