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Ovarian Transcriptome Analysis of Portunus trituberculatus Provides Insights into Genes Expressed during Phase III and IV Development.

Yang Y, Wang J, Han T, Liu T, Wang C, Xiao J, Mu C, Li R, Yu F, Shi H - PLoS ONE (2015)

Bottom Line: Also, we performed deep sequencing of ovaries in phases III and IV of sexual maturation in P. trituberculatus.Differential analysis of gene expression identified 506 significantly differentially expressed genes, which belong to 20 pathway, transporters, development, transcription factors, metabolism of other amino acids, carbohydrate and lipid, solute carrier family members, and enzymes.Taken together, our study provides the first comprehensive transcriptomic resource for P. trituberculatus ovaries, which will strengthen understanding of the molecular mechanisms underlying the sexual maturation process and advance molecular nutritional studies of P. trituberculatus.

View Article: PubMed Central - PubMed

Affiliation: Fisheries College of Zhejiang Ocean University, Zhoushan, China.

ABSTRACT
Enhancing the production of aquatic animals is crucial for fishery management and aquaculture applications. Ovaries are specialized tissues that play critical roles in producing oocytes and hormones. Significant biochemical changes take place during the sexual maturation of Portunus trituberculatus, but the genetics of this process has not been extensively studied. Transcriptome sequencing can be used to determine gene expression changes within specific periods. In the current study, we used transcriptome sequencing to produce a comprehensive transcript dataset for the ovarian development of P. trituberculatus. Approximately 100 million sequencing reads were generated, and 126,075 transcripts were assembled. Functional annotation of the obtained transcripts revealed important pathways in ovarian development, such as those involving the vitellogenin gene. Also, we performed deep sequencing of ovaries in phases III and IV of sexual maturation in P. trituberculatus. Differential analysis of gene expression identified 506 significantly differentially expressed genes, which belong to 20 pathway, transporters, development, transcription factors, metabolism of other amino acids, carbohydrate and lipid, solute carrier family members, and enzymes. Taken together, our study provides the first comprehensive transcriptomic resource for P. trituberculatus ovaries, which will strengthen understanding of the molecular mechanisms underlying the sexual maturation process and advance molecular nutritional studies of P. trituberculatus.

No MeSH data available.


Sequence length distribution of transcripts assembled from Illumina reads.
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pone.0138862.g001: Sequence length distribution of transcripts assembled from Illumina reads.

Mentions: Contigs (126,075) were generated from the library giving a total of ~100 million sequence reads (Table 2). There are 48,444 contigs with lengths up to 500 bp. The median size of the contigs (N50) was 1503 bp. The average size of the assembled contigs was 788 bp, and the lengths of contigs ranged from 200 bp to more than 16,000 bp (Fig 1). The Q30 bases rate, which is considered a benchmark for quality in next-generation sequencing, was up to 92.23%. All reads were deposited in the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with the accession number SRX1081182.


Ovarian Transcriptome Analysis of Portunus trituberculatus Provides Insights into Genes Expressed during Phase III and IV Development.

Yang Y, Wang J, Han T, Liu T, Wang C, Xiao J, Mu C, Li R, Yu F, Shi H - PLoS ONE (2015)

Sequence length distribution of transcripts assembled from Illumina reads.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591999&req=5

pone.0138862.g001: Sequence length distribution of transcripts assembled from Illumina reads.
Mentions: Contigs (126,075) were generated from the library giving a total of ~100 million sequence reads (Table 2). There are 48,444 contigs with lengths up to 500 bp. The median size of the contigs (N50) was 1503 bp. The average size of the assembled contigs was 788 bp, and the lengths of contigs ranged from 200 bp to more than 16,000 bp (Fig 1). The Q30 bases rate, which is considered a benchmark for quality in next-generation sequencing, was up to 92.23%. All reads were deposited in the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with the accession number SRX1081182.

Bottom Line: Also, we performed deep sequencing of ovaries in phases III and IV of sexual maturation in P. trituberculatus.Differential analysis of gene expression identified 506 significantly differentially expressed genes, which belong to 20 pathway, transporters, development, transcription factors, metabolism of other amino acids, carbohydrate and lipid, solute carrier family members, and enzymes.Taken together, our study provides the first comprehensive transcriptomic resource for P. trituberculatus ovaries, which will strengthen understanding of the molecular mechanisms underlying the sexual maturation process and advance molecular nutritional studies of P. trituberculatus.

View Article: PubMed Central - PubMed

Affiliation: Fisheries College of Zhejiang Ocean University, Zhoushan, China.

ABSTRACT
Enhancing the production of aquatic animals is crucial for fishery management and aquaculture applications. Ovaries are specialized tissues that play critical roles in producing oocytes and hormones. Significant biochemical changes take place during the sexual maturation of Portunus trituberculatus, but the genetics of this process has not been extensively studied. Transcriptome sequencing can be used to determine gene expression changes within specific periods. In the current study, we used transcriptome sequencing to produce a comprehensive transcript dataset for the ovarian development of P. trituberculatus. Approximately 100 million sequencing reads were generated, and 126,075 transcripts were assembled. Functional annotation of the obtained transcripts revealed important pathways in ovarian development, such as those involving the vitellogenin gene. Also, we performed deep sequencing of ovaries in phases III and IV of sexual maturation in P. trituberculatus. Differential analysis of gene expression identified 506 significantly differentially expressed genes, which belong to 20 pathway, transporters, development, transcription factors, metabolism of other amino acids, carbohydrate and lipid, solute carrier family members, and enzymes. Taken together, our study provides the first comprehensive transcriptomic resource for P. trituberculatus ovaries, which will strengthen understanding of the molecular mechanisms underlying the sexual maturation process and advance molecular nutritional studies of P. trituberculatus.

No MeSH data available.