Abstract
The transcriptome of the holothurian Apostichopus japonicus was sequenced at four developmental stages—blastula, gastrula, auricularia, pentactula—on an Illumina sequencer. Based on our RNA-seq data and the paired-end reads from 16 libraries obtained by other researchers earlier, we have achieved the currently most complete transcriptome assembly for A. japonicus with the best basic statistical parameters. An analysis of the obtained transcriptome has revealed 174 differentially expressed transcription factors, as well as stage-specific transcription factors that are most promising for further study. In addition, a total of 1,174,999 high-quality single nucleotide polymorphisms have been identified, including 58,932 indels. A GO enrichment analysis of contigs containing polymorphic loci shows the predominance of GO terms associated with immune response. The data obtained by us provide an additional basis for a deeper study of the mechanisms of the planktotrophic-type development in holothurians and can be used in commercial sea cucumber breeding programs.
Highlights
The transcriptome of the holothurian Apostichopus japonicus was sequenced at four developmental stages—blastula, gastrula, auricularia, pentactula—on an Illumina sequencer
A search for differentially expressed genes (DEGs) revealed a total of 11697 genes with significant changes in expression level relative to the blastula stage
The blastula stage in A. japonicus is largely characterized by cluster 1, which is formed by genes with maximum expression at this developmental stage (Fig. 5A)
Summary
The transcriptome of the holothurian Apostichopus japonicus was sequenced at four developmental stages—blastula, gastrula, auricularia, pentactula—on an Illumina sequencer. We tried to obtain the most complete transcriptome, to determine DEGs at the main developmental stages of A. japonicus and the transcription factors (TFs) regulating it, as well as to identify SNPs and to establish the role of genes containing SNPs in development of this species.
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