Boyko AV et al. (2019), Reference assembly and gene expression analysis...

ECB-ART-46934

Sci Rep 2019 Feb 04;91:1131. doi: 10.1038/s41598-018-37755-5.

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Reference assembly and gene expression analysis of Apostichopus japonicus larval development.

Boyko AV , Girich AS , Eliseikina MG , Maslennikov SI , Dolmatov IY .

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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.

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Genes referenced: LOC100887844 LOC583082

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References [+] :

Bankevich, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. 2012, Pubmed

	Figure 1. Scheme of the process of read filtering and assembling.
	Figure 2. Length distribution of contigs and basic features of assembly.
	Figure 3. Average logFC values and Venn diagrams for up-regulated and down-regulated DEGs.
	Figure 4. GO enrichment terms for four stages of development. The GO enrichment analysis for stages was modified to reveal the predominant, in terms of total TPM value, GO terms at a stage. Only the ten most predominant GO processes are shown.
	Figure 5. Expression profiles of gene clusters. (A) Clusters 1 and 2 having positive (cluster 1) and negative (cluster 2) peaks at blastula stage. (B) Clusters 3 and 4 having positive peaks at gastrula (cluster 3) and auricularia (cluster 4) stages. (C) Clusters 5 and 6 having positive (cluster 5) and negative (cluster 6) peaks at pentactula stage. (D) Clusters 7 and 8 with gradual increase and decrease in expression levels, respectively. (E) Clusters 9 and 10 having positive peaks at early (cluster 9) and later (cluster 10) stages of larval development. (F) Dynamics of expression of genes of clusters 11-13.
	Figure 6. TPM values of 25 most predominant transcription factors. (A) TFs with peak of expression at blastula stage. (B) TFs with peak of expression at gastrula stage. (C) TFs with peak of expression at auricularia stage. (D) TFs with peak of expression at pentactula stage.
	Figure 7. GO enrichment terms for highly polomorphic genes. On the abscissa axis is the percentage of the total number of contigs of the test set.