Reference assembly and gene expression analysis of Apostichopus japonicus larval development

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.

The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation

“…In addition, all sequences were removed in which the predicted protein matched the species protein which did not belong to deuterostomes. These sequences satisfied two conditions: the bitscore above 200; the lack of a match with the available protein sequences of Apostichopus japonicus, Parastichopus parvimensis, Cladolabes schmeltzii, Patiria miniata, Lytechinus variegatus, and Strongylocentrotus purpuratus [25][26][27] with a bitscore, which was more than 80% of the match bitscore in the nonredundant protein (NRP) NCBI database. We assessed the completeness of the assembly using BUSCO v3 28 .…”

“…Subsequently, the obtained sequences were assembled with HomoloCAP script as described in the article 26 . The resulting sequences were filtered according to the NCBI requirements and uploaded to the TSA NCBI Database with the index GHCL00000000.…”

Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

“…A quantitative real-time polymerase chain reaction (qRT-PCR) analysis was conducted to explore the expression characteristics of a potential candidate gene during the following A. japonicus larval developmental stages: fertilized egg, blastula, gastrula, early auricularia larva, mid-auricularia larva, late-auricularia larva, doliolaria larva, pentactula larva, and juvenile [ 23 , 24 ]. Samples were treated with RNAwait (Solarbio, Beijing, China) for the subsequent RNA extraction [ 25 ]. Three tissues (body wall, respiratory tree, and intestine) were collected from three randomly selected individuals for the gene expression analysis.…”

A Novel Full-Length Transcriptome Resource for Sea Cucumber Apostichopus japonicus Using Pacbio SMRT Sequencing

“…For instance, transcriptome analysis of sea cucumber during the anti-bacterial process provided a valuable database of the interactions of mRNA-miRNA and gene expression regulatory mechanisms (Zhang et al, 2013). Comparative transcriptome analysis of multiple sea cucumber tissues revealed the molecular mechanisms of larval development (Boyko et al, 2019), growth variation (Gao et al, 2017), color variation (Jo et al, 2016), tissue-specific expression (Zhou et al, 2016a), tissue development (Zhan et al, 2019) and regeneration (Sun et al, 2011), responses to environmental stress (Li et al, 2019), aestivation (Yang et al, 2021), evisceration behavior (Ding et al, 2019), tenderization (Dong et al, 2019), and immune responses (Guo et al, 2021).…”