The Sea Cucumber Apostichopus Japonicus PDF Download

From Abstract: Apostichopus californicus (A. californicus) is a commercially important sea cucumber species that is understudied and overharvested. Genomic information for A. californicus is not available, which hinders genetic and genomic studies. The closest relative with a high-quality genome assembly and annotation is Apostichopus japonicus (A. japonicus). While colosely related, using the A. japonicus genome as a template for A. californicus research raises questions regarding the accuracy of the results. To facilitate future genomic research of A. californicus and to validate previous research, a draft genome was assembled and annotated using Illumina short-reads and publicly available data. To improve the draft assemby, a second assembly was created using the A. japonicus genome assembly as a reference. A combination of BUSCO, RNA-seq mapping, functional annotation, and targeted gene curation found comparable gene content between assemblies. The reference-assisted assembly was more contiguous and had more complete genes. Three genes, Mortalin, Survivin, and Telomerase were selected for manual curation. When checking the published A. japonicus gene models, Telomerase and Mortalin were found to be incorrect. The only assembly that had a complete sea cucumber Telomerase was the reference-guided assembly, deomonstrating the effectiveness of this approach. Mortalin and Survivin were complete in both A. californicus assemblies with a high degree of conservation relative to other echinoderms. Having an annotated genome assembly availalbe creates the opportunity to confidently create primers for genes, validate gene structure, study gene expression using qPCR and RNA-seq, and generate phylogenetic trees. These techniques can be used to study population structure, disease susceptibility, and improve aquaculture of this commercially important sea cucumber species.