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Twenty-one microsatellite loci from sea cucumber Apostichopus japonicus (Selenka, 1867), an endangered species on the IUCN Red List.

ABSTRACT: The sea cucumber Apostichopus japonicus-an endangered species on the IUCN Red List-is economically and ecologically important echinoderm species. Here we describe a set of 21 amplified microsatellites for A. japonicus isolated through biotinylated probes for hybridization and a library screening method, which were used to genotype an artificially propagated stock of sea cucumber offspring from Lianyungang City of China. The observed and expected heterozygosity at the population level ranged from 0.2083 to 0.1000 and 0.6260 to 0.9304, respectively. The number of alleles varied between 6 and 19, and none of the loci deviated significantly from the Hardy-Weinberg equilibrium (P?

SUBMITTER: Dong Z

PROVIDER: S-EPMC6049811 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Twenty-one microsatellite loci from sea cucumber Apostichopus japonicus (Selenka, 1867), an endangered species on the IUCN Red List.

Dong Zhiguo Z Chen Yihua Y Xu Guangen G Kang Chuanlei C Fu Guanghui G Chen Baiyao B Li Jiale J

3 Biotech 20180717 8

The sea cucumber Apostichopus japonicus-an endangered species on the IUCN Red List-is economically and ecologically important echinoderm species. Here we describe a set of 21 amplified microsatellites for A. japonicus isolated through biotinylated probes for hybridization and a library screening method, which were used to genotype an artificially propagated stock of sea cucumber offspring from Lianyungang City of China. The observed and expected heterozygosity at the population lev ...[more]

PMID: 30034987

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Project description:BACKGROUND: Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus. RESULTS: In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome. CONCLUSION: Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.

Dataset Information

Twenty-one microsatellite loci from sea cucumber Apostichopus japonicus (Selenka, 1867), an endangered species on the IUCN Red List.

Publications

Twenty-one microsatellite loci from sea cucumber <i>Apostichopus japonicus</i> (Selenka, 1867), an endangered species on the IUCN Red List.

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