Development of novel polymorphic microsatellite markers for the blood clam Tegillarca granosa by pyrosequencing

Abstract

ABSTRACT. Large amounts of expressed sequence tags (ESTs) generated using next-generation sequencing technologies provide a cost-effective and valuable genomic resource for the development of microsatellite markers. In this study, we isolated 115 novel polymorphic microsatellite markers for the blood clam Tegillarca granosa from ESTs in 454 sequencing data. All the loci were characterized in 30 individual clams from a natural population in Xiangshan (Zhejiang Province, China). The number of alleles per locus varied from 2 to 10, with an average of 3.78. The observed and expected heterozygosities ranged from 0 to 1 and from 0.040 to 0.799, respectively. The polymorphic information content (PIC) ranged from 0.038 to 0.825, and 29 highly polymorphic loci (PIC ≥ 0.5) and 42 moderately polymorphic loci (0.25 < PIC < 0.5) were identified. Thirty-eight of the 115 loci deviated significantly from the Hardy-Weinberg equilibrium (P < 0.01) after a Bonferroni correction. A BlastX search revealed that 46 (40%) of the polymorphic loci identified were from transcript regions of known genes. The microsatellite markers developed in the present study 8977-8987 (2015) will greatly enrich the microsatellite resources of T. granosa, and are available for further population genetic analysis, genetic trait mapping, and molecular-assisted selection.

Signalling pathways and key genes involved in regulation of ovarian development of Sepia esculenta

“…For non‐model organisms for which genomic information is lacking, RNA‐Seq of specific tissues can be used to obtain functional gene information about genes that participate in specific biological processes (Jung et al, 2011; Künstner et al, 2010; Teaniniuraitemoana et al, 2014). RNA‐Seq of fish such as Oncorhynchus mykiss (Baron et al, 2005), Gadus morhua (Kleppe et al, 2014) and Morone saxatilis (Reading et al, 2012) and molluscs such as Ruditapes philippinarum (Fabrizio et al, 2012), Argopecten purpuratus (Boutet et al, 2008), Mytilus galloprovincialis (Craft et al, 2010) and Tegillarca granosa (Dong et al, 2015) has been used to study genetic evolution, genetic breeding and ecology. In this study, we conducted transcriptome analysis of the ovarian tissue of golden cuttlefish during the growth, spawning and post‐reproductive death periods and compared the results to identify genes related to reproduction and death and to clarify the differential expression of genes before and after egg laying.…”