De novo assembly, gene annotation, and marker development using Illumina paired-end transcriptome sequencing in the Crassadoma gigantea

Crassadoma gigantea is an important commercial marine bivalve species in Baja California and Mexico. In this study, we have applied RNA-Seq technology to profile the transcriptome of the C. gigantea for the first time. A total of 80,832,518 raw reads were produced from a Illumina HiSeq4000 platform, and 77,306,198 (95.64%) clean reads were generated after trimming the adaptor sequences. The transcriptome assembled into 158,855 transcripts with an N50 size of 1995 bp and an average size of 1008 bp. A number of DNA repair related genes, such as MSH3, EGF, TGF, IGF, FGF, encoding different groups of growth factors were found in the transcriptome data of C. gigantean. In addition, immune related genes Toll-like receptor (TLR) including TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, and TLR9 was also observed in C. gigantean. A set of 12 polymorphic microsatellite loci were firstly developed and characterized in C. gigantea. The results show that the number of alleles and expected heterozygosity ranged from 3 to 9 and from 0.254 to 0.820, respectively. The average polymorphic information content was 0.790. These microsatellite loci will facilitate future studies of population structure and conservation genetics in this species.