De novo assembly, gene annotation, and simple sequence repeat marker development using Illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima.

We analyzed the mantle transcriptome of pearl oyster Pinctada maxima and developed EST-SSR markers using Illumina HiSeq 2000 paired-end sequencing technology. A total of 49,500,748 raw reads were generated. De novo assembly generated 108,704 unigenes with an average length of 407 bp. Sequence similarity search with known proteins or nucleotides revealed that 30,200 (27.78%) and 25,824 (23.76%) consensus sequences were homologous with the sequences in the non-redundant protein and Swiss-Prot databases, respectively, and that 19,701 (18.12%) of these unigenes were possibly involved in approximately 234 known signaling pathways in the Kyoto Encyclopedia of Genes and Genomes database. Ninety one biomineralization-related unigenes were detected. In a cultured stock, 1764 simple sequence repeats were identified and 56 primer pairs were randomly selected and tested. The rate of successful amplification was 68.3%. The developed molecular markers are helpful for further studies on genetic linkage analysis, gene localization, and quantitative trait loci mapping.