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Bay scallop Argopecten irradians, one of the most important commercial bivalves in China, is an interesting subject of research since it is hermaphrodite and capable of self-fertilization.In order to generate a comprehensive survey of gene sequences for further use in gene expression studies, allelic variations investigation and comparative genomics research, we sequenced the transcriptome using Genome Sequencer FLX System from 454 Life Sciences.