Transcriptome Sequencing and Characterization of Japanese Scallop <i>Patinopecten yessoensis</i> from Different Shell Color Lines

Shell color is an important trait that is used in breeding the Japanese scallop Patinopecten yessoensis, the most economically important scallop species in China. We constructed four transcriptome libraries from different shell color lines of P. yessoensis: the left and right shell mantles of ordinary strains of P. yessoensis and the left shell mantles of the ‘Ivory’ and ‘Maple’ strains. These four libraries were paired-end sequenced using the Illumina HiSeq 2000 platform and contained 54,802,692 sequences, 40,798,962 sequences, 74,019,262 sequences, and 44,466,166 sequences, respectively. A total of 214,087,082 expressed sequence tags were assembled into 73,522 unigenes with an average size of 1,163 bp. When the data were compared against the public Nr and Swiss-Prot databases using BlastX, nearly 30.55% (22,458) of the unigenes were significantly matched to known unique proteins. Gene Ontology annotation and pathway mapping analysis using the Kyoto Encyclopedia of Genes and Genomes categorized unigenes according to their diverse biological functions and processes and identified candidate genes that were potentially involved in growth, pigmentation, metal transcription, and immunity. Expression profile analysis was performed on all four libraries and many differentially expressed genes were identified. In addition, 5,772 simple sequence repeats were obtained from the P. yessoensis transcriptomes, and 464,197, 395,646, and 310,649 single nucleotide polymorphisms were revealed in the ordinary strains, the ‘Ivory’ strain, and the ‘Maple’ strain, respectively. These results provide valuable information for future genomic studies on P. yessoensis and improve our understanding of the molecular mechanisms involved in the growth, immunity, shell coloring, and shell biomineralization of this species. These resources also may be used in a variety of applications, such as trait mapping, marker-assisted breeding, studies of population genetics and genomics, and work on functional genomics.壳色是养殖虾夷盘扇贝（Patinopecten yessoensis）的重要育种性状，该物种是中国经济价值最高的扇贝养殖品种。本研究从虾夷盘扇贝的不同壳色品系构建了4个转录组文库：普通品系的左、右外套膜组织，以及"象牙色（Ivory）"和"枫色（Maple）"品系的左外套膜组织。上述4个文库均采用Illumina HiSeq 2000平台进行双端测序，分别获得54,802,692条、40,798,962条、74,019,262条及44,466,166条原始序列。总计214,087,082条表达序列标签被组装为73,522条单基因簇（unigene），平均长度为1,163 bp。利用BlastX将单基因簇序列比对至公共Nr数据库与Swiss-Prot数据库后，近30.55%（22,458条）的单基因簇可与已知的独特蛋白质产生显著匹配。通过基因本体（Gene Ontology）注释与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路注释分析，本研究根据单基因簇的多样生物学功能与过程对其进行了分类，并筛选出潜在参与生长、色素沉着、金属转录及免疫调控的候选基因。对全部4个文库开展表达谱分析，鉴定得到大量差异表达基因。此外，本研究从虾夷盘扇贝转录组中挖掘得到5,772个简单序列重复（simple sequence repeats, SSR）位点；在普通品系、"象牙色（Ivory）"品系及"枫色（Maple）"品系中，分别发现464,197、395,646及310,649个单核苷酸多态性（single nucleotide polymorphisms, SNP）位点。本研究结果为虾夷盘扇贝的后续基因组学研究提供了宝贵的数据资源，同时加深了我们对该物种生长、免疫、壳色形成及贝壳生物矿化相关分子机制的理解。这些组学资源还可应用于诸多研究领域，包括性状定位、标记辅助育种、群体遗传学与基因组学研究，以及功能基因组学相关研究。