title: De novo assembly and characterization of foot transcriptome and microsatellite marker development for Paphia textile.
abstract: Paphia textile is an important, aquaculture bivalve clam species distributed mainly in China, Philippines, and Malaysia. Recent studies of P. textile have focused mainly on artificial breeding and nutrition analysis, and the transcriptome and genome of P. textile have rarely been reported. In this work, the transcriptome of P. textile foot tissue was sequenced on an Illumina HiSeq™ 2000 platform. A total of 20,219,795 reads were generated, resulting in 4.08 Gb of raw data. The raw reads were cleaned and assembled into 54,852 unigenes with an N50 length of 829 bp. Of these unigenes, 38.92% were successfully annotated based on their matches to sequences in seven public databases. Among the annotated unigenes, 14,571 were assigned Gene Ontology terms, 5448 were classified to Clusters of Orthologous Groups categories, and 6738 were mapped to 228 pathways in the Kyoto Encyclopedia of Genes and Genomes database. For functional marker development, 5605 candidate simple sequence repeats were identified in the transcriptome and 80 primer pairs were selected randomly and amplified in a wild population of P. textile. A total of 36 loci that exhibited obvious repeat length polymorphisms were detected. The transcriptomic data and microsatellite markers will provide valuable resources for future functional gene analyses, genetic map construction, and quantitative trait loci mapping in P. textile.
authors.affiliation: Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Chen
authors.affiliation: Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China.
authors.forename: Jiakai
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China.
authors.forename: Shijun
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Mariculture in the East China Sea, Ministry of Agriculture of China, Fisheries College, Jimei University, Xiamen 361021, China. Electronic address: xdliu@jmu.edu.cn.
authors.forename: Xiande
authors.initials: X
authors.lastname: Liu
mesh_terms: D000818:Animals; D049872:Bivalvia / Q000235:genetics*; D005819:Genetic Markers; D018895:Microsatellite Repeats / Q000235:genetics*; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: Marker discovery; Microsatellite markers; Paphia textile; RNA sequencing; Transcriptome