Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery

• DOI: 10.1371/journal.pone.0148622
• Publication Date: 2016-02-12T18:44:25Z
• Authors: Bharat Bhusan Pat...; Tae Hun Wang; Se Won Kang; Hee-Ju Hwang; So Young Park; Eun Bi Park; Jong Min Chung; Dae Kwon Song; Changmu Kim; Soonok Kim; Jun Sang Lee; Yeon Soo Han; Hong Seog Park; Yong Seok Lee
• Keywords: Freshwater bivalve

Background The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use pearl farming. have been listed as endangered South Korea the loss of natural habitats caused by anthropogenic activities. decreasing population and a lack genomic information on concerning for environmentalists conservationists. In this study, we conducted de novo transcriptome sequencing annotation analysis C. using Illumina HiSeq 2500 next-generation (NGS) technology, Trinity assembler, bioinformatics databases prepare sustainable resource identification candidate genes involved immunity, defense, reproduction. Results included total 286,152,584 raw reads 281,322,837 clean reads. assembly identified 453,931 contigs 374,794 non-redundant unigenes with average lengths 731.2 737.1 bp, respectively. Furthermore, 100% coverage mitochondrial within two supported quality assembler. total, 84,274 showed homology entries at least one database, 23,246 were allocated or more Gene Ontology (GO) terms. most prominent GO biological process, cellular component, molecular function categories (level 2) membrane, binding, A 4,776 mapped 123 pathways KEGG database. Based terms annotation, suggested be stress responses, sex-determination, 17,251 cDNA simple sequence repeats (cSSRs) from 61,141 (size >1 kb) abundant being dinucleotide repeats. Conclusions This dataset represents first mollusc, plicata. provides comprehensive conservation genetic enrichment development markers will assist improvement