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

Bharat Bhusan Patnaik; 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

doi:10.1371/journal.pone.0148622

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

PLoS One. 2016 Feb 12;11(2):e0148622. doi: 10.1371/journal.pone.0148622. eCollection 2016.

Authors

Affiliations

¹ Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea.
² Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar- 751024, Odisha, India.
³ National Institute of Biological Resources, Incheon, 404-170, Republic of Korea.
⁴ Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Republic of Korea.
⁵ College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-gu, Gwangju, 500-757, Republic of Korea.
⁶ Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea.

Abstract

Background: The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction.

Results: The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats.

Conclusions: This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Endangered Species*
Female
Gene Expression Profiling
Gene Ontology
High-Throughput Nucleotide Sequencing
Immunity, Innate
Male
Microsatellite Repeats
Reproduction
Sex Determination Processes
Transcriptome*
Unionidae / genetics*
Unionidae / immunology
Unionidae / physiology

Grants and funding

This work was supported by the grant entitled "The Genetic and Genomic Evaluation of Indigenous Biological Resources" funded by the National Institute of Biological Resources (NIBR201503202).