Transcriptome assembly statistics of <i>C</i>. <i>plicata</i> visceral mass using the Trinity analysis.

<p>Transcriptome assembly statistics of <i>C</i>. <i>plicata</i> visceral mass using the Trinity analysis.</p

Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.

<p>The <i>C</i>. <i>plicata</i> visceral mass unigenes were assigned to KEGG pathways (inner circle). The total number of enzymes ascribed within each KEGG pathway is shown in the outer circle. Each pathway is represented by a different color.</p

Summary of <i>C</i>. <i>plicata</i> visceral mass unigene (≥ 200 bp) sequences after Trinity assembly.

<p>Summary of <i>C</i>. <i>plicata</i> visceral mass unigene (≥ 200 bp) sequences after Trinity assembly.</p

Statistical summary of homology search of assembled unigenes against the PANM protein database.

<p><b>(A)</b> Score distribution of BLAST hits for each unigene with a cutoff E-value of 1E -5. <b>(B)</b> E-value distribution of each unigene using BLAST hits with a cutoff E-value of 1E -5. <b>(C)</b> Identity distribution of the top BLAST hits for each unigene. <b>(D)</b> Similarity distribution of the top BLAST hits for each unigene. <b>(E)</b> Lengths of unigenes compared with the presence or absence of BLAST hits.</p

Schematic representation of transcriptome assembly and annotation.

<p>A <i>C</i>. <i>plicata</i> visceral mass transcriptome was obtained using an Illumina HiSeq2500 NGS platform. The raw reads obtained were preprocessed using the Sickle software tool (quality: 20, length: 40) and Fastq_filter software to obtain clean reads. Trinity assembly (K-mer, 25; minimum contig length; 200) and TGICL clustering (Identity; 94%; overlap; 30 bp) generated 374,794 unigenes. The unigenes were used for functional annotation using the PANM, Unigene, COG, GO, and KEGG databases and structural annotation for SSR detection.</p

List of the top-hit 40 InterPro domains in <i>C</i>. <i>plicata</i> transcriptome.

<p>List of the top-hit 40 InterPro domains in <i>C</i>. <i>plicata</i> transcriptome.</p

GO classifications of the <i>C</i>. <i>plicata</i> transcriptome at level 2.

<p>GO analyses were performed for three major classification categories: <b>(A)</b> biological processes; <b>(B)</b> cellular components and <b>(C)</b> molecular functions.</p

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

<div><p>Background</p><p>The freshwater mussel <i>Cristaria plicata</i> (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 <i>de novo</i> transcriptome sequencing and annotation analysis of <i>C</i>. <i>plicata</i> 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.</p><p>Results</p><p>The <i>C</i>. <i>plicata</i> transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The <i>de novo</i> 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 <i>C</i>. <i>plicata</i> 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.</p><p>Conclusions</p><p>This dataset represents the first transcriptome analysis of the endangered mollusc, <i>C</i>. <i>plicata</i>. 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 <i>C</i>. <i>plicata</i>.</p></div

Frequency distribution of simple sequence repeats (SSRs) based on motif types found in <i>C</i>. <i>plicata</i> visceral mass unigene sequences.

<p>Frequency distribution of simple sequence repeats (SSRs) based on motif types found in <i>C</i>. <i>plicata</i> visceral mass unigene sequences.</p

Summary of simple sequence repeat (SSR) types based on the number of repeat units.

<p>Summary of simple sequence repeat (SSR) types based on the number of repeat units.</p