Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
8388010 | Marine Genomics | 2018 | 5 Pages |
Abstract
Starfish (Phylum Echinodermata) are of interest from an evolutionary perspective because as deuterostomian invertebrates they occupy an “intermediate” phylogenetic position with respect to chordates (e.g. vertebrates) and protostomian invertebrates (e.g. Drosophila). Furthermore, starfish are model organisms for research on fertilization, embryonic development, innate immunity and tissue regeneration. However, large-scale molecular data for starfish tissues/organs are limited. To provide a comprehensive genetic resource for the starfish Patiria pectinifera, we report de novo transcriptome assemblies and global gene expression analysis for six P. pectinifera tissues/organs - body wall (BW), coelomic epithelium (CE), tube feet (TF), stomach (SM), pyloric caeca (PC) and gonad (GN). A total of 408 million high-quality reads obtained from six cDNA libraries were assembled de novo using Trinity, resulting in a total of 549,598 contigs with a mean length of 835 nucleotides (nt), an N50 of 1473Â nt, and GC ratio of 42.5%. A total of 126,136 contigs (22.9%) were obtained as predicted open reading frames (ORFs) by TransDecoder, of which 102,187 were annotated with NCBI non-redundant (NR) hits, and 51,075 and 10,963 were annotated with Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) using the Blast2GO program, respectively. Gene expression analysis revealed that tissues/organs are grouped into three clusters: BW/CE/TF, SM/PC, and GN, which likely reflect functional relationships. 2408, 8560, 2687, 1727, 3321, and 2667 specifically expressed genes were identified for BW, GN, PC, CE, SM and TF, respectively, using the ROKU method. This study provides a valuable transcriptome resource and novel molecular insights into the functional biology of different tissues/organs in starfish as a model organism.
Keywords
FPKMFDRAICORFsRSEMKOGDEGsRNA-Seq by Expectation MaximizationEukaryotic Orthologous GroupsPCACoelomic epitheliumEchinodermMolecular functionPrincipal component analysisTranscriptomecellular componentKEGG یا Kyoto Encyclopedia of Genes and Genomes Kyoto Encyclopaedia of Genes and Genomesdifferential expressed genesBody wallStarfishPyloric caecaNon-redundantbiological processOpen reading framesStomachAkaike's Information Criterionfalse discovery rateGene ontologyDifferentially expressed genesGonad
Related Topics
Physical Sciences and Engineering
Earth and Planetary Sciences
Earth and Planetary Sciences (General)
Authors
Chan-Hee Kim, Hye-Jin Go, Hye Young Oh, Yong Hun Jo, Maurice R. Elphick, Nam Gyu Park,