De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology

Abstract

Abstract:The soft-shelled turtle Pelodiscus sinensis is a high-profile turtle species because of its nutritional and medicinal value in Asian countries. However, little is known about the genes that are involved in formation of their nutritional quality traits, especially the molecular mechanisms responsible for unsaturated fatty acid and collagen biosynthesis. In the present study, the transcriptomes from six tissues from Pelodiscus sinensis were sequenced using an Illumina paired-end sequencing platform. We obtained more than 47 million sequencing reads and 73 954 unigenes with an average size of 754 bp by de-novo assembly. In total, 55.19% of the unigenes (40 814) had significant similarity with proteins in the National Center of Biotechnology Information (NCBI) non-redundant protein database and Swiss-Prot database (E-value <10 −5 ). Of these annotated unigenes, 9 156 and 11 947 unigenes were assigned to 52 gene ontology categories (GO) and 25 clusters of orthologous groups (COG), respectively. In total, 26 496 (35.83%) unigenes were assigned to 242 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we found a number of highly expressed genes involved in the regulation of P. sinensis unsaturated fatty acid biosynthesis and collagen formation, including desaturases, growth factors, transcription factors, and extracellular matrix components. Our data represent the most comprehensive sequence resource available for the Chinese soft-shelled turtle and could provide a basis for new research on this turtle as well as the molecular genetics and functional genomics of other terrapins. To our knowledge, we report for the first time, the large-scale RNA sequencing (RNA-Seq) of terrapin animals and would enrich the knowledge of turtles for future research.

Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles

“…We first acquired genomic data of six vertebrate species from the Amniota Orthology Dataset ( http://www.deep-phylogeny.org/hamstr/download/datasets/hmmer3/ ), which include green anole ( Anolis carolinensis ), chicken ( Gallus gallus ), human ( Homo sapiens ), opossum ( Monodelphis domestica ), zebra finch ( Taeniopygia guttata ), and western clawed frog ( Xenopus tropicalis ). Additionally, we downloaded transcriptomic data of the soft-shelled turtle ( Pelodiscus sinensis ), Nile crocodile ( Crocodylus niloticus ), royal python ( Python regius ), and tuatara ( Sphenodon punctatus ) [1] , [66] – [68] . After adding the Chinese pond turtle, our dataset included a total of 11 species, and had at least two representatives of each major lineage of living amniotes (with the exception of a single crocodilian).…”

Comparative studies of the expression of creatine kinase isoforms under immune stress in Pelodiscus sinensis

“…The sequence of PSCK-S containing the whole CDS (coding region) was obtained from the transcriptome sequencing data of P. sinensis in our previous study [17], in which de-novo characterization of the softshelled turtle (P. sinensis) transcriptome was performed using Illumina RNA-Seq technology. The gene was defined by overlap PCR amplification and splicing was performed after positive and negative monoclonal sequencing.…”

Research Article A comparative study on genetic characteristics of two new varieties of Pelodiscus sinensis and their hybrid.

“…The concentration and purity of the total RNA were determined with Agilent Bioanalyzer (nucleic acid/protein analyzer) with (OD 260 /OD 280 ) greater than 2.0, RNA 28S:18S ≥ 1, RIN ≥ 8. RNA samples were saved in dry ice immediately and sent to the ILLUMINA Gene Company for mRNA sequencing (Wang et al, 2013). Clean reads were compared with mapped genomic sequence of P. sinensis by using Tophat v. 2.0.5 (Trapnell et al, 2009).…”