Chinese softshell turtle assembly and gene annotation


The Chinese softshell turtle (Pelodiscus sinensis) genome was produced by the RIKEN institute. The genome is 2.1Gb in length; composed of 205,379 contigs with an N50 value of 22kb and 19,903 scaffolds with an N50 value of 3.37Mb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000230535.1

Gene annotation

The gene set was built using a mixed approach. Due to the lack of species specific sequences and the availability of RNASeq data for Chinese softshell turtle from RIKEN and BGI Institutes, the final gene set comprises of models based orthologous proteins from the vertebrate division of UniProtKB in addition to models from RNASeq data. The RNASeq data contained samples from TK7, TK9, TK11, TK13, TK15, TK17, TK23, gastrula and neurula developmental stages, together with pooled data set and combined data from all nine stages. 8,070 gene models were made exclusively from RNASeq data. The data was also used to add UTR to gene models.

RNASeq data set

In addition to the main set, we have predicted gene models for each tissue type using the RNASeq pipeline. We did a BLASTp of these models against UniProt proteins with protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

Developmental stageNumber of gene models
All nine stages29847

More information

General information about this species can be found in Wikipedia.



AssemblyPelSin_1.0, INSDC Assembly GCA_000230535.1, Oct 2011
Database version82.1
Base Pairs2,106,639,384
Golden Path Length2,202,483,752
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedNov 2011
Genebuild releasedJul 2012
Genebuild last updated/patchedFeb 2014

Gene counts

Coding genes18,189
Non coding genes1,042
Small non coding genes1,006
Misc non coding genes36
Gene transcripts21,808


Genscan gene predictions48,910