Chinese softshell turtle assembly and gene annotation

Assembly

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
TK722581
TK922479
TK1122299
TK1322412
TK1522778
TK1722223
TK2322777
Gastrula23290
Neurual22387
Pooled32727
All nine stages29847

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyPelSin_1.0, INSDC Assembly GCA_000230535.1, Oct 2011
Database version75.1
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 genes

Genes and/or transcript that contains an open reading frame (ORF).

18,189
Short non coding genes

Short non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

1,042
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

97
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.21,808

Other

Genscan gene predictions48,910

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