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Painted turtle assembly and gene annotation

Assembly

The Chrysemys_picta_bellii-3.0.3 assembly was submitted by Painted turtle genome sequencing consortium on March 2014. The assembly is on chromosome level, consisting of 262,326 contigs assembled into 78,631 scaffolds. From these sequences, 18 chromosomes have been built. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 21,349 while the scaffold N50 is 6,605,846.

Gene annotation

The painted turtle (Chrysemys picta) is the most widespread native turtle of North America. It lives in slow-moving fresh waters, from southern Canada to Louisiana and northern Mexico, and from the Atlantic to the Pacific. The turtle is the only species of the genus Chrysemys, which is part of the pond turtle family Emydidae.

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome. lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyChrysemys_picta_bellii-3.0.3, INSDC Assembly GCA_000241765.2, Mar 2014
Base Pairs2,365,766,571
Golden Path Length2,365,766,571
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2018
Genebuild releasedDec 2018
Genebuild last updated/patchedMar 2020
Database version100.303

Gene counts

Coding genes21,186
Non coding genes5,523
Small non coding genes1,183
Long non coding genes2,799
Misc non coding genes1,541
Pseudogenes108
Gene transcripts46,230

Other

Genscan gene predictions145,617

About this species

HASH(0x22996898)