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West African mud turtle assembly and gene annotation

Assembly

The Pelusios_castaneus-1.0 assembly was submitted by McDonnell Genome Institute - Washington University School of Medicine on August 2019. The assembly is on scaffold level, consisting of 112,514 contigs assembled into 69,036 scaffolds. 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 74,864 while the scaffold N50 is 14,055,032.

Gene annotation

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

AssemblyPelusios_castaneus-1.0, INSDC Assembly GCA_007922175.1, Aug 2019
Base Pairs2,044,278,682
Golden Path Length2,044,278,682
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedDec 2019
Database version100.1

Gene counts

Coding genes19,343
Non coding genes771
Small non coding genes599
Long non coding genes157
Misc non coding genes15
Pseudogenes101
Gene transcripts27,962

Other

Genscan gene predictions98,832

About this species

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