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Pachon cavefish assembly and gene annotation

Assembly

The Astyanax_mexicanus-1.0.2 assembly was submitted by Aquatic Genome Models on April 2019. The assembly is on scaffold level, consisting of 121,345 contigs assembled into 10,735 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 14,739 while the scaffold N50 is 1,775,308.

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

AssemblyAstyanax_mexicanus-1.0.2, INSDC Assembly GCA_004802775.1, Apr 2019
Base Pairs1,191,242,572
Golden Path Length1,191,242,572
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJun 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedJun 2019
Database version100.102

Gene counts

Coding genes22,263
Non coding genes3,087
Small non coding genes388
Long non coding genes2,692
Misc non coding genes7
Pseudogenes137
Gene transcripts62,405

Other

Genscan gene predictions47,951

About this species

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