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Hagfish assembly and gene annotation

Assembly

The Eburgeri_3.2 assembly was submitted by Riken Center For Development Biology on 2017-10-24. The assembly is on the scaffold level, consisting of 10846 scaffolds. The total length is 2608383542 of which 1172995459 positions are gaps.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_900186335.2

Gene annotation

Hagfish, are eel-shaped, slime-producing marine fish (occasionally called slime eels). They are the only known living animals that have a skull but no vertebral column, although hagfish do have rudimentary vertebrae. Along with lampreys, hagfish are jawless; they are the sister group to jawed vertebrates, and living hagfish remain similar to hagfish from around 300 million years ago.

The gene annotation of the hagfish was created via a combination of RNA-seq based annotation of nine adult tissues, three development stages and one artificially merged set of all reads. This was combined with protein-to-genome alignments of a subset of vertebrate proteins. Cut-off parameters for the alignments were relaxed to account for the distant nature of hagfish to most other vertebrates. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. 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

AssemblyEburgeri_3.2, INSDC Assembly GCA_900186335.2, Oct 2017
Base Pairs2,608,383,542
Golden Path Length2,608,383,542
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2017
Genebuild releasedJun 2018
Genebuild last updated/patchedJun 2018
Database version94.32

Gene counts

Coding genes16,513
Non coding genes733
Small non coding genes271
Long non coding genes455
Misc non coding genes7
Gene transcripts29,049

Other

Genscan gene predictions39,464

About this species