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Live sharksucker assembly and gene annotation

Assembly

The fEcheNa1.1 assembly was submitted by SC on April 2019. The assembly is on chromosome level, consisting of 178 contigs assembled into 38 scaffolds. From these sequences, 24 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 12,371,513 while the scaffold N50 is 23,287,306.

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

AssemblyfEcheNa1.1, INSDC Assembly GCA_900963305.1, Apr 2019
Base Pairs544,212,633
Golden Path Length544,212,633
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJul 2019
Genebuild releasedDec 2019
Genebuild last updated/patchedAug 2019
Database version100.11

Gene counts

Coding genes21,655
Non coding genes976
Small non coding genes714
Long non coding genes201
Misc non coding genes61
Pseudogenes276
Gene transcripts56,376

Other

Genscan gene predictions31,426

About this species

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