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Channel catfish assembly and gene annotation

Assembly

The IpCoco_1.2 assembly was submitted by Auburn University on June 2016. The assembly is on chromosome level, consisting of 34,544 contigs assembled into 9,975 scaffolds. From these sequences, 29 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 77,201 while the scaffold N50 is 7,726,806.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001660625.1

Gene annotation

The channel catfish (Ictalurus punctatus) is North America's most numerous catfish species. It is the official fish of Kansas, Missouri, Iowa, Nebraska, and Tennessee, and is informally referred to as a "channel cat". In the United States, they are the most fished catfish species with around 8 million anglers targeting them per year. The popularity of channel catfish for food has contributed to the rapid expansion of aquaculture of this species in the United States.

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

AssemblyIpCoco_1.2, INSDC Assembly GCA_001660625.1, Jun 2016
Base Pairs783,274,721
Golden Path Length783,274,721
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.12

Gene counts

Coding genes23,651
Non coding genes1,431
Small non coding genes1,411
Long non coding genes5
Misc non coding genes15
Pseudogenes36
Gene transcripts39,017

Other

Genscan gene predictions41,812

About this species