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New Caledonian crow assembly and gene annotation

Assembly

The UO_Cmon_1.0 assembly was submitted by University of Otago on November 2019. The assembly is on scaffold level, consisting of 11,985 contigs assembled into 2,996 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 331,397 while the scaffold N50 is 4,457,533.

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

AssemblyUO_Cmon_1.0, INSDC Assembly GCA_009650515.1, Nov 2019
Base Pairs1,056,558,033
Golden Path Length1,056,558,033
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedFeb 2020
Genebuild releasedMay 2020
Genebuild last updated/patchedFeb 2020
Database version101.1

Gene counts

Coding genes15,356
Non coding genes1,358
Small non coding genes361
Long non coding genes994
Misc non coding genes3
Pseudogenes82
Gene transcripts30,038

Other

Genscan gene predictions44,434

About this species

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