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Green anole assembly and gene annotation

The Carolina anole (Anolis carolinensis) is an arboreal anole lizard native to the southeastern United States (west to Texas) and introduced elsewhere. This species has been chosen as a model reptile for genomics by the NHGRI because of the ease and low cost of laboratory breeding and evolutionary value of the diversity of the genus.

Assembly

The AnoCar2.0 assembly was submitted by Broad Institute on September 2011. The assembly is on chromosome level, consisting of 41,987 contigs assembled into 6,646 scaffolds. From these sequences, 13 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 79,867 while the scaffold N50 is 4,033,265.

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

AssemblyAnoCar2.0v2, INSDC Assembly GCA_000090745.2, Jan 2011
Base Pairs1,799,143,587
Golden Path Length1,799,143,587
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2020
Genebuild releasedMar 2021
Genebuild last updated/patchedOct 2020
Database version104.2

Gene counts

Coding genes21,555
Non coding genes4,098
Small non coding genes919
Long non coding genes3,176
Misc non coding genes3
Pseudogenes826
Gene transcripts38,557

Other

Genscan gene predictions95,447

About this species

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