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.
AnoCar2.0 (GCA_000090745.1) is an assembly of the anole lizard, provided by the Genome Sequencing Platform, the Genome Assembly Team, Broad Institute of MIT and Harvard. This assembly is used by UCSC to create their anoCar2 database.
The anole lizard genome is composed of 13 chromosomes, assembled from 41.9861 contigs and 2.143 scaffolds. The total number of bases in the genome is 1.78Gb.
The gene set for anole lizard was built using the Ensembl genebuild pipeline. Gene models are based on genewise alignments of chicken proteins as well as genetically distant proteins from other species, including most vertebrates from Uniprot. To improve the accuracy of models generated from distant species, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. The protein based gene models were then extended using anole lizard cDNA and EST alignments as well as chicken cDNA. Potentially missing predictions and partial gene predictions were identified by examining the human-chicken one-to-one orthologs, which were then used to build new gene models.
RNASeq data set
In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt vertebrate proteins of protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.
The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:
|Tissue||Number of gene models|
General information about this species can be found in Wikipedia.
|Assembly||AnoCar2.0, INSDC Assembly GCA_000090745.1, May 2010|
|Golden Path Length||1,799,143,587|
|Annotation method||Full genebuild|
|Genebuild started||Sep 2010|
|Genebuild released||Dec 2010|
|Genebuild last updated/patched||Jul 2016|
|Non coding genes||7,168|
|Small non coding genes||2,883|
|Long non coding genes||4,008|
|Misc non coding genes||277|
|Genscan gene predictions||107,132|