Anole lizard assembly and gene annotation

Assembly

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 genome assembly represented here corresponds to GenBank Assembly ID GCA_000090745.1

Other assemblies

Gene annotation

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:

TissueNumber of gene models
adrenal gland22213
brain23145
dewlap25201
heart23246
liver23169
lung22811
merged27722
ovary25003
skeletal muscle22316
whole embryo22958

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAnoCar2.0, INSDC Assembly GCA_000090745.1, May 2010
Database version81.2
Base Pairs1,701,353,770
Golden Path Length1,799,143,587
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedSep 2010
Genebuild releasedDec 2010
Genebuild last updated/patchedFeb 2013

Gene counts

Coding genes18,596
Non coding genes3,160
Small non coding genes2,883
Misc non coding genes277
Pseudogenes157
Gene transcripts22,494

Other

Genscan gene predictions107,132