Argentine black and white tegu (HLtupMer3)

Argentine black and white tegu assembly and gene annotation

Assembly

The HLtupMer3 assembly was submitted by Center for Systems Biology Dresden on September 2018. The assembly is on scaffold level, consisting of 38,189 contigs assembled into 5,988 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 167,260 while the scaffold N50 is 28,146,161.

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

AssemblyHLtupMer3, INSDC Assembly GCA_003586115.1, Sep 2018
Base Pairs2,026,218,827
Golden Path Length2,026,218,827
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedDec 2018
Database version111.3

Gene counts

Coding genes19,342
Non coding genes4,299
Small non coding genes2,221
Long non coding genes1,791
Misc non coding genes287
Pseudogenes52
Gene transcripts36,061

Other

Genscan gene predictions99,120