The genome of the Australian dragon lizard Pogona vitticeps.

Dataset type: Genomic
Data released on September 22, 2015

Georges A; Li Q; Lian J; OMeally D; Deakin J; Wang Z; Zhang P; Fujita M; Patel HR; Holleley CE; Zhou Y; Zhang X; Matsubara K; Waters P; Graves JAM; Sarre SD; Zhang G (2015): The genome of the Australian dragon lizard Pogona vitticeps. GigaScience Database. http://dx.doi.org/10.5524/100166

DOI10.5524/100166

We present a genomic resource for a wild-caught male ZZ Central Bearded Dragon Pogona vitticeps, from Australia. The genomic sequence, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (185x raw read depth) from 13 insert libraries ranging from 250 bp to 40 Kbp. After filtering for low quality and duplicated reads, a total of 146 Gbp of data (86x) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % SNP plus indels) complicated assembly, nevertheless 96.4% of reads mapped back to the assembled scaffolds indicating that the assembly included most of the sequenced genome. The total length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp, with an N50 of 2.29 Mbp.
We also present transcriptome data from brain, heart, lung, liver, kidney, skeletal muscle and gonads of male and female P. vitticeps, assembled these datasets (from seven individuals) into 595,564 contigs.
Genes were annotated on the basis of de novo prediction, similarity to Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and Pogona vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63% of which had intact open reading frames. Our assembly captured 99% (246 of 248) of the core CEGMA genes, with 93% (231) being complete.
The annotated Pogona genome can be accessed through a genome browser available here.

Additional details

Read the peer-reviewed publication(s):

Georges, A., Li, Q., Lian, J., O’Meally, D., Deakin, J., Wang, Z., … Zhang, G. (2015). High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. GigaScience, 4(1). doi:10.1186/s13742-015-0085-2

Genome browser:

https://genomics.canberra.edu.au

Accessions (data included in GigaDB):

BioProject: PRJEB5206





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Fabian103695 central bearded dragonPogona vitticeps Alternative names:UCID 001003387339
Sex:male
Genotype:ZZ
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsBIGWIG164.38 MB2015-09-22
Coding sequenceFASTA31.38 MB2015-09-04
AnnotationGFF626.06 KB2015-09-04
AnnotationGFF78.81 MB2015-09-04
AnnotationGFF145.11 MB2015-09-04
AnnotationGFF472.54 MB2015-09-04
AnnotationGFF99.52 MB2015-09-04
AnnotationGFF14.18 MB2015-09-04
Protein sequenceFASTA11.22 MB2015-09-04
SAMPLE:1985454ReadmeTEXT1.31 KB2015-09-04
Displaying 1-10 of 10 File(s).
Date Action
September 22, 2015 Dataset publish
September 22, 2015 Description updated from : We present a genomic resource for a wild-caught male ZZ Central Bearded Dragon Pogona vitticeps, from Australia. The genomic sequence, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (185x raw read depth) from 13 insert libraries ranging from 250 bp to 40 Kbp. After filtering for low quality and duplicated reads, a total of 146 Gbp of data (86x) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % SNP plus indels) complicated assembly, nevertheless 96.4% of reads mapped back to the assembled scaffolds indicating that the assembly included most of the sequenced genome. The total length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp, with an N50 of 2.29 Mbp.
We also present transcriptome data from brain, heart, lung, liver, kidney, skeletal muscle and gonads of male and female P. vitticeps, assembled these datasets (from seven individuals) into 595,564 contigs.
Genes were annotated on the basis of de novo prediction, similarity to Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and Pogona vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63% of which had intact open reading frames. Our assembly captured 99% (246 of 248) of the core CEGMA genes, with 93% (231) being complete.
The annotated Pogona genome can be accessed through a genome browser available at https://genomics.canberra.edu.au.
October 8, 2015 Manuscript Link added : 10.1186/s13742-015-0085-2
October 14, 2015 File georges_et_al.tar updated
October 14, 2015 File Pogona_vitticeps.male.pep updated
October 15, 2015 File georges_et_al.tar updated
October 15, 2015 File georges_et_al.tar updated
October 15, 2015 File Pogona_vitticeps.male.cds updated
October 15, 2015 File Pogona_vitticeps.male.fa.ltr_finder.gff updated
October 16, 2015 File Pogona_vitticeps.male.cds updated
October 21, 2015 File Pogona_vitticeps.male.cds updated
October 21, 2015 File georges_et_al.tar updated
October 26, 2015 File Pogona_vitticeps.male.cds updated
October 28, 2015 File georges_et_al.tar updated
November 5, 2015 File georges_et_al.tar updated
November 9, 2015 File Pogona_vitticeps.male.cds updated