| Title |
High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps
|
|---|---|
| Published in |
Giga Science, September 2015
|
| DOI | 10.1186/s13742-015-0085-2 |
| Pubmed ID | |
| Authors |
Arthur Georges, Qiye Li, Jinmin Lian, Denis O’Meally, Janine Deakin, Zongji Wang, Pei Zhang, Matthew Fujita, Hardip R. Patel, Clare E. Holleley, Yang Zhou, Xiuwen Zhang, Kazumi Matsubara, Paul Waters, Jennifer A. Marshall Graves, Stephen D. Sarre, Guojie Zhang |
| Abstract |
The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Pogona vitticeps. The genomic sequence for P. vitticeps, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (179X raw read depth) from 13 insert libraries ranging from 250 bp to 40 kbp. After filtering for low-quality and duplicated reads, 146 Gbp of data (83X) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4 % of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome. Length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp. N50 was 2.29 Mbp. Genes were annotated on the basis of de novo prediction, similarity to the green anole Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and P. 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 core CEGMA genes, with 93 % (231) being complete. The quality of the P. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotated P. vitticeps genome can be accessed through a genome browser available at https://genomics.canberra.edu.au. |
X Demographics
The data shown below were collected from the profiles of 35 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Australia | 5 | 14% |
| United Kingdom | 5 | 14% |
| United States | 3 | 9% |
| Canada | 3 | 9% |
| Germany | 2 | 6% |
| France | 1 | 3% |
| South Africa | 1 | 3% |
| Hong Kong | 1 | 3% |
| Georgia | 1 | 3% |
| Other | 1 | 3% |
| Unknown | 12 | 34% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 21 | 60% |
| Members of the public | 11 | 31% |
| Science communicators (journalists, bloggers, editors) | 3 | 9% |
Mendeley readers
The data shown below were compiled from readership statistics for 114 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Portugal | 1 | <1% |
| Netherlands | 1 | <1% |
| France | 1 | <1% |
| Brazil | 1 | <1% |
| Japan | 1 | <1% |
| United States | 1 | <1% |
| Unknown | 108 | 95% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 28 | 25% |
| Researcher | 28 | 25% |
| Student > Master | 14 | 12% |
| Student > Bachelor | 10 | 9% |
| Student > Doctoral Student | 6 | 5% |
| Other | 10 | 9% |
| Unknown | 18 | 16% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 44 | 39% |
| Biochemistry, Genetics and Molecular Biology | 32 | 28% |
| Environmental Science | 5 | 4% |
| Engineering | 2 | 2% |
| Pharmacology, Toxicology and Pharmaceutical Science | 1 | <1% |
| Other | 6 | 5% |
| Unknown | 24 | 21% |
Attention Score in Context
This research output has an Altmetric Attention Score of 27. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 March 2017.
All research outputs
#1,443,809
of 26,017,215 outputs
Outputs from Giga Science
#243
of 1,176 outputs
Outputs of similar age
#20,033
of 289,148 outputs
Outputs of similar age from Giga Science
#5
of 14 outputs
Altmetric has tracked 26,017,215 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,176 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 21.8. This one has done well, scoring higher than 79% of its peers.
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We're also able to compare this research output to 14 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 64% of its contemporaries.