While reptiles represent one of the most morphologically diverse vertebrate groups, there are only a very limited number of species sequenced. Among the lepidosauria, the only families with sequenced species include the Dactyloidae (green anole, Anolis carolinensis), Pythonidae (Burmese python, Python bivittatus), and the Elapidae (king cobra, Ophiophagus hannah), despite representing more than 35 squamate families. The Agamidae are a species-rich family of lizards, and the complete genome sequence of an agamid species has not been previously carried out.

Georges et al. present the high-coverage sequencing and genome annotation of the first agamid, the Australian dragon lizard Pogona vitticeps, which has a ZZ/ZW chromosomal sex determination system. The authors used both Illumina HiSeq2000 small insert as well as a range of mate-pair libraries, and using SOAPdenovo assembly achieved a contig N50 of 31.3 kb and a scaffold N50 of 2,290.5 kb, which is very high for post-Sanger, next-generation sequencing assemblies. They employ a well established genome annotation pipeline, with Trinity-based assembly of eight separate adult tissues. This yielded 19,406 annotated genes, which approaches the annotations of A. carolinensis, the chicken, mouse, and human. CEGMA scores are high for partial and full coverage. Overall, the investigators have generated a high quality genome sequence build and annotation for P. vitticeps that should be very valuable for the reptile comparative genomics and studies of vertebrate sex determination, and no issues about the genome sequencing and annotation were identified in this work.

Some specific issues were identified and the following minor essential revisions should be made prior to publication:
1. As required by journal editorial policy for the collection of tissues from a vertebrate species, a description of compliance with institutional or national guidelines and approval by an appropriate review committee, if required, should be included.
2. The authors refer to comparison with genome of the Africa clawed frog, Xenopus laevis, presented in Table 7. However, the X. laevis genome is not officially published yet, and there is not a JGI 4.2 build. Instead, the genome of the western clawed frog, Xenopus tropicalis, has been published [Hellsten et al. Science 328, 633 (2010)] and there is a JGI 4.2 build. This seems like this is a mislabeling of the data set?
3. Table 7: To be consistent about use of common names, “cobra” should be “king cobra”, “sea turtle” should be “green sea turtle”, and “pond turtle” should instead be “western painted turtle” if referring to Chrysemys picta bellii.
4. Line 160: Amplicon Express seems to have changed its URL to now be http://ampliconexpress.com since the one used redirects there.
Level of interest An article of outstanding merit and interest in its field
Quality of written English Acceptable
Statistical review No, the manuscript does not need to be seen by a statistician.
Declaration of competing interests I declare that I have no competing interests

Authors' response to reviews: (http://www.gigasciencejournal.com/imedia/1555691691835752_comment.pdf)

The reviewed version of the manuscript can be seen here:
http://www.gigasciencejournal.com/imedia/1445750077178132_manuscript.pdf
All revised versions are also available:
Draft - http://www.gigasciencejournal.com/imedia/1445750077178132_manuscript.pdf