I have read the data note submitted to GigaScience regarding the Ophisaurus gracilis draft genome. This will be an important contribution to genomics as it represents the second lizard genome to be sequenced. I think the data should be available as soon as possible, but the authors should consider the following suggestions, all Minor Essential Revisions:

First, the authors make repeated suggestions that Ophisaurus is an “intermediate” species between a lizard and snake. Or, that it is a “limbless relative” to lizard. Ophisaurus IS a lizard, not an intermediate, not a relative. And, while it is true that the genome will be an important resource for understanding limb loss, it will be so only in the context of Anguidae; snakes are quite divergent from anguids, and the developmental and genomic underpinnings of limb loss may be divergent as well. So while it is tempting to compare the limb loss between snakes and lizards, the authors should be aware that they are not the same and in fact are convergent traits.

Second, I am a little uneasy about the statement that the genome is 100% represented when it is based on an “estimate” of genome size. I would be ok with a different wording, perhaps “likely complete” coverage.

Third, there are inconsistencies with the reporting. In the abstract, the authors use the full sequencing volume to say the genome is covered at 154X, but in the paper they state 86X because nearly half the reads are thrown out. Please stick to one set of numbers (preferably the 86X, which represents the data actually used in the assembly).

There are some spelling errors, such as “gnome” for “genome” in the abstract. Level of interest An article of importance in its field Quality of written English Needs some language corrections before being published 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.

Author response:

http://www.gigasciencejournal.com/imedia/5685823071629165_comment.pdf