Major Compulsory Revisions: To assess the workflow used in library construction and assembly, more details are needed. Researchers hoping to use this genome in future studies will want to know how this data was generated in greater detail. 1. Please include more details on the library construction. How was genomic DNA fragmented and size selected? 2. What programs/thresholds were used to filter duplicates and low quality reads? 3. What parameters were used in SOAPdenovo? If default were used, please specify this.

Minor Essential Revisions 1. Need some information on the individual O. gracilis that was sequenced. Is the specimen accessioned in a museum? What was the gender, age, type of tissue sampled? From what locality was is taken from? 2. O. gracilis is a lizard, not a relative of lizards. The phrase “a limbless relative to” will need need to be rewritten to reflect this fact. Include a specific statement of where (at what facility) and when (month and year) the sequencing took place. 3. What quality scoring system was used? 4. The morphology of this lizard to snakes may be similar but please include a brief statement about their phylogenetic relationship to each other, including a citation. If divergence time has been estimated, this would be good to include. 5. Table 1. The common name should be Asian glass lizard, not slowworm. The European species have the common name slowworm.

Minor Issues Not for Publication

1. Punctation - there are number of places where commas need to be inserted to separate out clauses. Ex. “The sequencing of Ophisaurus gracilis, a limbless relative [….] closer to snake, …”
2. Abstract/Background: Change “with elongated” to “with an elongated”; Change “studying genetic basis” to “studying the genetic basis”.
3. Abstract/Findings: Change “using HiSeq2000” to “using a HiSeq2000”; Change to “was subsequently filtered and assembled. The final assembly consisted of 1.78 Gbp comprising 6,717 scaffolds (N50 = 1.27 Mbp, maximum scaffold = 6.68 Mbp).”; Delete comma from “predicted, and 884.06”.
4. Abstract/Conclusions: Change “gnome” to “genome”
5. Data description: Change “Seven Paired” to “Seven paired”; change “size of O. gracilis” to “size of the O. gracilis”; change “chiken Galus galus” to “chicken Gallus gallus”; italicize “de novo”; change “accounted approximately” to “accounted for approximately”; change “snakes’ genomes, the ” to “snake genomes: the”; change “In summary, we provided” to “in summary, we provide”; delete “as we present in this study”.
6. Clarify in abstract/findings what the clause “occupying approximately half of the genome” is referring to.
7. Last sentence of abstract/findings needs to be rewritten.
8. Acknowledgements are missing.

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

Minor Revisions: 1. Integers 1-10 should be written out in full (e.g. one through ten). 2. Delete "here" from "In summary, here we provide". 3. When referring to this as the "second lizard genome" please see last years publication of the S. occidentalis genomic resources in Molecular Ecology Resources' Genomic Resources Notes: http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12340/full

Level of interest An article of importance 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.

Author response:

http://www.gigasciencejournal.com/imedia/2089389292163631_comment.pdf