Kirill Grigorev, Sergey Kliver, Pavel Dobrynin, Aleksey Komissarov, Walter Wolfsberger, Ksenia Krasheninnikova, Yashira M Afanador-Hernández, Liz A Paulino, Rosanna Carreras, Luis E Rodríguez, Adrell Núñez, Filipe Silva, David Hernández-Martich, Audrey J Majeske, Agostinho Antunes, Alfred L Roca, Stephen J O'Brien, Juan Carlos Martinez-Cruzado, Taras K Oleksyk
Review posted on 29th August 2017
Grigorev et al demonstrate how low coverage sequencing of several individuals with low levels of heterozygosity, combined with a string-graph based assembly approach, can produce a useful, quality, genome assembly. The different assembly approaches used were thoroughly tested before drawing the conclusion that a string-graph based approach produced a higher quality assembly. The authors were sensitive to the limitations of this approach more generally, noting its being computationally intensive makes it generally a more undesirable approach for higher sequence coverage genomes as is its sensitivity to sequence variation. Nevertheless, a strong case was made for using this approach for low coverage genomes, particularly for threatened species were obtaining material for high coverage sequencing may be an issue.
The utility of the data presented in this manuscript was explored in several ways, including assisting in determining the phylogenetic position, identification of potential venom genes and microsatellites for conservation genetics. Although the analysis of the venom genes is challenged by the lack of a saliva sample for transcriptomics, the comparative genomic analysis provides a good starting point for future studies if such a sample should become available in the future.
Overall, I felt that the authors presented an excellent approach for utilizing low genome coverage data while recognizing the limitations of their data (e.g. the limitations of using a low coverage genome to accurately assess repeat content of the genome) and therefore, the discussion of their findings was appropriate and not overstated.
Prior to publication, the authors should check for typos in Tables S3 and S4 (e.g. varified should be verified; wodii should be woodi etc).
Review posted on 11th September 2016
There is a paucity of reptile genomes given the number of species within this vertebrate group, making any additional reptile genome assembly an important additional to the list. The manuscript "Draft genome of the leopard gecko, Eublepaharis macularius" by Xiong et al reports a brief description of the assembly and gene content analysis of the leopard gecko genome. Being able to now compare genomes with atypical gecko features to that of Gekko japonicas will help to uncover the genomic features contributing to the more typical gecko features. The authors have generated a genome assembly and gene build of similar quality to Gekko japonicas and it will be useful for comparative genomic investigations.
Table S2: Assembly statistics for Pogona vitticeps should be added to this table for completeness [Georges et al (2015) Gigascience 4:45]. The text in the manuscript relating to this table would also need to be updated and should be changed to "Comparison of assembly N50s of leopard gecko and the eleven other published reptile genomes…"
Line 102: change to "…captured 225 (91%) of the 248…"
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