Review for "Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola"

Completed on 29 Aug 2017 by Janine Deakin .

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Comments to author

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.

Minor comment:

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).