Abstract
Background: Chinese clearhead icefish, Protosalanx hyalocranius, is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests. Findings: A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly. Conclusion: We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.
Highlights
We made revisions based on your suggestions
Related point-by-point responses to the comments of reviewers are provided as follows for your consideration
The queries related to the discarded sequences and a potential error in our genome size calculation, from the reviewer 1, were answered in detail
Summary
We made revisions based on your suggestions. Related point-by-point responses (in the blue color) to the comments of reviewers are provided as follows for your consideration. The queries related to the discarded sequences and a potential error in our genome size calculation, from the reviewer 1, were answered in detail. We took necessary filtering processes to remove 3 and 1 low-quality bases in left and right edges of the raw reads and to discard those duplicated reads produced by sequencing PCRs. Usually, around 20-30% of raw reads were removed in our previous reports (You et al 2014, Nature Communications, 5:5594; Yang et al, 2015, BMC Biology, 14:1; Bian et al, 2016, Scientific Reports, 6:24501; Chen et al, 2016, GigaScience, 5:39; Lin et al, 2016, Nature, in press) when the same processes were applied.
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