Genome assembly of the deep-sea coral Lophelia pertusa
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Abstract
Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio CLR data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.
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Abstract
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.78), and has published the reviews under the same license. These are as follows.
Reviewer 1. Takeshi Takeuchi
Is there sufficient data validation and statistical analyses of data quality?
Scaffolding with the Chicago and Hi-C libraries did not significantly improve the assembly. In general, Hi-C scaffolding can produce a chromosome-scale assembly. I would suggest that the authors describe the quality of the Chicago and Hi-C sequence data. For example, the mapping rates of the Chicago/Hi-C reads to the assembly should be informative.
**Reviewer 2. Yang Zhou **
This is a fascinating study on the assembly of the first deep-sea scleractinian coral, Lophelia pertusa. The manuscript is well-written and easy to follow. I …
Abstract
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.78), and has published the reviews under the same license. These are as follows.
Reviewer 1. Takeshi Takeuchi
Is there sufficient data validation and statistical analyses of data quality?
Scaffolding with the Chicago and Hi-C libraries did not significantly improve the assembly. In general, Hi-C scaffolding can produce a chromosome-scale assembly. I would suggest that the authors describe the quality of the Chicago and Hi-C sequence data. For example, the mapping rates of the Chicago/Hi-C reads to the assembly should be informative.
**Reviewer 2. Yang Zhou **
This is a fascinating study on the assembly of the first deep-sea scleractinian coral, Lophelia pertusa. The manuscript is well-written and easy to follow. I have gone through your manuscript and would like you to address the following concerns/comments before publication.
Line 47: 1.2 454 pyrosequencing reads means 1.2Gb 454 pyrosequencing reads? Line 51-52: Please add some references. Line 72: As far as I know, the DNA extraction process of stony corals is affected by calcium carbonate skeletons. How did you deal with this problem during the DNA extraction process? References: Please double-check the references for errors. Italics for species names, capitalization of journal titles, and so on.
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