General comment:
The author has done a well-designed study of an effective hybrid genome model for Chinese herbal plant danshen. To improve the genome assembly, authors propose a novel computational pipeline for danshen combining Illumina data and PacBio data. The genome-related experiment is well-justified, and the method will help other researchers to further dig out assembling related genome in other population groups. However, I have several comments on this manuscript.

1. In the Danshen genomic DNA sequencing on Illumina platforms, what is the standard used in assigning the clean data?

- In total, 1.88 billion and 225 Gb -> 147 Gb clean data were obtained.

2. In the Gene family clustering analysis, why don't evaluate the your homology-based samples (i.e., Arabidopsis thaliana, … , and Ensembl 33 other plants)?

- To confirm or verify the 1,147 unique genes, author only use to compare the using 4 accessions including Coffea canephora (i.e., It is NOT homology-based samples) for clustering analysis. If homology based prediction of Coffea canephora analysis result is described, I think which it is another evidence for your proposal model.

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