Chromosome-level genome assembly and DNA methylation data of the oleaginous astaxanthin-producing alga Chromochloris zofingiensis

Chromochloris zofingiensis has emerged as a promising economic microalgal strain owing to its capacity for the integrated production of triacylglycerol (TAG) and astaxanthin. To advance its development as a robust model alga for studying lipid metabolism and astaxanthin biosynthesis, we performed a comprehensive genome sequencing strategy integrating Nanopore long-reads and Illumina short-reads, together with Hi-C and PacBio full-length transcriptome sequencing. This enabled an improved chromosome-level genome assembly comprising of 17 chromosomes with a total size of 57.09 Mb and a scaffold N50 of 3.18 Mb. In total, 94.85% of the assembled sequences are anchored on 17 chromosomes. Compared to the sole published genome draft, the new assembly exhibits substantial enhancements in completeness and accuracy, with 12,480 protein-coding genes predicted. Furthermore, we presented the first genome-wide DNA methylation landscape of C. zofingiensis through the combined analysis of Nanopore and Bisulfite sequencing data. In summary, this improved, chromosome-scale genome provides a valuable genetic resource for in-depth molecular research and genetic engineering of this oleaginous astaxanthin-producing alga.