Haematococcus lacustris genome assembly and annotation reveal diploid genetic traits and stress-induced gene expression patterns

Abstract

The green alga <i>Haematococcus lacustris</i> (formerly <i>Haematococcus pluvialis</i>) is a primary source of astaxanthin, a ketocarotenoid with high antioxidant activity and several industrial applications. Here, the <i>Haematococcus lacustris</i> highly repetitive genome was reconstructed by exploiting next-generation sequencing integrated with Hi-C scaffolding, obtaining a 151 Mb genome assembly in 32 scaffolds at a near-chromosome level with high continuity. Surprisingly, the distribution of the single-nucleotide-polymorphisms identified demonstrates a diploid configuration for the <i>Haematococcus</i> genome, further validated by Sanger sequencing of heterozygous regions. Functional annotation and RNA-seq data enabled the identification of 13,946 nuclear genes, with >5000 genes not previously identified in this species, providing insights into the molecular basis for metabolic rear-rangement in stressing conditions such as high light and/or nitrogen starvation, where astaxanthin biosynthesis is triggered. These data constitute a rich genetic resource for biotechnological manipulation of <i>Haematococcus lacustris</i> highlighting potential targets to improve astaxanthin and carotenoid productivity.