Chromosome-level genome assembly and transcriptome of the green algaChromochloris zofingiensisilluminates astaxanthin production

Abstract

Microalgae have potential to help meet energy and food demands without exacerbating environmental problems. There is interest in the unicellular green alga Chromochloris zofingiensis, because it produces lipids for biofuels and a highly valuable carotenoid nutraceutical, astaxanthin. To advance understanding of its biology and facilitate commercial development, we present a C. zofingiensis chromosome-level nuclear genome, organelle genomes, and transcriptome from diverse growth conditions. The assembly, derived from a combination of short-and long-read sequencing in conjunction with optical mapping, revealed a compact genome of ∼58 Mbp distributed over 19 chromosomes containing 15,274 predicted protein-coding genes. The genome has uniform gene density over chromosomes, low repetitive sequence content (∼6%), and a high fraction of protein-coding sequence (∼39%) with relatively long coding exons and few coding introns. Functional annotation of gene models identified orthologous families for the majority (∼73%) of genes. Synteny analysis uncovered localized but scrambled blocks of genes in putative orthologous relationships with other green algae. Two genes encoding beta-ketolase (BKT), the key enzyme synthesizing astaxanthin, were found in the genome, and both were up-regulated by high light. Isolation and molecular analysis of astaxanthin-deficient mutants showed that BKT1 is required for the production of astaxanthin. Moreover, the transcriptome under high light exposure revealed candidate genes that could be involved in critical yet missing steps of astaxanthin biosynthesis, including ABC transporters, cytochrome P450 enzymes, and an acyltransferase. The high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production.Chlorophyceae | carotenoid biosynthesis | de novo genome | genome mapping | RNA-Seq

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

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Novel insights into salinity-induced lipogenesis and carotenogenesis in the oleaginous astaxanthin-producing alga Chromochloris zofingiensis: a multi-omics study

“…The alga is also able to synthesize high-value ketocarotenoids and is thought to be a candidate astaxanthin producer alternative to Haematococcus pluvialis [16]. The robustness in concurrent accumulation of TAG and astaxanthin [11,14,17] and availability of chromosome-level genome sequence [18] enable C. zofingiensis as an emerging model alga for both fundamental studies and industrial applications. While many studies deal with the engineering of culture conditions for TAG and astaxanthin production by C. zofingiensis [9,11,12,14,17,[19][20][21][22], the molecular mechanisms underlying their biosynthesis are less touched and remain to be fully explored in a system-level manner.…”

Comparative genomics ofChlamydomonas

“…shown that the centromeric repeats in the Chlorophyceae species Chromochloris zofingiensis 383 consist of LTR elements from the Copia superfamily (Roth et al 2017). Secondly, the apparent 384 absence of ZeppL elements from Y. unicocca and V. carteri suggest that these elements are not 385 required for centromere formation in these species.…”