New genomic insights into long-chain alkenone biosynthesis by the coccolithophorid marine alga Gephyrocapsa huxleyi

Abstract Background Gephyrocapsa huxleyi is a coccolithophoric haptophyte widespread across most marine ecosystems that plays an important role in the carbon cycle. G. huxleyi is one of the few haptophytes known to produce long-chain alkenones (LCAs), which are lipids composed of C 35 -C 42 n -alkyl chains, with two to four trans-double bonds and a keto group at either the 2nd or 3rd carbon positions, which are widely used as proxies for paleotemperature reconstruction. Despite the biomarker value of LCAs, little is known about their biosynthesis, which severely limits the understanding of the regulation of their production under different conditions, and thus their predictive nature. Differences in gene expression under different conditions may help to unravel the LCA biosynthetic pathway, but require annotated reference genomes. Although a large number of G. huxleyi strains inhabiting diverse ecosystems exist, only one such genome (i.e. of strain CCMP1516) is currently available. Results To evaluate differences in LCA biosynthesis under changing conditions, we developed a tailored approach to decontaminate and assemble the genomes of two additional non-axenic G. huxleyi strains (strains CCMP1742 and CCMP2758) that produce LCAs with two to four double bonds, one of which (CCMP2758) also produces unusually short (C 35 -C 36 ) LCAs. We identified a polyketide synthase (PKS) in strain CCMP1516, which we propose as a candidate to carry out LCA formation based on the structure and composition of its modules. Additionally, we identified several CCMP1742 and CCMP2758 PKSs that were differentially expressed between temperatures and across time that closely resemble this PKS and are likely to be involved in LCA formation. Based on differences in gene expression between two different growth temperatures, we also identified a limited number of desaturases which are potentially responsible for the addition of the third and fourth double bonds in the LCAs produced by these strains. Conclusions Here, we advance the understanding of biosynthesis of LCAs, important molecules for paleotemperature reconstruction, in the marine haptophyte G. huxleyi . By assembling the genomes of two LCA-producing strains, we were able to overcome the limitations of the scarcity of reference genomes of this group, enabling the analysis of gene expression under varying growth conditions and the identification of PKSs and desaturases potentially involved in LCA biosynthesis. These findings constitute a step forward in elucidating the genetic basis for LCA production and regulation in G. huxleyi , which not only advances our understanding on how LCAs are formed but also aids in the improvement of LCA-based paleotemperature reconstructions.