Abstract
The heterotrophic stramenopile Cafeteria roenbergensis is a globally distributed marine bacterivorous protist. This unicellular flagellate is host to the giant DNA virus CroV and the virophage mavirus. We sequenced the genomes of four cultured C. roenbergensis strains and generated 23.53 Gb of Illumina MiSeq data (99–282 × coverage per strain) and 5.09 Gb of PacBio RSII data (13–45 × coverage). Using the Canu assembler and customized curation procedures, we obtained high-quality draft genome assemblies with a total length of 34–36 Mbp per strain and contig N50 lengths of 148 kbp to 464 kbp. The C. roenbergensis genome has a GC content of ~70%, a repeat content of ~28%, and is predicted to contain approximately 7857–8483 protein-coding genes based on a combination of de novo, homology-based and transcriptome-supported annotation. These first high-quality genome assemblies of a bicosoecid fill an important gap in sequenced stramenopile representatives and enable a more detailed evolutionary analysis of heterotrophic protists.
Highlights
Background & SummaryThe diversity of eukaryotes lies largely among its unicellular members, the protists
We recently showed that mavirus can exist as an integrated provirophage in C. roenbergensis and provide resistance against CroV infection on a host-population level[10]
We selected and sequenced four strains of C. roenbergensis isolated from different locations in the Atlantic (Woods Hole, MA, USA; British Virgin Islands) and the Pacific (Yaquina Bay, OR, USA; South Pacific Ocean, 2200 km off the coast of Chile) (Table 1)
Summary
The diversity of eukaryotes lies largely among its unicellular members, the protists. Genomic exploration of eukaryotic microbes lags behind that of animals, plants, and fungi[1] One of these neglected groups is the Bicosoecida within the Stramenopiles, which contains the widespread marine heterotrophic flagellate, Cafeteria roenbergensis[2,3,4,5,6]. Based on read coverage we estimate that CrCflag carries 18 haploid copies of the operon, CrRCC970-E3 21, CrBVI 63 and CrE4-10P 83. Variation on this scale has been observed as a common feature of marine eukaryotic plankton[26], it is surprising to find this much variation among such closely related strains. The Cafeteria genome may provide insights into possible sexual processes and how its evolution is influenced by mobile genetic elements
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