Analysis of three-cell amplified genomes of the Choanoflagellate Monosiga Brevicollis reveals single-cell genomics as a limited approach for evolutionary purposes

Abstract

Environmental metabarcoding data is providing a new view of the real protist diversity. This new diversity often occupies key phylogenetic positions which can led to important insights in the evolution of different eukaryotic lineages. This is the case of the Opisthokonta, in which the identification of new unicellular lineages close to animals has the potential to improve our understanding of the transition towards animal multicellularity. However, isolating these new organisms is a challenge. Instead, single-cell genomics (SCG) seems a prominsing approach to obtain directly the genomes from the environment. However, SCG technologies, which have mainly been employed in prokaryotes, are affected by important biases, specially during the whole genome amplification step. The potential of SGC for eukaryotes remains unclear. To test the potential of this technique for evolutionary studies in eukaryotes, we here analyze three environmental single amplified genomes (SAGs) from the choanoflagellate Monosiga brevicollis, whose genome is already sequenced. We show the genome recovery obtained from our SAGs was low (between 30-5%, around 3,684 out of 9,175 genes). Interestingly, the percentatge of pylogenomic markers that our SAGs contains is good (almost 100% for some datasets). We also explored different techniques to improve the quality and the recovery of the assemblies obtained. We found that genome recovery increased up to 48% by pooling the data from the three different SAGs. Current SCG technologies seem a limited approach for adressing some questions but has the potential to provide enough data for phylogenomic analyses.