Is single-cell genomics a useful technique to address evolutionary questions? Insights from three Monosiga brevicollis single-cell amplified genomes

Single-cell genomics techniques suffer from biases at whole genome amplification step which can lead to extremely variable numbers of genome recovery (5-100%). Thus, it is unclear whether this technique can be useful to address biological questions. To provide some insights into this, we analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known, with the aim to investigate whether the genomic information recovered by SCG is useful enough for evolutionary questions. Our results show that each SAG has a different, independent biases, yielding different levels of genome recovery (up to 36%). Genes can appear fragmented and often splitted in more genes during the annotation. However, protein domain recovery can be up to 55%. Meaning that the genomic information recovered from one single SAG can be enough to perform phylogenomics analyses, as well as to investigate interesting protein domains. However, gene/domain loses, gene architectures, sinteny and other genomic features can not be addressed with a SAG alone. We also confirm that co-assembly of several SAGs improves the general genomic recovery. Overall, SAGs can provide important insights from uncultured organisms, but it has some limitations that will be needed to be taken into account