Abstract
Single-cell genomics (SCG) appeared as a powerful technique to get genomic information from uncultured organisms. However, SCG techniques suffer from biases at the whole genome amplification step that can lead to extremely variable numbers of genome recovery (5–100%). Thus, it is unclear how useful can SCG be to address evolutionary questions on uncultured microbial eukaryotes. To provide some insights into this, we here analysed 3 single-cell amplified genomes (SAGs) of the choanoflagellate Monosiga brevicollis, whose genome is known. Our results show that each SAG has a different, independent bias, yielding different levels of genome recovery for each cell (6–36%). Genes often appear fragmented and are split into more genes during annotation. Thus, analyses of gene gain and losses, gene architectures, synteny and other genomic features can not be addressed with a single SAG. However, the recovery of phylogenetically-informative protein domains can be up to 55%. This means SAG data can be used to perform accurate phylogenomic analyses. Finally, we also confirm that the co-assembly of several SAGs improves the general genomic recovery. Overall, our data show that, besides important current limitations, SAGs can still provide interesting and novel insights from poorly-known, uncultured organisms.
Highlights
In the last decade, molecular techniques based in the sequence of 18 S rDNA gene have deciphered an impressive amount of hidden eukaryotic diversity[1,2,3,4,5]
As Multiple Displacement Amplification (MDA) can lead to the generation of chimeric DNA fragments[36] and the amplification of sample contaminants, we first mapped these reads to the M. brevicollis reference genome and observed that the number of aligned reads varied widely among the different single-cell amplified genomes (SAGs)
Even though MB2 presented a higher percentage of read mapping, those reads were extremely biased towards a few genomic regions (Fig. 1a)
Summary
Molecular techniques based in the sequence of 18 S rDNA gene have deciphered an impressive amount of hidden eukaryotic diversity[1,2,3,4,5]. A study focused in an uncultured group of marine stramenopiles (MAST)[29], showed that by co-assembling different SAGs from different cells the genome recovered increased substantially[28]. It remains yet unclear the full potential of this methodology and how to best approach the analyses of the data recovered from SAGs. it remains yet unclear the full potential of this methodology and how to best approach the analyses of the data recovered from SAGs These are important questions because the scientific community is generating more SCG data. We show that co-assembly of several SAGs improves the general genomic recovery
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