Towards a complete description of the genomes of marine uncultured stramenopiles using single cell genomics

Abstract

The emergence of single cell genomics in microbial ecology has offered a promising technology to retrieve genomic information from organisms that are ecologically relevant but still refractory to being cultured. However, single amplified genomes (SAGs) are based on whole-genome amplification and may suffer amplification bias, which questions about the possibility of acquiring complete genomes. A way to improve the completeness of the retrieved genomes is to co-assembly the sequencing data from cells that are supposed to derive from the same population. In this case, however, tests are needed to justify the mixing of different SAGs. In this study, several individual SAGs from 9 protistan stramenopiles ¿ribogroups¿ belonging to uncultured MASTs and Chrysophyceae have been firstly assembled and their respective tetranucleotide frequencies analysed using the ESOM tool. SAGs with similar tetranucleotide frequency profiles were then co-assembly and their completion estimated using CEGMA. Finally, the contribution of the different individual SAGs to the overall genome assembly has been analysed for estimating how many SAGs may be needed to complete different protists genomes, and whether this number changes in taxa of similar genome size