View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

Chlamydomonas reinhardtii is a single-celled green alga and model organism of the plant kingdom exhibiting high intraspecies diversity with a small, relatively well-characterized genome ~110 Mb in size. These features, combined with its haplontic, easily manipulable life cycle and existing mating and tetrad separation protocols, make it an optimal species in which to study meiotic recombination. After mating a pair of divergent parental lines, genome-wide recombination patterns were analyzed across a set of ~1.5 million variant positions in ~500 strains from ~200 tetrads. This analysis led to the identification of chromosomal regions of suspected misassembly in the reference genome. This discovery, in combination with the existence of several dozen known unmapped scaffolds, prompted us to develop a novel genome reassembly protocol using linkage analysis to properly reconstruct the C. reinhardtii reference genome. Reassembly procedures that use linkage analysis traditionally involve using a set of independent samples that are each genotyped with high confidence at the same set of loci. This approach, however, is rather limited because sequencing depth, contamination rates and genotyping error rates can vary greatly depending on genomic content, budgetary constraints, and sequencing protocols. We developed a procedure that borrows information from neighboring genotyped variant positions to smooth out uncertainties in genotype caused by low sequencing depth, non-negligible contamination, and other sources of error, and we additionally accounted for the correlation in genotype between samples from the same tetrad. Using this robust approach, we then chose optimal locations to break existing chromosomes/scaffolds into new contigs that were reassembled into groups of ordered sets, making up new chromosomes. The accuracy of these new chromosomes was then confirmed and improved upon using discordant reads of various template sizes. In total, our linkage analysis yielded several dozen large-scale changes to the genome, the vast majority of which were strongly supported by the presence of discordant read connections spanning contig boundaries. Over the coming months, we will be explicitly comparing our new reference genome to the recently released JGI C. reinhardtii genome assembled using third-generation sequencing. With this new JGI genome, we will generate the recombination landscape to document the genome-wide profile of crossover and gene conversion events for the first time in unicellular algae.

Genome reassembly in Chlamydomonas reinhardtii: A novel approach

**Genome reassembly in Chlamydomonas reinhardtii: A novel approach**