Saccharomyces cerevisiae strain:UOA_M2 Genome sequencing and assembly. Saccharomyces cerevisiae strain:UOA_M2

Two commercial winemaking yeasts, M2 and F15, were crossed and 96 recombinant F2 progeny were dissected from the F1 generation. Both parents and the 96 progeny strains were sequenced using 2nd generation sequencing platforms. The genome of M2 was assembled against a reference genome sequence as well as de novo. Sequence variant sites and copy number variants were identified between M2 and F15 on both assemblies and the 96 recombinant progeny were genotyped at these loci. A genetic map was built using the variant loci as markers. We used genetic linkage data to improve the whole genome assembly of one parent strain. First, duplication/translocation events detected through copy number variations were correctly mapped in the genome. Second, linkage data within de novo contigs was used to detect wrongly assembled contigs. Finally, linkage data between contigs was used to concatenate them into scaffolds and, eventually, whole chromosomes. This method represents an alternative and complementary approach to finishing genomes and may be particularly useful for assembling genomic sequences without a reference genome.