Phased Diploid Genome Assemblies for Three Strains of from Oak Trees.

Although normally a harmless commensal, , it is also one of the most common causes of bloodstream infections in the U.S. has long been considered an obligate commensal, however, recent studies suggest it can live outside animal hosts. Here, we have generated PacBio sequences and phased genome assemblies for three strains from oak trees (NCYC 4144, NCYC 4145, and NCYC 4146). PacBio datasets are high depth (over 400 fold coverage) and more than half of the sequencing data are contained in reads longer than 15 kb. Primary assemblies showed high contiguity with several chromosomes for each strain recovered as single contigs, and greater than half of the alternative haplotype sequence was assembled in haplotigs at least 174 kb long. Using these assemblies we were able to identify structural polymorphisms, including a polymorphic inversion over 100 kb in length. These results show that phased diploid assemblies for can enable the study of genomic variation within and among strains of an important fungal pathogen.