Fig. 1.

Whole chromosome pairwise alignments of the mat chromosome of N. tetrasperma against N. crassa. The mat chromosome (chromosome 1) of the 10 high-quality de novo assemblies (eight N. tetrasperma, one N. sitophila and one N. intermedia) generated for this study (Table 1), together with two mat chromosomes from Lineage 6³⁰, were aligned to the N. crassa OR74A assembly³¹. Chromosomes are scaled in Mbp and only inverted regions larger than 100 kbp are shown. For N. tetrasperma, genomes of each of the two mating types from a single heterokaryon were sequenced separately. Each heterokaryon represent a phylogenetically distinct lineage (Lineages 1, 6, 7, 8 and 9)^27,33,34. The previously identified set of inversions in 2508 mat A (Lineage 6)³⁰ is the biggest inverted region identified in N. tetrasperma. Strain 965 mat A (Lineage 9) carries a 1.9 Mbp inversion surrounding the mat locus, CJ86 mat a (Lineage 8) carries a 260 kbp inversion and CJ73 mat A (Lineage 7) a 320 kbp inversion. Both mating type strains of Lineage 1 completely lack large inversions on this chromosome, as do the N. sitophila and N. intermedia genomes