Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma

Abstract

Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of nondegenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes.We found that suppressed recombination extends across at least 6 Mbp (∼ 63%) of the mating-type (mat) chromosome in N. tetrasperma and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six of eight lineages show introgression into one of their mat chromosomes, with multiple Neurospora species acting as donors. The introgressed tracts have been fixed within lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one lineage. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.

Figure 1.

The global pattern of variation in N. tetrasperma. (A) The phylogenetic relationships of all N. tetrasperma strains used in this study, inferred from 2,259,433 variable sites on the autosomes. A subtree excluding N. discreta, N. crassa, and N. hispaniola is shown. Numbers on the branches indicate the bootstrap support for that relationship expressed as a proportion. (B) Principal component analysis (PCA) of genetic variation (509,199 biallelic autosomal SNPs) across the global sample of N. tetrasperma strains. The first two principal components are shown. (C) Population structure of N. tetrasperma inferred from 9000 SNPs (1500 from each of the six autosomes) using InStruct at K = 6. Lineages color coded in A, B, and C according to the legend in B. (LA) Louisiana; (NZ) New Zealand; (UK) United Kingdom; (HI) Hawaii; (MX) Mexico; (LB) Liberia.

Figure 2.

Pair-wise divergences between the mat A and mat a homokaryons sampled from the same heterokaryon for the mat chromosomes (linkage group I) and six autosomes (II–VII) of representatives from all N. tetrasperma lineages. Each linkage group is shown in a separate row (labeled on the right). The pair-wise divergences were calculated as the fraction of differences (in bp) between the sequences, using a 100-kb sliding window (step size 20 kb). (LA) Louisiana; (NZ) New Zealand; (UK) United Kingdom; (HI) Hawaii; (MX) Mexico; (LB) Liberia.

Figure 3.

Patterns of genetic variation across the mat chromosome for N. tetrasperma lineages L5, L8, and L10. (A) Linkage disequilibrium given as the mean Pearson's correlation coefficient (r²). The vertical black line shows the position of the mat a locus in the 2509 reference genome. (B) Nucleotide diversity (π), Tajima's D (Tajima 1989), and Fay and Wu's H (Fay and Wu 2000). For all variables, we used a 100-kb window size (step size 20 kb). The values for each window are represented by the gray points, and smooth lines were plotted with stat_smooth in the ggplot2 R package using the gam method with a span of 0.2. Dashed vertical lines indicate lineage-specific limits of the SR region.

Figure 4.

Introgression of large chromosomal regions from heterothallic Neurospora to N. tetrasperma. (A) Diagrams showing the genealogy of the mat chromosome SR region in a N. tetrasperma lineage when suppression of recombination had begun at SR Time. The shaded regions show that a lineage is in SR. The models from left to right show expected relationships in the absence of introgression, SR A introgression, and SR a introgression. (B) Box plots of mean divergence between L10, L7, and L9 in the SR region. Asterisks above the horizontal black lines are the P-values for the Mann-Whitney U test between SR regions within a lineage: (***) P < 0.001; (n.s.) nonsignificant. (C) Pair-wise divergences between the mat chromosomes of N. tetrasperma strains and the heterothallic species N. crassa, N. hispaniola, and N. sitophila. Each row in the figure shows the sequence divergence between a strain of N. tetrasperma and the heterothallic species indicated in the heading of the column, using a nonoverlapping sliding window of 25 kb. N. tetrasperma strains are sorted by lineage and according to mating type. Regions lacking a sufficient number of sites (2500 sites) are colored gray. A maximum divergence of up to 0.06 is plotted, and windows exceeding this are colored gray.

Figure 5.

The phylogenetic relationships of Neurospora strains in the PAR and SR regions common to all N. tetrasperma lineages. The SR tree was reconstructed from a concatenated data set of six genes and the PAR tree from two genes (see Supplemental Table 12). The heterothallic species are in blue, and N. tetrasperma lineages in red. Numbers on the branches are bootstrap support values expressed as a percentage; values below 70 are not shown.