An Inversion Polymorphism Under Balancing Selection, Involving Giant Mobile Elements, in an Invasive Fungal Pathogen

Area of Science:

• Genomics
• Evolutionary Biology
• Mycology

Background:

• Recombination suppression can drive evolution on sex chromosomes or supergenes.
• A genomic region in Cryphonectria parasitica was previously suggested to be nonrecombining and linked to the mating-type (MAT) locus.

Purpose of the Study:

• To investigate the recombination status and evolutionary history of the MAT-proximal region in Cryphonectria parasitica.
• To characterize the genetic makeup and diversity of haplotypes within this region.

Main Methods:

• Analysis of hundreds of existing C. parasitica genomes.
• Generation of new high-quality genome assemblies.
• Comparative genomic analyses to identify structural variations and sequence divergence.

Main Results:

• A ~1.2 Mb region proximal to the MAT locus lacks recombination in C. parasitica.
• Two highly differentiated haplotypes segregate in balanced proportions, with one showing an inversion in the invaded range.
• This region harbors specific genes, including transposable elements (Starships), and shows enrichment in nonsynonymous substitutions and gene presence/absence polymorphism.

Conclusions:

• A large, nonrecombining region linked to the MAT locus is maintained by balancing selection in C. parasitica.
• These haplotypes, possibly involved in adaptation, exhibit distinct evolutionary histories and genetic features.
• The findings illuminate mechanisms of adaptation in a significant tree pathogen.