Biology Department, Duke University, 130 Science Dr, Durham, NC 27708, USA.
Integrative Biology, University of Colorado, 1151 Arapahoe St, SI 2071, Denver, CO 80204, USA.
Genetics. 2023 May 26;224(2). doi: 10.1093/genetics/iyad069.
Studying the signatures of evolution can help to understand genetic processes. Here, we demonstrate how the existence of balancing selection can be used to identify the breeding systems of fungi from genomic data. The breeding systems of fungi are controlled by self-incompatibility loci that determine mating types between potential mating partners, resulting in strong balancing selection at the loci. Within the fungal phylum Basidiomycota, two such self-incompatibility loci, namely HD MAT locus and P/R MAT locus, control mating types of gametes. Loss of function at one or both MAT loci results in different breeding systems and relaxes the MAT locus from balancing selection. By investigating the signatures of balancing selection at MAT loci, one can infer a species' breeding system without culture-based studies. Nevertheless, the extreme sequence divergence among MAT alleles imposes challenges for retrieving full variants from both alleles when using the conventional read-mapping method. Therefore, we employed a combination of read-mapping and local de novo assembly to construct haplotypes of HD MAT alleles from genomes in suilloid fungi (genera Suillus and Rhizopogon). Genealogy and pairwise divergence of HD MAT alleles showed that the origins of mating types predate the split between these two closely related genera. High sequence divergence, trans-specific polymorphism, and the deeply diverging genealogy confirm the long-term functionality and multiallelic status of HD MAT locus in suilloid fungi. This work highlights a genomics approach to studying breeding systems regardless of the culturability of organisms based on the interplay between evolution and genetics.
研究进化的特征可以帮助我们理解遗传过程。在这里，我们展示了如何利用平衡选择的存在，从基因组数据中识别真菌的繁殖系统。真菌的繁殖系统由自交不亲和基因座控制，这些基因座决定潜在交配伙伴之间的交配类型，从而导致基因座上的强烈平衡选择。在真菌门担子菌中，有两个这样的自交不亲和基因座，即 HD MAT 基因座和 P/R MAT 基因座，控制着配子的交配类型。一个或两个 MAT 基因座的功能丧失会导致不同的繁殖系统，并使 MAT 基因座摆脱平衡选择的束缚。通过研究 MAT 基因座上平衡选择的特征，我们可以在无需进行基于培养的研究的情况下推断出一个物种的繁殖系统。然而，MAT 等位基因之间的极端序列分化给使用传统的读映射方法从两个等位基因中检索完整变体带来了挑战。因此，我们采用了读映射和局部从头组装的组合方法，从 Suilloid 真菌（Suillus 和 Rhizopogon 属）的基因组中构建了 HD MAT 等位基因的单倍型。HD MAT 等位基因的系统发育和成对分歧表明，交配类型的起源早于这两个密切相关的属的分化。高序列分化、跨种多态性和深度分化的系统发育证实了 HD MAT 基因座在 Suilloid 真菌中的长期功能和多等位基因状态。这项工作强调了一种基于进化和遗传学相互作用的基因组学方法，无论生物体是否可培养，都可以用来研究繁殖系统。
