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Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi.

Publication ,  Journal Article
Ke, Y-H; Branco, S; Bazzicalupo, AL; Nguyen, NH; Liao, H-L; Kennedy, P; Bruns, TD; Kuo, A; LaButti, K; Barry, K; Grigoriev, I; Vilgalys, R
Published in: Genetics
May 2023

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.

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Published In

Genetics

DOI

EISSN

1943-2631

ISSN

0016-6731

Publication Date

May 2023

Volume

224

Issue

2

Start / End Page

iyad069

Related Subject Headings

  • Polymorphism, Genetic
  • Plant Breeding
  • Phylogeny
  • Genomics
  • Genes, Mating Type, Fungal
  • Fungi
  • Evolution, Molecular
  • Developmental Biology
  • Basidiomycota
  • 3105 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
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Ke, Y.-H., Branco, S., Bazzicalupo, A. L., Nguyen, N. H., Liao, H.-L., Kennedy, P., … Vilgalys, R. (2023). Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi. Genetics, 224(2), iyad069. https://doi.org/10.1093/genetics/iyad069
Ke, Yi-Hong, Sara Branco, Anna L. Bazzicalupo, Nhu H. Nguyen, Hui-Ling Liao, Peter Kennedy, Thomas D. Bruns, et al. “Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi.Genetics 224, no. 2 (May 2023): iyad069. https://doi.org/10.1093/genetics/iyad069.
Ke Y-H, Branco S, Bazzicalupo AL, Nguyen NH, Liao H-L, Kennedy P, et al. Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi. Genetics. 2023 May;224(2):iyad069.
Ke, Yi-Hong, et al. “Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi.Genetics, vol. 224, no. 2, May 2023, p. iyad069. Epmc, doi:10.1093/genetics/iyad069.
Ke Y-H, Branco S, Bazzicalupo AL, Nguyen NH, Liao H-L, Kennedy P, Bruns TD, Kuo A, LaButti K, Barry K, Grigoriev I, Vilgalys R. Genomic determination of breeding systems and trans-specific evolution of HD MAT genes in suilloid fungi. Genetics. 2023 May;224(2):iyad069.

Published In

Genetics

DOI

EISSN

1943-2631

ISSN

0016-6731

Publication Date

May 2023

Volume

224

Issue

2

Start / End Page

iyad069

Related Subject Headings

  • Polymorphism, Genetic
  • Plant Breeding
  • Phylogeny
  • Genomics
  • Genes, Mating Type, Fungal
  • Fungi
  • Evolution, Molecular
  • Developmental Biology
  • Basidiomycota
  • 3105 Genetics