Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing

Michael G. Milgroom, Maria Del Mar Jimenez Gasco, Concepción Olivares-García, Milton T. Drott, Rafael M. Jiménez-D́iaz

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Abstract

Most asexual species of fungi have either lost sexuality recently, or they experience recombination by cryptic sexual reproduction. Verticillium dahliae is a plant-pathogenic, ascomycete fungus with no known sexual stage, even though related genera have well-described sexual reproduction. V. dahliae reproduces mitotically and its population structure is highly clonal. However, previously described discrepancies in phylogenetic relationships among clonal lineages may be explained more parsimoniously by recombination than mutation; therefore, we looked for evidence of recombination within and between clonal lineages. Genotyping by sequencing was performed on 141 V. dahliae isolates from diverse geographic and host origins, resulting in 26,748 single-nucleotide polymorphisms (SNPs). We found a strongly clonal population structure with the same lineages as described previously by vegetative compatibility groups (VCGs) and molecular markers. We detected 443 recombination events, evenly distributed throughout the genome. Most recombination events detected were between clonal lineages, with relatively few recombinant haplotypes detected within lineages. The only three isolates with mating type MAT1-1 had recombinant SNP haplotypes; all other isolates had mating type MAT1-2. We found homologs of eight meiosis-specific genes in the V. dahliae genome, all with conserved or partially conserved protein domains. The extent of recombination and molecular signs of sex in (mating-type and meiosis-specific genes) suggest that V. dahliae clonal lineages arose by recombination, even though the current population structure is markedly clonal. Moreover, the detection of new lineages may be evidence that sexual reproduction has occurred recently and may potentially occur under some circumstances. We speculate that the current clonal population structure, despite the sexual origin of lineages, has arisen, in part, as a consequence of agriculture and selection for adaptation to agricultural cropping systems.

Original languageEnglish (US)
Article numbere106740
JournalPloS one
Volume9
Issue number9
DOIs
StatePublished - Jan 1 2014

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Verticillium
Verticillium dahliae
Fungi
Genetic Recombination
genotyping
Genes
population structure
fungi
sexual reproduction
Polymorphism
Nucleotides
meiosis
Reproduction
single nucleotide polymorphism
haplotypes
Meiosis
teleomorphs
Haplotypes
Population
Single Nucleotide Polymorphism

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Milgroom, Michael G. ; Jimenez Gasco, Maria Del Mar ; Olivares-García, Concepción ; Drott, Milton T. ; Jiménez-D́iaz, Rafael M. / Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing. In: PloS one. 2014 ; Vol. 9, No. 9.
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abstract = "Most asexual species of fungi have either lost sexuality recently, or they experience recombination by cryptic sexual reproduction. Verticillium dahliae is a plant-pathogenic, ascomycete fungus with no known sexual stage, even though related genera have well-described sexual reproduction. V. dahliae reproduces mitotically and its population structure is highly clonal. However, previously described discrepancies in phylogenetic relationships among clonal lineages may be explained more parsimoniously by recombination than mutation; therefore, we looked for evidence of recombination within and between clonal lineages. Genotyping by sequencing was performed on 141 V. dahliae isolates from diverse geographic and host origins, resulting in 26,748 single-nucleotide polymorphisms (SNPs). We found a strongly clonal population structure with the same lineages as described previously by vegetative compatibility groups (VCGs) and molecular markers. We detected 443 recombination events, evenly distributed throughout the genome. Most recombination events detected were between clonal lineages, with relatively few recombinant haplotypes detected within lineages. The only three isolates with mating type MAT1-1 had recombinant SNP haplotypes; all other isolates had mating type MAT1-2. We found homologs of eight meiosis-specific genes in the V. dahliae genome, all with conserved or partially conserved protein domains. The extent of recombination and molecular signs of sex in (mating-type and meiosis-specific genes) suggest that V. dahliae clonal lineages arose by recombination, even though the current population structure is markedly clonal. Moreover, the detection of new lineages may be evidence that sexual reproduction has occurred recently and may potentially occur under some circumstances. We speculate that the current clonal population structure, despite the sexual origin of lineages, has arisen, in part, as a consequence of agriculture and selection for adaptation to agricultural cropping systems.",
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Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing. / Milgroom, Michael G.; Jimenez Gasco, Maria Del Mar; Olivares-García, Concepción; Drott, Milton T.; Jiménez-D́iaz, Rafael M.

In: PloS one, Vol. 9, No. 9, e106740, 01.01.2014.

Research output: Contribution to journalArticle

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