Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species

Jane E Stewart; Masato Kawabe; Zaid Abdo; Tsutomu Arie; Tobin L Peever

doi:10.1371/journal.pone.0020083

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Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species

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Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species

Jane E Stewart, Masato Kawabe, Zaid Abdo, Tsutomu Arie and Tobin L Peever

PloS one, Vol.6(5), pp.e20083-e20083

2011

DOI: https://doi.org/10.1371/journal.pone.0020083

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https://hdl.handle.net/2376/100386

PMCID: PMC3098265

PMID: 21625561

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Abstract

Biology

Sexual reproduction in heterothallic ascomycete fungi is controlled by a single mating-type locus called MAT1 with two alternate alleles or idiomorphs, MAT1-1 and MAT1-2 . These alleles lack sequence similarity and encode different transcriptional regulators. A large number of phytopathogenic fungi including Alternaria spp. are considered asexual, yet still carry expressed MAT1 genes. The molecular evolution of Alternaria MAT1 was explored using nucleotide diversity, nonsynonymous vs. synonymous substitution ( dn/ds ) ratios and codon usage statistics. Likelihood ratio tests of site-branch models failed to detect positive selection on MAT1-1-1 or MAT1-2-1 . Codon-site models demonstrated that both MAT1-1-1 and MAT1-2-1 are under purifying selection and significant differences in codon usage were observed between MAT1-1-1 and MAT1-2-1 . Mean GC content at the third position (GC3) and effective codon usage (ENC) were significantly different between MAT1-1-1 and MAT1-2-1 with values of 0.57 and 48 for MAT1-1-1 and 0.62 and 46 for MAT1-2-1 , respectively. In contrast, codon usage of Pleospora spp. (anamorph Stemphylium ), a closely related Dothideomycete genus, was not significantly different between MAT1-1-1 and MAT1-2-1 . The purifying selection and biased codon usage detected at the MAT1 locus in Alternaria spp. suggest a recent sexual past, cryptic sexual present and/or that MAT1 plays important cellular role(s) in addition to mating.

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Title: Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species
Creators: Jane E Stewart
Masato Kawabe
Zaid Abdo
Tsutomu Arie
Tobin L Peever
Publication Details: PloS one, Vol.6(5), pp.e20083-e20083
Academic Unit: Plant Pathology, Department of
Publisher: Public Library of Science; San Francisco, USA
Identifiers: 99900546573501842
Language: English
Resource Type: Journal article