Pseudogenization in pathogenic fungi with different host plants and lifestyles might reflect their evolutionary past

Summary Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non‐ or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identifica...

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Published inMolecular plant pathology Vol. 15; no. 2; pp. 133 - 144
Main Authors van der Burgt, Ate, Karimi Jashni, Mansoor, Bahkali, Ali H., de Wit, Pierre J. G. M.
Format Journal Article
LanguageEnglish
Published England Blackwell Publishing Ltd 01.02.2014
John Wiley & Sons, Inc
John Wiley and Sons Inc
Subjects
Botrytis cinerea
Cladosporium fulvum
Fungi
Fungi - genetics
Fungi - pathogenicity
gene
Genes
Genes, Fungal
Genomes
genomics
locus
Lycopersicon esculentum
Mutation
Mycosphaerella fijiensis
Original
Plants - microbiology
prediction
proteins
Pseudogenes
resistance
software
update
Verticillium dahliae
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Summary:Summary Pseudogenes are genes with significant homology to functional genes, but contain disruptive mutations (DMs) leading to the production of non‐ or partially functional proteins. Little is known about pseudogenization in pathogenic fungi with different lifestyles. Here, we report the identification of DMs causing pseudogenes in the genomes of the fungal plant pathogens Botrytis cinerea, Cladosporium fulvum, Dothistroma septosporum, Mycosphaerella fijiensis, Verticillium dahliae and Zymoseptoria tritici. In these fungi, we identified 1740 gene models containing 2795 DMs obtained by an alignment‐based gene prediction method. The contribution of sequencing errors to DMs was minimized by analyses of resequenced genomes to obtain a refined dataset of 924 gene models containing 1666 true DMs. The frequency of pseudogenes varied from 1% to 5% in the gene catalogues of these fungi, being the highest in the asexually reproducing fungus C. fulvum (4.9%), followed by D. septosporum (2.4%) and V. dahliae (2.1%). The majority of pseudogenes do not represent recent gene duplications, but members of multi‐gene families and unitary genes. In general, there was no bias for pseudogenization of specific genes in the six fungi. Single exceptions were those encoding secreted proteins, including proteases, which appeared more frequently pseudogenized in C. fulvum than in D. septosporum. Most pseudogenes present in these two phylogenetically closely related fungi are not shared, suggesting that they are related to adaptation to a different host (tomato versus pine) and lifestyle (biotroph versus hemibiotroph).
Bibliography:Fig. S1 Distance of pseudogenes to repetitive sequence or scaffold boundary.Fig. S2 Distance of pseudogenes from repeat-induced point mutation (RIP) loci.Fig. S3 Inter-pseudogene distances.Table S1 The 28 informant species used for Alignment-Based Fungal Gene Prediction (ABFGP).Table S2 Expression evidence of pseudogenes and false discovery estimation of disruptive mutations (DMs) by Alignment-Based Fungal Gene Prediction (ABFGP) measured on unigene data.Table S3 Sequences of primers used for resequencing disruptive mutations in secreted proteases of Cladosporium fulvum.Table S4 Six strains of Cladosporium fulvum used to confirm the presence of predicted disruptive mutations (DMs) in secreted proteases.Table S5 Pseudogene distribution over the chromosomes of Zymoseptoria tritici.Table S6 Pseudogene distribution over the chromosomes of Dothistroma septosporum.Table S7 Directly adjacent pseudogenized gene pairs and triplet in Dothistroma septosporum.Table S8 Directly adjacent pseudogenized gene pairs and triplet in Cladosporium fulvum.Table S9 Functional prediction of 924 pseudogenes by assignment of PFAM domains.Table S10 Hundreds of additional pseudogenes in the Capnodiales species Cladosporium fulvum, Dothistroma septosporum and Zymoseptoria tritici detected on the basis of similarity to known proteins.Table S11 Twenty-two pseudogenes shared between Cladosporium fulvum and Dothistroma septosporum.Method S1 Removal of sequence errors from predicted disruptive mutations (DMs) by comparison with next-generation sequencing assemblies of four genomes with low coverage.Method S2 Observed pattern of substitutions is explained by determinants of random DNA mutation alone.Method S3 Additional pseudogenes in Cladosporium fulvum, Dothistroma septosporum and Zymoseptoria tritici identified by pairwise comparisons.Datafile S1 Protein sequences of 924 pseudogenes including 1662 disruptive mutations.Datafile S2 General Feature Format (GFF) annotation of 674 additional pseudogenes identified in the Capnodiales species Cladosporium fulvum, Dothistroma septosporum and Zymoseptoria tritici.
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ArticleID:MPP12072
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content type line 23
ISSN:1464-6722
1364-3703
DOI:10.1111/mpp.12072