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mpp12072-sup-0002-figures1.doc55K

Fig. S1 Distance of pseudogenes to repetitive sequence or scaffold boundary.

mpp12072-sup-0003-figures2.doc56K

Fig. S2 Distance of pseudogenes from repeat-induced point mutation (RIP) loci.

mpp12072-sup-0004-figures3.doc42K

Fig. S3 Inter-pseudogene distances.

mpp12072-sup-0008-tables1.doc64K

Table S1 The 28 informant species used for Alignment-Based Fungal Gene Prediction (ABFGP).

mpp12072-sup-0009-tables2.doc58K

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.

mpp12072-sup-0010-tables3.doc52K

Table S3 Sequences of primers used for resequencing disruptive mutations in secreted proteases of Cladosporium fulvum.

mpp12072-sup-0011-tables4.doc46K

Table S4 Six strains of Cladosporium fulvum used to confirm the presence of predicted disruptive mutations (DMs) in secreted proteases.

mpp12072-sup-0012-tables5.doc41K

Table S5 Pseudogene distribution over the chromosomes of Zymoseptoria tritici.

mpp12072-sup-0013-tables6.doc45K

Table S6 Pseudogene distribution over the chromosomes of Dothistroma septosporum.

mpp12072-sup-0014-tables7.doc49K

Table S7 Directly adjacent pseudogenized gene pairs and triplet in Dothistroma septosporum.

mpp12072-sup-0015-tables8.doc70K

Table S8 Directly adjacent pseudogenized gene pairs and triplet in Cladosporium fulvum.

mpp12072-sup-0016-tables9.doc1438K

Table S9 Functional prediction of 924 pseudogenes by assignment of PFAM domains.

mpp12072-sup-0017-tables10.doc44K

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.

mpp12072-sup-0018-tables11.doc53K

Table S11 Twenty-two pseudogenes shared between Cladosporium fulvum and Dothistroma septosporum.

mpp12072-sup-0005-methods1.doc71K

Method S1 Removal of sequence errors from predicted disruptive mutations (DMs) by comparison with next-generation sequencing assemblies of four genomes with low coverage.

mpp12072-sup-0006-methods2.doc67K

Method S2 Observed pattern of substitutions is explained by determinants of random DNA mutation alone.

mpp12072-sup-0007-methods3.doc53K

Method S3 Additional pseudogenes in Cladosporium fulvum, Dothistroma septosporum and Zymoseptoria tritici identified by pairwise comparisons.

mpp12072-sup-0001-datas1.docx390K

Datafile S1 Protein sequences of 924 pseudogenes including 1662 disruptive mutations.

mpp12072-sup-0001-data_s2.tar.zip0K

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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