Abstract
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
B
otrytis cinerea
,
C
ladosporium fulvum
,
D
othistroma septosporum
,
M
ycosphaerella fijiensis
,
V
erticillium dahliae
and
Z
ymoseptoria 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).