The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization

Abstract

We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

“…This yielded 9,129 gene models ( Table 1). This total is relatively close to the number of gene models in N. crassa 12 , but is roughly 2,500 fewer than the number of predicted genes in Fusarium graminearum 13 (anamorph, Gibberella zeae)-a surprising difference, given that F. graminearum and T. reesei share the most recent common ancestor among the genomes listed in Table 1 (ref. 14).…”

“…To gain insight into the effect of the environment on genome evolution, we constructed a comparative map by calculating syntenic regions shared by T. reesei, F. graminearum 13 and N. crassa 12 (Supplementary Table 2 online). As noted in other studies 15 , this map ( Fig.…”

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

“…To generate the species tree, a total of 90 orthologous genes from P. chrysogenum, P. marneffei (GenBank ABAR00000000), T. stipitatus (GenBank ABAS00000000), A. niger 16 , A. nidulans 10 , A. oryzae 15 , A. fumigatus 12 , A. clavatus (GenBank AAKD00000000), A. terreus (Refseq NT_165925-NT_165951), Neosartorya fischeri (GenBank AAKE00000000) and Gibberella zeae (anamorph Fusarium graminearum) 49 were aligned at the amino acid level (Supplementary Table 22 online). To minimize the effect of incorrect or incongruent gene models, these proteins were chosen on the basis of having identical numbers of introns in each species and similar lengths (95% overlap).…”

Genome-Wide Analysis of the Fusarium oxysporum mimp Family of MITEs and Mobilization of Both Native and De Novo Created mimps

“…Alternatively, the observed discrepancy between insertional preference of endogenous mimp2 elements in F. oxysporum and newly transposed mimp2 copies in F. graminearum could be due to structural differences between the two genomes. The genome of F. graminearum is characterized by a high gene density and a remarkable paucity in repeated sequences (Cuomo et al 2007). In contrast, F. oxysporum genome exhibits a high expansion of repeated sequences together with the occurrence of several large segmental duplications.…”