Lieschen De Vos

IMA Genome-F 2: Ceratocystis manginecans, Ceratocystis moniliformis, Diplodia sapinea: Draft genome sequences of Diplodia sapinea, Ceratocystis manginecans, and Ceratocystis moniliformis.

The draft nuclear genomes of Diplodia sapinea, Ceratocystis moniliformis s. str., and C. manginecans are presented. Diplodia sapinea is an important shoot-blight and canker pathogen of Pinus spp., C. moniliformis is a saprobe associated with wounds on a wide range of woody angiosperms and C. manginecans is a serious wilt pathogen of mango and Acacia mangium. The genome size of D. sapinea is estimated at 36.97 Mb and contains 13 020 predicted genes. Ceratocystis moniliformis includes 25.43 Mb and is predicted to encode at least 6 832 genes. This is smaller than that reported for the mango wilt pathogen C. manginecans which is 31.71 Mb and is predicted to encode at least 7 494 genes. The latter is thus more similar to C. fimbriata s.str., the type species of the genus. The genome sequences presented here provide an important resource to resolve issues pertaining to the taxonomy, biology and evolution of these fungi.

IMA Genome-F 4: Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata.

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.

Molecular Characterization of Fusarium globosum Strains from South African Maize and Japanese Wheat

The fungus Fusarium globosum was first isolated from maize in South Africa and subsequently from wheat in Japan. Here, multiple analyses revealed that, despite morphological similarities, South African maize and Japanese wheat isolates of the fungus exhibit multiple differences. An amplified fragment length polymorphism-based similarity index for the two groups of isolates was only 45%. Most maize isolates produced relatively high levels of fumonisins, whereas wheat isolates produced little or no fumonisins. The fumonisin biosynthetic gene FUM1 was detected in maize isolates by Southern blot analysis but not in the wheat isolates. In addition, most of the maize isolates produced sclerotia, and all of them produced large orange to dark purple sporodochia in carrot agar culture, whereas wheat isolates did not produce either structure. In contrast, individual isolates from both maize and wheat carried markers for both mating type idiomorphs, which indicates that the fungus may be homothallic. However, a sexual stage of F. globosum was not formed under standard self-fertilization conditions developed for other homothallic species of Fusarium. The inability to produce the sexual stage is consistent with the high similarity of 87–100% and GST index of 1.72 for the maize isolates, which suggests that these isolates are undergoing asexual but not sexual reproduction. Together, the results suggest that the South African maize and Japanese wheat isolates of F. globosum are distinct populations and could be different species.

Genome-Wide Macrosynteny among Fusarium Species in the Gibberella fujikuroi Complex Revealed by Amplified Fragment Length Polymorphisms

The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including Fusarium circinatum, Fusarium fujikuroi and Fusarium verticillioides, each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between Fusarium temperatum and F. circinatum, together with genomic sequence data, was utilized to consider the level of synteny between the three Fusarium genomes. Regions that are homologous amongst the Fusarium genomes examined were identified using in silico and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to F. fujikuroi and F. verticillioides. This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in F. verticillioides and F. fujikuroi, as well as to assign two previously unmapped supercontigs of F. verticillioides to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of F. circinatum and F. temperatum. Overall, a remarkable level of macrosynteny was observed among the three Fusarium genomes, when comparing AFLP fragments. This study not only demonstrates how in silico AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.

Genetic analysis of growth, morphology and pathogenicity in the F1 progeny of an interspecific cross between Fusarium circinatum and Fusarium subglutinans

Fusarium circinatum and Fusarium subglutinans are two distinct species in the Gibberella fujikuroi species complex. A genetic linkage map produced from an interspecific cross between these species was used to identify quantitative trait loci (QTLs) associated with variation in mycelial growth and morphology of colony margins (CMs) in the 94 F(1) progeny. Mycelial growth was assessed by measuring culture size at 25°C and 30°C, while CM morphology was characterized in the parents and assessed in their F(1) progeny. In order to test the pathogenicity of the progeny, Pinus patula seedlings were inoculated and lesion lengths were measured after 3weeks. Seven putative QTLs were associated with mycelial growth, three for growth at 25°C and four at 30°C. One highly significant QTL (P<0.001) was present at both growth temperatures. For CM morphology, a QTL was identified at the same position (P<0.001) as the QTL responsible for growth at the two temperatures. The putative QTLs accounted for 45 and 41% of the total mycelial growth variation at 25°C and 30°C, respectively, and for 21% of the variation in CM morphology. Only one of the 94 F(1) progeny was pathogenic on P. patula seedlings. This observation could be explained by the genetic constitution of this F(1) isolate, namely that ∼96% of its genome originated from the F. circinatum parent. This F(1) individual also grew significantly faster at 25°C than the F. circinatum parent (P<0.05), as well as more rapidly than the average growth for the remaining 93 F(1) progeny (P<0.05). However, no association was found between mycelial growth and pathogenicity at 25°C. The highly significant QTL associated with growth at two temperatures, suggests that this is a principal genomic region involved in mycelial growth at both temperatures, and that the same region is also responsible for CM morphology.

Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips

The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. Fusarium pininemorale and H. decipiens are not known to cause significant disease but are closely related to species of economic importance. The genome sizes range from 25.99 Mb in the case of O. ips to 4.82 Mb for H. lignivorus. These genomes include the first reports of a genome from the genus Hawksworthiomyces. The availability of these genome data will allow the resolution of longstanding questions regarding the taxonomy of these species. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these species or close relatives cause disease.

Multiple independent origins for a subtelomeric locus associated with growth rate in Fusarium circinatum

Fusarium is a diverse assemblage that includes a large number of species of considerable medical and agricultural importance. Not surprisingly, whole genome sequences for many Fusarium species have been published or are in the process of being determined, the availability of which is invaluable for deciphering the genetic basis of key phenotypic traits. Here we investigated the distribution, genic composition, and evolutionary history of a locus potentially determining growth rate in the pitch canker pathogen F. circinatum. We found that the genomic region underlying this locus is highly conserved amongst F. circinatum and its close relatives, except for the presence of a 12 000 base pair insertion in all of the examined isolates of F. circinatum. This insertion encodes for five genes and our phylogenetic analyses revealed that each was most likely acquired through horizontal gene transfer from polyphyletic origins. Our data further showed that this region is located in a region low in G+C content and enriched for repetitive sequences and transposable elements, which is situated near the telomere of Chromosome 3 of F. circinatum. As have been shown for other fungi, these findings thus suggest that the emergence of the unique 12 000 bp region in F. circinatum is linked to the dynamic evolutionary processes associated with subtelomeres that, in turn, have been implicated in the ecological adaptation of fungal pathogens.