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Comparative Genomics Reveals Horizontal Gene Transfer in Pathogenic Fungus

By Andrea Anderson

NEW YORK (GenomeWeb News) – The fungal plant pathogen Fusarium oxysporum is capable of horizontal gene transfer similar to that seen in bacteria, a new comparative genomics study suggests.

An international team sequenced the genomes of two plant pathogens in the Fusarium genus — F. verticillioides and F. oxysporum f.sp lycopersici — and compared them with the genome of the previously sequenced species F. graminearum. In the process, the team found four chromosomes carrying pathogenesis-related genes that can hop from one F. oxysporum strain to another.

The power to detect these so-called "pathogenicity chromosomes" is a direct result of the comparative genomics approach, lead author Li-Jun Ma, a researcher with the Broad Institute's Fungal Genome Initiative, told GenomeWeb Daily News.

The study appears online today in Nature.

In an effort to understand Fusarium pathogenicity, the researchers focused on F. verticillioides and F. graminearum, which mainly infect cereal crops, and the tomato wilt-causing pathogen F. oxysporum, which can also infect a relatively broad range of other plants and even some animals.

They used whole-genome shotgun with the Sanger approach to tackle the genomes of the F. verticillioides strain 7600 and the F. oxysporum f.sp lycopersici strain 4287.

After assembling the genomes, they then used both manual and automated annotation methods to predict genes in the newly sequenced genomes and re-annotate an updated assembly of the F. graminearum genome.

When they compared the genomes, the researchers found that F. oxysporum f.sp lycopersici's genome is 65 percent larger than the F. graminearum genome and 44 percent larger than the genome of the more closely related F. verticillioides.

While the F. verticillioides genome appears to be housed on 11 chromosomes and the F. graminearum on four chromosomes, the F. oxysporum genome assembly involved 15 chromosomes — 11 resembling F. verticillioides chromosomes and four containing many sequences not found in the other two species.

The team's subsequent analyses of the unique F. oxysporum sequences showed that these lineage-specific regions contain almost three-quarters of the transposable elements in the fungus' genome and house relatively few known protein-coding genes.

In addition, most of the known genes in these regions correspond to those found in other fungal species, consistent with the notion that lineage-specific regions in F. oxysporum came from a horizontal gene transfer source.

"[T]he tomato strain had 11 chromosomes very similar to the other fungi, but then an additional four chromosomes that looked like nothing we'd ever seen before," co-corresponding author Corby Kistler, a researcher with the US Department of Agriculture's Agricultural Research System, who is also affiliated with the University of Minnesota, said in a statement. "These chromosomes had many features that made them look like they came from a completely different species."

The researchers also garnered evidence suggesting different strains contain distinct pathogenicity chromosomes, Ma explained, which may correspond to the particular plants that they infect. For instance, the researchers found that strains infecting Arabidopsis and cotton have different lineage-specific regions than those found in the tomato pathogen.

And by incubating a non-pathogenic strain with a pathogenic strain, the team found that at least one of the chromosomes — chromosome 14 — can hop from one strain to the next, making the recipient strain pathogenic.

"Prior to this we've believed that fungi were generally confined to vertical gene transfer or conventional inheritance, a slower type of genetic change based on the interplay of DNA mutation, recombination and the effects of selection," co-author Michael Freitag, a biochemistry and biophysics researcher at Oregon State University, said in a statement. "[W]e found fungi able to transfer an infectious capability to a different strain in a single generation."

The researchers are now using a combination of optical mapping and targeted sequencing to characterize pathogenicity chromosomes in additional fungal isolates, Ma said, noting that they currently have funding to look at about a dozen strains.

Such work is expected to help inform future studies of plant disease — and provide insights that may help combat agriculturally important plant infections. "Because of this work, we know more about the toolbox fungi have to cause disease," Kistler said in statement. "Our job now is to develop tools of our own aimed at those traits that make fungi harmful to plants."

In addition, the findings suggest Fusarium may serve as a useful model system for studying eukaryotic genome stability and dynamics, Ma noted, since researchers can compare a species such as F. oxysporum, which has a very flexible genome, with closely related species that have stable genomes under tight control. As such, she added, the study offers "a new view of eukaryotic dynamics and evolution."

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