T-Toxin Virulence Genes: Unconnected Dots in a Sea of Repeats
[1];
[3];
[4];
[2];
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Section of Plant Pathology &, Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA, Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
- Functional and systems Biology Group, Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA, DOE Joint BioEnergy Institute, Emeryville, California, USA
In 1970, the Southern Corn Leaf Blight epidemic ravaged U.S. fields to great economic loss. The outbreak was caused by never-before-seen, supervirulent, Race T of the fungus Cochliobolus heterostrophus. The functional difference between Race T and O, the previously known, far less aggressive strain, is production of T-toxin, a host-selective polyketide. Supervirulence is associated with ~1 Mb of Race T-specific DNA; only a fraction encodes T-toxin biosynthetic genes (Tox1). Tox1 is genetically and physically complex, with unlinked loci (Tox1A, Tox1B) genetically inseparable from breakpoints of a Race O reciprocal translocation that generated hybrid Race T chromosomes. Previously, we identified 10 genes for T-toxin biosynthesis. Unfortunately, high-depth, short-read sequencing placed these genes on four small, unconnected scaffolds surrounded by repeated A+T rich sequence, concealing context. To sort out Tox1 topology and pinpoint the hypothetical Race O translocation breakpoints corresponding to Race T-specific insertions, we undertook PacBio long-read sequencing which revealed Tox1 gene arrangement and the breakpoints. Six Tox1A genes are arranged as three small islands in a Race T-specific sea (~634 kb) of repeats. Four Tox1B genes are linked, on a large loop of Race T-specific DNA (~210 kb). The race O breakpoints are short sequences of race O-specific DNA; corresponding positions in race T are large insertions of race T-specific, A+T rich DNA, often with similarity to transposable (predominantly Gypsy) elements. Nearby, are ‘Voyager Starship’ elements and DUF proteins. These elements may have facilitated Tox1 integration into progenitor Race O and promoted large scale recombination resulting in race T.
- Research Organization:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Grant/Contract Number:
- AC02-05CH11231; 10.46936/10.25585/60001208; AC05-76RL01830
- OSTI ID:
- 1960447
- Alternate ID(s):
- OSTI ID: 1969975; OSTI ID: 1973239
- Report Number(s):
- PNNL-SA-181983; e00261-23
- Journal Information:
- mBio (Online), Journal Name: mBio (Online) Vol. 14 Journal Issue: 2; ISSN 2150-7511
- Publisher:
- American Society for MicrobiologyCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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