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Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis

GND
1058930834
Zugehörigkeit
Julius Kühn-Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Germany
Sedaghatjoo, Somayyeh;
Zugehörigkeit
Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
Mishra, Bagdevi;
Zugehörigkeit
Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Vöttinger Straße 38, 85354 Freising, Germany
Forster, Monika K.;
GND
1170372171
Zugehörigkeit
Julius Kühn-Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Germany
Becker, Yvonne;
GND
1013858662
Zugehörigkeit
Julius Kühn-Institute (JKI), Institute for Biosafety in Plant Biotechnology, Germany
Keilwagen, Jens;
GND
124632750
Zugehörigkeit
Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Vöttinger Straße 38, 85354 Freising, Germany
Killermann, Berta;
GND
131405853
Zugehörigkeit
Faculty of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max‑von‑Laue‑Str. 13, 60438 Frankfurt am Main, Germany
Thines, Marco;
Zugehörigkeit
Molecular Phytopathology and Mycotoxin Research, University of Goettingen, Grisebachstrasse 6, 37077 Goettingen, Germany
Karlovsky, Petr;
GND
12412514X
Zugehörigkeit
Julius Kühn-Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Germany
Maier, Wolfgang

Tilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intraspecies variation in these species and the genetic basis of their separation is unknown. We sequenced the genome of four T. caries, five T. controversa, and two T. laevis and extended this dataset with five publicly available ones. The genomes of the three species displayed microsynteny with up to 94.3% pairwise aligned regions excluding repetitive regions. The majority of functionally characterized genes involved in pathogenicity, life cycle, and infection of corn smut, Ustilago maydis, were found to be absent or poorly conserved in the draft genomes and the biosynthetic pathway for trimethylamine in Tilletia spp. could be different from bacteria. Overall, 75% of the identified protein-coding genes comprising 84% of the total predicted carbohydrate utilizing enzymes, 72.5% putatively secreted proteins, and 47.4% of effector-like proteins were conserved and shared across all 16 isolates. We predicted nine highly identical secondary metabolite biosynthesis gene clusters comprising in total 62 genes in all species and none were species-specific. Less than 0.1% of the protein-coding genes were species-specific and their function remained mostly unknown. Tilletia controversa had the highest intraspecies genetic variation, followed by T. caries and the lowest in T. laevis. Although the genomes of the three species are very similar, employing 241 single copy genes T. controversa was phylogenetically distinct from T. caries and T. laevis, however these two could not be resolved as individual monophyletic groups. This was in line with the genome-wide number of single nucleotide polymorphisms and small insertions and deletions. Despite the conspicuously different teliospore ornamentation of T. caries and T. laevis, a high degree of genomic identity and scarcity of species-specific genes indicate that the two species could be conspecific.

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