Population genomics of speciation and host adaptation in fungal plant pathogens
T.A. Duong1, A. Viljoen1, P. Shaw1, L. Sebapu1, A. Hammerbacher2, M.J. Wingfield1, B. Slippers1, S.F. Chen1,3, R. Chang1, F.F. Liu1,3, B.D. Wingfield1
1Department of Biochemistry, Genetics and Microbiology, 2Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa. 3China Eucalypt Research Centre, Chinese Academy of Forestry, Zhanjiang 524022, China.

Species of the Ceratocystis fimbriata sensu lato ( s.l .) complex are important pathogens of forestry and agricultural crops worldwide. Members of this complex are causal agents of wilting diseases in several forestry and fruit tree species, as well as root rot of sweet potato around the world. Recognizing species boundaries in this complex has been under considerable debate, which has resulted in taxonomic confusion. We generated genome sequences for a collection of isolates of C. fimbriata s.l. from five hosts and 11 countries across five continents. Population genomic analyses revealed three distinct lineages, defined by their patterns of host association. The first lineage included isolates only from sweet potato (member of the Solanales ), representing C. fimbriata sensu stricto . The second lineage included isolates infecting Eucalyptus and Punica (members of the Myrtales ), known as C. eucalypticola . The last lineage consisted of isolates infecting Acacia and Mangifera (members of the Fabales and Sapindales ), known as C. manginecans . Hybrids of C. eucalypticola and C. manginecans were identified from regions where they co-occur, but there were no hybrids between C. fimbriata and the other two species. Further analyses into gene composition, alternative isoforms, and gene expression between C. eucalypticola and C. fimbriata indicated a high level of gene conservation, but isoform usage and gene expression patterns differ significantly. Overall, our results reveal signatures of host specialization and cryptic speciation in these fungi. These findings form the basis for our understanding of their ecology and evolution.

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