Gene genealogies provide evidence for genetic divergence and multiple origins in Alternaria spp. collected from tomato and potato in North Carolina and Wisconsin

Authors: ADHIKARI, TIKA - NORTH CAROLINA STATE UNIVERSITY; INGRAM, THOMAS - NORTH CAROLINA STATE UNIVERSITY; MEADOWS, INGA - NORTH CAROLINA STATE UNIVERSITY; Halterman, Dennis; LOUWS, FRANK - NORTH CAROLINA STATE UNIVERSITY

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/18/2020
Publication Date: 6/18/2020
Citation: Adhikari, T.B., Ingram, T., Meadows, I., Halterman, D.A., Louws, F.J. 2020. Gene genealogies provide evidence for genetic divergence and multiple origins in Alternaria spp. collected from tomato and potato in North Carolina and Wisconsin. Phytopathology. p.1-16. https://doi.org/10.1094/PHYTO-12-19-0487-R.
DOI: https://doi.org/10.1094/PHYTO-12-19-0487-R

Interpretive Summary: Fungal plant pathogens belonging to the Genus Alternaria cause diseases of potato and tomato, including early blight, leaf blight, and stem canker. Samples of Alternaria species were collected from potato and tomato fields in North Carolina and Wisconsin in order to study the population diversity. Using sequences of genes within collected fungal isolates, we determined that the population of Alternaria linariae from tomato was distinct from the population of A. solani from potato, supporting the hypothesis of genetic divergence. Based on similarities with other Alternaria strains, we found that many Alternaria strains share similarities with those from Brazil, suggesting that NC and WI isolates were introduced from Brazil. We found no evidence that populations are recombining, which suggests that mutation and balancing selection with the hosts is the driving force behind diversification. Our findings will impact future investigations into the differences that exist in evolving populations of Alternaria species from tomato and potato. The results will also impact the development of effective disease management strategies for Alternaria in tomato and potato.

Technical Abstract: Alternaria alternata (Fr.) Keissler causes leaf blight and stem canker on tomato, and A. linariae (Neerg.) Simmons and A. solani (Ell. and Mart.) Jones and Grout incites early blight (EB) on tomato and potato, respectively are considered destructive pathogens of vegetables in North Carolina (NC) and Wisconsin (WI). We used the gene genealogical approach to investigate evolutionary processes and geographical origins in the panel of 152 isolates of three closely related Alternaria spp. collected from tomato in NC and from potato in WI. Sequences of the single-copy two nuclear genes: the glyceraldehyde-3-phosphate dehydrogenase (GPDH) and RNA polymerase second largest subunit (RPB2), and the rDNA internal transcribed spacer (ITS) region were analyzed to infer nucleotide and haplotype diversity informative data. Little or no polymorphisms in the ITS region was detected; however, high levels of non-coding sequence variations were obtained for the GPDH and RPB2 genes. The coalescent gene genealogy and phylogenetic analysis classified Alternaria spp. into three distinct clusters and each cluster represented by a species. The population of A. linariae from tomato was genetically distinct from the population of A. solani from potato based on the 15 variable nucleotide sites detected at the RPB2 gene, supporting the hypothesis of genetic divergence. Of the 13 haplotypes detected, six haplotypes H1 to H6 were shared with Brazilian haplotypes, consistent with the hypothesis of introduction of the pathogens to NC and WI from Brazil. In addition, seven new haplotypes H7 to H13 were identified, providing most specific evidence for the presence of endemic haplotypes of A. linariae and A. solani. Nucleotide diversity and mutation parameter (Watterson’s Tw) estimates were higher in A. alternata and lower in A. linariae and A. solani populations. Neutrality tests indicated no evidence for recombination but an excess of recent mutations, population expansion and balancing selection could play an important role in shaping the genetic structure of Alternaria spp. Overall, this study demonstrates that the nuclear genes can provide valuable information on DNA sequence variations in Alternaria spp. and that clonal populations consist of genetically distinct admixtures of introduced and endemic haplotypes adapting to tomato and potato production areas in NC and WI.