Global analysis of Hemileia vastatrix populations shows clonal reproduction for the coffee leaf rust pathogen throughout most of its range

Hemileia vastatrix is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee-growing region in the world. The development of coffee varieties resistant to H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix to infer the reproductive mode of the fungus across most of its geographic range including Central Africa, SE Asia, the Caribbean, and South and Central America. The population structure of H. vastatrix was determined using eight simple sequence repeat markers (SSRs) developed for this study. The analyses of the standardized index of association, Hardy Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.

Recent clonal reproduction of Cryptomeria japonica in a snowy region revealed by a survey of small-sized ramets

Clonal reproduction may contribute to population maintenance in areas where disturbance caused by snow limits tree recruitment. To understand the importance of clonal reproduction in the population dynamics of canopy tree species, it is necessary to determine the frequency of clonal reproduction in the early stages of seedling establishment. We found 106 ramets, including “small-sized” ramets of less than 5 cm in diameter at breast height, aggregated within 4 patches in a 70 × 50 m plot and also identified 20 genets among these ramets with the use of nuclear microsatellite markers. The size structure of the ramets revealed an inverse J-shaped distribution, suggesting that continuous recruitment of new ramets occurs. However, the number of intermediate-sized ramets (around 10 cm DBH) at the present study site was small, suggesting that most new ramets die while they are still small by pressure from heavy snow. Of the 20 genets, 12 included one or more small-sized ramets, which indicated recent recruitment. Of the 12 genets, 3 included only a single small-sized ramet, which suggested seedling recruitment, whereas the other 9 included multiple ramets (39 small-sized ramets in total), which indicated clonal recruitment. The frequency (9/12) and number (39/9) of recent clonal recruits suggest that clonal reproduction effectively maintains the population of Cryptomeria japonica in snowy regions.

Fungal clones win the battle, but recombination wins the war

Clonal reproduction is common in fungi and fungal-like organisms during epidemics and invasion events. The success of clonal fungi shaped systems for their classification and some pathogens are tacitly treated as asexual. We argue that genetic recombination driven by sexual reproduction must be a starting hypothesis when dealing with fungi for two reasons: (1) Clones eventually crash because they lack adaptability; and (2) fungi find a way to exchange genetic material through recombination, whether sexual, parasexual, or hybridisation. Successful clones may prevail over space and time, but they are the product of recombination and the next successful clone will inevitably appear. Fungal pathogen populations are dynamic rather than static, and they need genetic recombination to adapt to a changing environment.