BackgroundIn February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields.ResultsReinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae.ConclusionOur findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-016-0309-7) contains supplementary material, which is available to authorized users.

Background: In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. Results: Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae.

25The wheat blast disease has been a serious constraint for wheat production in Latin America 26 since the late 1980s. We used a population genomics analysis including 95 genome 27 sequences of the wheat blast pathogen Pyricularia graminis-tritici (Pygt) and other 28Pyricularia species to show that Pygt is a distinct, highly diverse pathogen species with a 29 broad host range. We assayed 11 neutral SSR loci in 526 Pygt isolates sampled from wheat 30 and other grasses distributed across the wheat-growing region of Brazil to estimate gene 31 flow, assess the importance of sexual reproduction, and compare the genetic structures of 32Pygt populations infecting wheat and nearby grasses. Our results suggest a mixed 33 reproductive system that includes sexual recombination as well as high levels of gene flow 34 among regions, including evidence for higher gene flow from grass-infecting populations and 35 into wheat-infecting populations than vice versa. The most common virulence groups were 36 shared between the grass-and wheat-infecting Pygt populations, providing additional 37 evidence for movement of Pygt between wheat fields and nearby grasses. Analyses of 38 fruiting body formation found that proto-perithecia and perithecia developed on senescing 39 stems of wheat and other grass hosts, suggesting that sexual reproduction occurs mainly 40 during the saprotrophic phase of the disease cycle on dead residues. Phalaris canariensis 41 (canarygrass) supported the fullest development of perithecia, suggesting it is a promising 42 candidate for identifying the teleomorph in the field. Based on these findings, we formulated 43 a more detailed disease cycle for wheat blast that includes an important role for grasses 44 growing near wheat fields. Our findings strongly suggest that widely grown pasture grasses 45 function as a major reservoir of wheat blast inoculum and provide a temporal and spatial 46 bridge that connects wheat fields across Brazil. 47. CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/203455 doi: bioRxiv preprint first posted online Oct. 16, 2017; 3 Author summary (200 words) 48 After the first wheat blast epidemic occurred in 1985 in Paraná, Brazil, the disease 49 spread to Bolivia, Argentina, and Paraguay, and was introduced into Bangladesh in 2016 50 followed by India in 2017. Wheat blast is caused by Pyricularia graminis-tritici (Pygt), a 51 highly diverse pathogen species related to the rice blast fungus P. oryzae, but with an 52 independent origin and a broader host range. We conducted a large scale contemporary 53 sampling of Pygt from symptomatic wheat and other grass species across Brazil and analyzed 54 the genetic structure of Pygt populations. Pygt populations on both wheat and other grasses 55 had high genotypic and virulence diversity, a genetic structure consistent with a ...