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Phytophthora colocasiae from Vietnam, China, Hawaii and Nepal: intra- and inter-genomic variations in ploidy and a long-lived, diploid Hawaiian lineage.

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Abstract

Phytophthora colocasiae is an important pathogen of taro and is widely distributed. Our goal was to develop whole genome sequence and single nucleotide polymorphism (SNP) markers to characterize historical and current populations from Hawaii (2010 and 2016, HA), historical isolates from Vietnam and China (2010, VN and CH) and current isolates from Nepal (2016, NEP). Seven isolates (VN = 2, CH = 1, HA = 1, NEP = 3) were sequenced (NCBI BioProject PRJNA378784) and compared using the reference genome of the closely related vegetable pathogen P. capsici. Genome-wide SNP analysis using 27,537 markers revealed genomes of diploid, triploid, tetraploid and higher ploidy. Ploidy varied within and between populations, with HA being primarily diploid, CH primarily triploid, VN containing diploid and triploid isolates, and NEP having predominantly triploid, tetraploid and higher ploidy. A total of 37 SNP markers were genotyped in 89 samples (grown in culture or directly from infected tissue) using targeted-sequencing. Analyses indicate a single clonal lineage dominated populations in HA from 2010 to 2016 and targeted-sequencing was useful to estimate ploidy. The implications for adaptation and evolution of P. colocasiae are discussed, as well as consequences for selection and breeding of resistant taro cultivars.

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Acknowledgements

Permission to harvest infected taro leaves was obtained from all landowners and taro producers, and shipment and processing of isolates was conducted under USDA permit P526P-16-02522 to Kurt Lamour.

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Authors and Affiliations

  1. Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA

    Sandesh Kumar Shrestha & Kurt Lamour

  2. Department of Tropical Plant & Soil Sciences, University of Hawai’i, Hilo, HI, USA

    Susan C. Miyasaka

  3. College of Agriculture, Forestry and Natural Resource Management, University of Hawai’i at Hilo, 200 W. Kawili St, Hilo, HI, 96720, USA

    Michael Shintaku

  4. Department of Entomology and Plant Pathology, University of Tennessee, Jackson, TN, USA

    Heather Kelly

Authors
  1. Sandesh Kumar Shrestha
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  2. Susan C. Miyasaka
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  3. Michael Shintaku
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  4. Heather Kelly
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  5. Kurt Lamour
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Correspondence to Kurt Lamour.

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Section Editor: Marco Thines

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Supplementary Fig. 1

Ploidy estimates for P. colocasiae isolates recovered from Hawaii, China, Vietnam and Nepal based on linkage groups defined for the closely related vegetable pathogen, P. capsici. (PDF 204 kb)

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Shrestha, S.K., Miyasaka, S.C., Shintaku, M. et al. Phytophthora colocasiae from Vietnam, China, Hawaii and Nepal: intra- and inter-genomic variations in ploidy and a long-lived, diploid Hawaiian lineage.. Mycol Progress 16, 893–904 (2017). https://doi.org/10.1007/s11557-017-1323-z

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  • DOI: https://doi.org/10.1007/s11557-017-1323-z

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