Discerning the global phylogeographic distribution of Phyllosticta citricarpa by means of whole genome sequencing.

Autor: Coetzee B; Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: beatrix@sun.ac.za., Carstens E; Citrus Research International, Nelspruit, South Africa. Electronic address: ec@cri.co.za., Fourie PH; Citrus Research International, Nelspruit, South Africa; Department of Plant Pathology, Stellenbosch University, Stellenbosch, South Africa. Electronic address: phf@cri.co.za., Dewdney MM; Department of Plant Pathology, Citrus Research and Education Centre, University of Florida, Lake Alfred, USA. Electronic address: mmdewdney@ufl.edu., Rollins JA; Department of Plant Pathology, University of Florida, Gainesville, FL, USA. Electronic address: rollinsj@ufl.edu., Manzano León AM; Research Institute for Tropical Fruit Crops, Havana, Cuba. Electronic address: fitopatologia17@iift.cu., Donovan NJ; Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Menangle, New South Wales, Australia. Electronic address: nerida.donovan@dpi.nsw.gov.au., Glienke C; Department of Genetics, Federal University of Paraná, Curitiba, Brazil. Electronic address: ch.glienke@gmail.com., Miles AK; Superior Production Company Pty Ltd, Emerald, Australia. Electronic address: andrewmiles@2ph.com.au., Li H; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China. Electronic address: hyli@zju.edu.cn., Bester-van der Merwe AE; Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: aeb@sun.ac.za.
Jazyk: angličtina
Zdroj: Fungal genetics and biology : FG & B [Fungal Genet Biol] 2022 Sep; Vol. 162, pp. 103727. Date of Electronic Publication: 2022 Jul 21.
DOI: 10.1016/j.fgb.2022.103727
Abstrakt: Phyllosticta citricarpa is a fungal pathogen causing citrus black spot (CBS). As a regulated pest in some countries, the presence of the pathogen limits the export of fruit and is therefore of agricultural and economic importance. In this study, we used high throughput sequencing data to infer the global phylogeographic distribution of this pathogen, including 71 isolates from eight countries, Argentina, Australia, Brazil, China, Cuba, Eswatini, South Africa and the United States of America. We assembled draft genomes and used a pairwise read mapping approach for the detection and enumeration of variants between isolates. We performed SSR marker discovery based on the assembled genome with the best assembly statistics, and generated genotype profiles for all isolates with 1987 SSR markers in silico. Furthermore, we identified 32,560 SNPs relative to a reference sequence followed by population genetic analyses based on the three datasets; pairwise variant counts, SSR genotypes and SNP genotypes. All three analysis approaches gave similar overall results. Possible pathways of dissemination among the populations from China, Australia, southern Africa and the Americas are postulated. The Chinese population is the most diverse, and is genetically the furthest removed from all other populations, and is therefore considered the closest to the origin of the pathogen. Isolates from Australia, Eswatini and the South African province Mpumalanga are closely associated and clustered together with those from Argentina and Brazil. The Eastern Cape, North West, and KwaZulu-Natal populations in South Africa grouped in another cluster, while isolates from Limpopo are distributed between the two aforementioned clusters. Southern African populations showed a close relationship to populations in North America, and could be a possible source of P. citricarpa populations that are now found in North America. This study represents the largest whole genome sequencing survey of P. citricarpa to date and provides a more comprehensive assessment of the population genetic diversity and connectivity of P. citricarpa from different geographic origins. This information could further assist in a better understanding of the epidemiology of the CBS pathogen, its long-distance dispersal and dissemination pathways, and can be used to refine phytosanitary regulations and management programmes for the disease.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2022 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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