Characterization of Globodera ellingtonae Populations from Chile Utilizing Whole Genome Sequencing

被引:3
作者
Hesse, C. N. [1 ]
Moreno, I [2 ]
Pardo, O. Acevedo [2 ]
Fuentes, H. Pacheco [2 ]
Grenier, E. [3 ]
Dandurand, L. M. [4 ]
Zasada, I. A. [1 ]
机构
[1] USDA ARS, Hort Crops Res Unit, Corvallis, OR 97330 USA
[2] Serv Agr & Ganadero SAG, Div Protecc Agr & Forestal & Red SAG Labs, Santiago, Chile
[3] Univ Rennes 1, IGEPP, INRAE, Agrocampus Ouest, F-35650 Le Rheu, France
[4] Univ Idaho, 875 Perimeter Dr MS 2329, Moscow, ID 83844 USA
基金
新加坡国家研究基金会;
关键词
Genome; Globodera ellingtonae; Population genetics; Potato cyst nematode; VARIANT CALL FORMAT; DNA; MORPHOLOGY; ALIGNMENT; PACKAGE;
D O I
10.21307/jofnem-2021-088
中图分类号
Q95 [动物学];
学科分类号
071002 ;
摘要
Globodera ellingtonae was originally described from populations collected in the United States. In the original description, ribosomal DNA loci from Globodera sp. collected in Chile and Argentina were similar to G. ellingtonae, suggesting this nematode originated in this region of South America. In an effort to find additional populations of G. elllingtonae, collection trips were conducted in 2017 and 2020 in the Antofagasta and Arica y Parinacota Regions in Northern Chile, respectively. Globodera sp. were more prevalent in Antofagasta (17 samples collected, 53% positive for Globodera sp.) than in Arica y Parincota (16 samples collected, 13% positive for Globodera sp.). The genomes of single cysts (N >= 3) from four fields were sequenced. Additionally, the genomes of the G. ellingtonae population from Oregon and a Globodera sp. population originally collected in Antofagasta Region but maintained in culture in France were also sequenced. Based upon a HSP90 sequenced data mined from WSG data, all of the populations from the Antofagasta Region were G. ellingtonae and grouped in a monophyletic clade. A population collected from the Arica y Parincota Region was identified as G. rostochiensis based upon HSP90 data. Genome-wide SNP patterns of the G. ellingtonae populations showed strong clustering based on geographic location indicating that G. ellingtonae has high genetic diversity within Chile. A phylogenetic tree derived from 168,354 binary SNPs in the nuclear genome showed separate but distinct clustering of the Oregon population and the population from Antofagasta maintained in France. The Oregon G. ellingtonae population subtended the Chilean clades and placed on a long branch representing approximately twice the genetic variation observed among all Chilean G. ellingtonae populations. The possibility remains that G. ellingtonae from Chile may be sufficiently diverged to constitute a new species from G. ellingtonae originally described from a population collected in Oregon.
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页数:9
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