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Genetic entanglement between Cercospora species associating soybean purple seed stain

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Abstract

Soybean purple seed stain (S-PSS) is a destructive, worldwide distributed fungal disease caused by several Cercospora species. This work aims to shed light on the nature of the genealogical and genetic relationships amongst S-PSS causal agents. Fungal isolates were obtained from Argentina and Brazil, which belong to the leading countries in soybean production worldwide. DNA sequences were obtained from eight loci across the collection of isolates. Relationships were evaluated through Bayesian phylogenetic inferences, and distance and character-based network analyses and discriminant analyses. The occurrence of reticulate evolutionary events was tested with recombination tests. The high haplotype diversity (H = 1.0) was arranged in four validated haplogroups. Reticulate network topologies were evident, and 11 recombination events were validated through several tests. Five of these events occurred across species boundaries. Comparison with sequences from 70 Cercospora species indicated that at least five monophyletic groups of S-PSS-causing agents are currently present in South America. The provided evidence supports the hypothesis that interspecific genetic exchange plays a significant role in the evolutionary dynamics of Cercospora species in this region. The occurrence of interspecific recombination has implications for understanding epidemiological threats to soybean production that appear to be more serious than previously anticipated.

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Abbreviations

S-PSS:

Soybean purple seed stain

GCPSR:

Genealogical Concordance Phylogenetic Species Recognition

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Acknowledgements

We would like to express our sincere gratitude to the farmers and field technicians who provided assistance during field trips and sampling. We also wish to express our gratitude to B. Ferrari, M. Quiroga, E. Pozzo, D. Girotti, N. García Dutriez and M. Franco from “Don Mario Semillas” for supplying infected materials from different locations in Argentina. This research was financially supported by “Programa de Proyectos Conjuntos de Investigación SPU-CAPES MERCOSUR” (2011-PPC015), “Instituto Nacional de Tecnología Agropecuaria (INTA, Argentina)”, the Minas Gerais State Foundation of Research Aid—FAPEMIG (PPM 00561-15), the National Council of Scientific and Technological Development—CNPq (478752/2013-0 and 305827/2015-4) and the CAPES Foundation—Brazilian Ministry of Education (PPCP-Mercosul 015/2011 and AUX-PE PNPD 2927/2010).

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Authors and Affiliations

  1. Instituto de Genética “Ewald A. Favret”, CNIA, INTA Castelar, Buenos Aires, Argentina

    Eduardo A. Guillin

  2. Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, Brazil

    Luiz Orlando de Oliveira

  3. Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina

    Pablo E. Grijalba

  4. Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires—IEGEBA (UBA-CONICET), 4to piso, Laboratorio 61-62, Pabellón II C1428EHA, Buenos Aires, Argentina

    Alexandra M. Gottlieb

  5. Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET—Universidad de Buenos Aires, Buenos Aires, Argentina

    Alexandra M. Gottlieb

Authors
  1. Eduardo A. Guillin
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  2. Luiz Orlando de Oliveira
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  3. Pablo E. Grijalba
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  4. Alexandra M. Gottlieb
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Correspondence to Alexandra M. Gottlieb.

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Section Editor: Hans-Josef Schroers

Electronic supplementary material

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Supplementary Table S1

Materials used in this study, including geographic origin of isolates and GenBank accession numbers; the tentative identification of isolates follows Soares et al. (2015) where possible (DOC 131 kb)

Supplementary Table S2

Additional materials used in this study, including numbers of isolates, host names, geographic origin and GenBank accession numbers. Species names are those proposed in Groenewald et al. (2013). The numbers of ex-type isolates are indicated (DOC 250 kb)

Supplementary Table S3

Results of CADM tests performed pairwise amongst single loci matrices from dataset 1. Kendall test values (below the diagonal) and Mantel probabilities (above the diagonal) are shown. All probabilities are based upon 999 permutations (DOC 37 kb)

Supplementary Table S4

Results of CADM tests performed pairwise amongst single loci matrices from dataset 2. Kendall test values (below the diagonal) and Mantel probabilities (above the diagonal) are shown. All probabilities are based upon 999 permutations (DOC 28.5 kb)

Fig. S1

Median-joining network derived from dataset 1, excluding C. sojina (484 sites; 66 terminals). The colours in terminals indicate species identification: C. kikuchii and C. aff. kikuchii (blue); C. cf. flagellaris (red); C. cf. sigesbeckiae (purple); Cercospora sp. Q (green); C. alchemillicola (pink); Cercospora sp. H (orange); Cercospora sp. (black). The black squares represent putative or not sampled haplotypes (GIF 22.2 kb)

High resolution image (TIF 596 kb)

Fig. S2

Graphical haplotypes and haplogroups defined for dataset 1. The top line shows the gene order and the approximate size of each gene locus, as follows: act (bases 1–151), cal (152–395), cfp (396–1265), cyt-b (1266–1918), ef (1919–2154) and tub1/2 (2155–3351). Each grey block represents a unique haplotype; variable sites are depicted by vertical lines. The coloured small dots indicate species identification: C. kikuchii and C. aff. kikuchii (blue); C. cf. flagellaris (red); C. cf. sigesbeckiae (purple); Cercospora sp. Q (green); C. alchemillicola (pink); Cercospora sp. H (orange); Cercospora sp. (black). The black arrows indicate interlocus recombinants and the pink arrow shows a putative intralocus recombinant. Haplogroups (H) are delimited on the right, with the equivalent DAPC group assignment shown in parentheses (G) (GIF 148 kb)

High resolution image (TIF 1336 kb)

Fig. S3

DAPC analyses of dataset 1 (excluding C. sojina; 3351 sites; 66 terminals). a Scatter plot depicting relative intragroup and among-group genetic distances. The first three axes explain 74%, 15.7% and 10.3% of the variation, respectively. The colours correspond to those used to delimit haplogroups. Individual isolates cannot be distinguished within each group and inertia ellipses are not apparent in the scatter plot due to the scale defined by the intragroup/intergroup variation rate. b Group assignment. The red blocks indicate full assignment probability (p = 1.0). Isolates are coloured according to their species identification: C. kikuchii and C. aff. kikuchii (blue); C. cf. flagellaris (red); C. cf. sigesbeckiae (purple); Cercospora sp. Q (green); C. alchemillicola (pink); Cercospora sp. H (orange); Cercospora sp. (black) (GIF 50.3 kb)

High resolution image (TIF 336 kb)

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Guillin, E.A., de Oliveira, L.O., Grijalba, P.E. et al. Genetic entanglement between Cercospora species associating soybean purple seed stain. Mycol Progress 16, 593–603 (2017). https://doi.org/10.1007/s11557-017-1289-x

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