Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

doi:10.1186/s12864-019-5774-2

. 2019 May 17;20(1):385.

doi: 10.1186/s12864-019-5774-2.

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Mahsa Mousavi-Derazmahalleh¹, Steven Chang², Geoff Thomas³, Mark Derbyshire², Phillip E Bayer^{4

5}, David Edwards^{4

5}, Matthew N Nelson^{1

5

6

7}, William Erskine^{1

5}, Francisco J Lopez-Ruiz², Jon Clements³, James K Hane^{8

9}

Affiliations

¹ UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
² Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
³ Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
⁴ School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
⁵ UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
⁶ Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.
⁷ Current address: Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, 6913, Australia.
⁸ Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia. james.hane@curtin.edu.au.
⁹ Curtin Institute for Computation, Curtin University, Bentley, WA, 6102, Australia. james.hane@curtin.edu.au.

PMID: 31101009
PMCID: PMC6525431
DOI: 10.1186/s12864-019-5774-2

Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Mahsa Mousavi-Derazmahalleh et al. BMC Genomics. 2019.

. 2019 May 17;20(1):385.

doi: 10.1186/s12864-019-5774-2.

Authors

Affiliations

¹ UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
² Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
³ Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
⁴ School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
⁵ UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
⁶ Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.
⁷ Current address: Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, 6913, Australia.
⁸ Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia. james.hane@curtin.edu.au.
⁹ Curtin Institute for Computation, Curtin University, Bentley, WA, 6102, Australia. james.hane@curtin.edu.au.

PMID: 31101009
PMCID: PMC6525431
DOI: 10.1186/s12864-019-5774-2

Abstract

Background: Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea - both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts.

Results: Genomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents.

Conclusions: Detection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens.

Keywords: Botrytis cinerea; Comparative genomics; Lupin; Sclerotinia sclerotiorum.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

**Fig. 1**
Genome features, mutation profiles and presence-absence variations across isolates of *Botrytis cinerea* and *Sclerotinia sclerotiorum*. Chromosomes of reference isolates *Botrytis cinerea* B05.10 (a) and *Sclerotinia sclerotiorum* 1980-UF (b) are visualised alongside (from the innermost ring outwards): genome features including G:C content, gene and repeat densities; ratios of non-synonymous to synonymous mutations (Dn/Ds) relative to alignments of lupin-infecting isolates over 100 kb intervals, and the percent of 100 kb regions that aligned to lupin-infecting isolate assemblies. Yellow boxes indicate large regions of absence in the reference isolate relative to lupin-infecting isolates (Additional file 2)

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References

1. Gladstones J. Distribution, origin, taxonomy, history and importance. In: ‘Lupins as crop plants—biology, production and utilization’.(Eds JS Gladstones, C Atkins, J Hamblin) pp. 1–40. In. Cambridge: Cambridge University Press. p. 1998.
1. Caballero B, Finglas P, Toldrá F. Encyclopedia of food and health, 1st edn: academic. 2015.
1. Clements JC, Wilson J, Sweetingham MW, Quealy J, Francis G. Male sterility in three crop Lupinus species. Plant Breed. 2012;131(1):155–163.
1. Western Australian lupin industry [https://www.agric.wa.gov.au/grains-research-development/western-australi...].
1. White P, French B, McLarty A: Producing lupins. In. Edited by Department of Agriculture and Food, 2nd edn. Perth: South Perth, W.a. : Department of Agriculture and Food; 2008.

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[1] Gladstones J. Distribution, origin, taxonomy, history and importance. In: ‘Lupins as crop plants—biology, production and utilization’.(Eds JS Gladstones, C Atkins, J Hamblin) pp. 1–40. In. Cambridge: Cambridge University Press. p. 1998.

[2] Gladstones J. Distribution, origin, taxonomy, history and importance. In: ‘Lupins as crop plants—biology, production and utilization’.(Eds JS Gladstones, C Atkins, J Hamblin) pp. 1–40. In. Cambridge: Cambridge University Press. p. 1998.

[3] Caballero B, Finglas P, Toldrá F. Encyclopedia of food and health, 1st edn: academic. 2015.

[4] Caballero B, Finglas P, Toldrá F. Encyclopedia of food and health, 1st edn: academic. 2015.

[5] Clements JC, Wilson J, Sweetingham MW, Quealy J, Francis G. Male sterility in three crop Lupinus species. Plant Breed. 2012;131(1):155–163.

[6] Clements JC, Wilson J, Sweetingham MW, Quealy J, Francis G. Male sterility in three crop Lupinus species. Plant Breed. 2012;131(1):155–163.

[7] Western Australian lupin industry [https://www.agric.wa.gov.au/grains-research-development/western-australi...].

[8] Western Australian lupin industry [https://www.agric.wa.gov.au/grains-research-development/western-australi...].

[9] White P, French B, McLarty A: Producing lupins. In. Edited by Department of Agriculture and Food, 2nd edn. Perth: South Perth, W.a. : Department of Agriculture and Food; 2008.

[10] White P, French B, McLarty A: Producing lupins. In. Edited by Department of Agriculture and Food, 2nd edn. Perth: South Perth, W.a. : Department of Agriculture and Food; 2008.

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Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

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Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

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