Genetic Diversity and Population Structure of Rice Pathogen Ustilaginoidea Virens in China

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2013 Oct 8

PMID 24098811

Citations 24

Authors

Xianyun Sun

Shu Kang

Yongjie Zhang

Xinqiu Tan

Yufei Yu

Haiyong He

Xinyu Zhang

Yongfeng Liu

Shu Wang

Wenxian Sun

Lei Cai

Shaojie Li

Affiliations

Soon will be listed here.

Abstract

Rice false smut caused by the fungal pathogen Ustilaginoidea virens is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two U. virens isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of U. virens in China. A total of 56 multilocus sequence types (haplotypes) were identified out of 162 representative isolates from 15 provinces covering five major rice-growing areas in China. However, the phylogeny, based on sequences at individual SNP-rich regions, strongly conflicted with each other and there were significant genetic differences between different geographical populations. Gene flow between the different geographical populations and genetic differentiation within each geographical population were also detected. In addition, genetic recombination and genetic isolation resulting from geographic separation was also found.

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References

Taylor J, Fisher M . Fungal multilocus sequence typing--it's not just for bacteria. Curr Opin Microbiol. 2003; 6(4):351-6. DOI: 10.1016/s1369-5274(03)00088-2. View

Xu J . Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol. 2006; 15(7):1713-31. DOI: 10.1111/j.1365-294X.2006.02882.x. View

Kepler R, Sung G, Harada Y, Tanaka K, Tanaka E, Hosoya T . Host jumping onto close relatives and across kingdoms by Tyrannicordyceps (Clavicipitaceae) gen. nov. and Ustilaginoidea_(Clavicipitaceae). Am J Bot. 2012; 99(3):552-61. DOI: 10.3732/ajb.1100124. View

Brooks S, Anders M, Yeater K . Effect of Cultural Management Practices on the Severity of False Smut and Kernel Smut of Rice. Plant Dis. 2019; 93(11):1202-1208. DOI: 10.1094/PDIS-93-11-1202. View

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S . MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28(10):2731-9. PMC: 3203626. DOI: 10.1093/molbev/msr121. View

Excoffier L, Lischer H . Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2011; 10(3):564-7. DOI: 10.1111/j.1755-0998.2010.02847.x. View

Xu J . Fundamentals of fungal molecular population genetic analyses. Curr Issues Mol Biol. 2006; 8(2):75-89. View

Luduena R, Roach M, Prasad V, Banerjee M, Koiso Y, Li Y . Interaction of ustiloxin A with bovine brain tubulin. Biochem Pharmacol. 1994; 47(9):1593-9. DOI: 10.1016/0006-2952(94)90537-1. View

Pritchard J, Stephens M, Donnelly P . Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2):945-59. PMC: 1461096. DOI: 10.1093/genetics/155.2.945. View

10.

Peakall R, Smouse P . GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update. Bioinformatics. 2012; 28(19):2537-9. PMC: 3463245. DOI: 10.1093/bioinformatics/bts460. View

11.

Kasuga T, White T, Koenig G, McEwen J, Restrepo A, Castaneda E . Phylogeography of the fungal pathogen Histoplasma capsulatum. Mol Ecol. 2003; 12(12):3383-401. DOI: 10.1046/j.1365-294x.2003.01995.x. View

12.

Stamatakis A, Hoover P, Rougemont J . A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008; 57(5):758-71. DOI: 10.1080/10635150802429642. View

13.

Rush M, Shahjahan A, Jones J, Groth D . Outbreak of False Smut of Rice in Louisiana. Plant Dis. 2019; 84(1):100. DOI: 10.1094/PDIS.2000.84.1.100D. View

14.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

15.

Koiso Y, Li Y, Iwasaki S, Hanaoka K, Kobayashi T, Sonoda R . Ustiloxins, antimitotic cyclic peptides from false smut balls on rice panicles caused by Ustilaginoidea virens. J Antibiot (Tokyo). 1994; 47(7):765-73. DOI: 10.7164/antibiotics.47.765. View

16.

Meyer W, Aanensen D, Boekhout T, Cogliati M, Diaz M, Esposto M . Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii. Med Mycol. 2009; 47(6):561-70. PMC: 2884100. DOI: 10.1080/13693780902953886. View

17.

Librado P, Rozas J . DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25(11):1451-2. DOI: 10.1093/bioinformatics/btp187. View

18.

Miyazaki S, Matsumoto Y, Uchihara T, Morimoto K . High-performance liquid chromatographic determination of ustiloxin A in forage rice silage. J Vet Med Sci. 2009; 71(2):239-41. DOI: 10.1292/jvms.71.239. View

19.

Li J, Fan S, Liu X, Li D, Nie Z, Li F . Biased genotype distributions of Candida albicans strains associated with vulvovaginal candidosis and candidal balanoposthitis in China. Clin Infect Dis. 2008; 47(9):1119-25. DOI: 10.1086/592249. View

20.

Kim K, Park E . Ultrastructure of spined conidia and hyphae of the rice false smut fungus Ustilaginoidea virens. Micron. 2006; 38(6):626-31. DOI: 10.1016/j.micron.2006.09.006. View