The Genetic Structure of Phellinus noxius and Dissemination Pattern of Brown Root Rot Disease in Taiwan.
Since the 1990s, brown root rot caused by Phellinus noxius (Corner) Cunningham has become a major tree disease in Taiwan. This fungal pathogen can infect more than 200 hardwood and softwood tree species, causing gradual to fast decline of the trees. For effective control, we must determine how the pathogen is disseminated and how the new infection center of brown root rot is established. We performed Illumina sequencing and de novo assembly of a single basidiospore isolate Daxi42 and obtained a draft genome of ~40 Mb. By comparing the 12,217 simple sequence repeat (SSR) regions in Daxi42 with the low-coverage Illumina sequencing data for four additional P. noxius isolates, we identified 154 SSR regions with potential polymorphisms. A set of 13 polymorphic SSR markers were then developed and used to analyze 329 P. noxius isolates collected from 73 tree species from urban/agricultural areas in 14 cities/counties all around Taiwan from 1989 to 2012. The results revealed a high proportion (~98%) of distinct multilocus genotypes (MLGs) and that none of the 329 isolates were genome-wide homozygous, which supports a possible predominant outcrossing reproductive mode in P. noxius. The diverse MLGs exist as discrete patches, so brown root rot was most likely caused by multiple clones rather than a single predominant strain. The isolates collected from diseased trees near each other tend to have similar genotype(s), which indicates that P. noxius may spread to adjacent trees via root-to-root contact. Analyses based on Bayesian clustering, FST statistics, analysis of molecular variance, and isolation by distance all suggest a low degree of population differentiation and little to no barrier to gene flow throughout the P. noxius population in Taiwan. We discuss the involvement of basidiospore dispersal in disease dissemination.
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan; Master Program for Plant Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Chia-Lin
CL
Chung
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Shun-Yuan
SY
Huang
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Yu-Ching
YC
Huang
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Shean-Shong
SS
Tzean
Plant Pathology Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist., Taichung City 41362, Taiwan.
Pao-Jen
PJ
Ann
Plant Pathology Division, Taiwan Agricultural Research Institute, No. 189, Zhongzheng Rd., Wufeng Dist., Taichung City 41362, Taiwan.
Jyh-Nong
JN
Tsai
Master Program for Plant Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Chin-Cheng
CC
Yang
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Hsin-Han
HH
Lee
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Tzu-Wei
TW
Huang
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Hsin-Yu
HY
Huang
Division of Forest Protection, Taiwan Forestry Research Institute, No. 53, Nanhai Rd., Zhongzheng Dist., Taipei City 10066, Taiwan.
Tun-Tschu
TT
Chang
Department of Crop Environment, Taitung District Agricultural Research and Extension Station, No. 675, Sec. 1, Zhonghua Rd., Taitung City 95055, Taiwan.
Hui-Lin
HL
Lee
Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan; Master Program for Plant Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 10617, Taiwan.
Ruey-Fen
RF
Liou
D005800:Genes, Fungal; D005838:Genotype; D018895:Microsatellite Repeats; D009181:Mycoses / Q000235:genetics*; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology*; D011110:Polymorphism, Genetic; D013172:Spores, Fungal / Q000235:genetics*; D013624:Taiwan