Journal
GIGASCIENCE
Volume 5, Issue -, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1186/s13742-016-0108-7
Keywords
Black shank; Phytophthora nicotianae; Genomes; Hybrid assembly; RxLR effector
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Funding
- China National Tobacco Corporation [110201201003 [JY-03], 110201301006 [JY-06]]
- Yunnan Tobacco Corporation [2012YN01, 2013YN01]
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Background: Black shank is a severe plant disease caused by the soil-borne pathogen Phytophthora nicotianae. Two physiological races of P. nicotianae, races 0 and 1, are predominantly observed in cultivated tobacco fields around the world. Race 0 has been reported to be more aggressive, having a shorter incubation period, and causing worse root rot symptoms, while race 1 causes more severe necrosis. The molecular mechanisms underlying the difference in virulence between race 0 and 1 remain elusive. Findings: We assembled and annotated the genomes of P. nicotianae races 0 and 1, which were obtained by a combination of PacBio single-molecular real-time sequencing and second-generation sequencing (both HiSeq and MiSeq platforms). Gene family analysis revealed a highly expanded ATP-binding cassette transporter gene family in P. nicotianae. Specifically, more RxLR effector genes were found in the genome of race 0 than in that of race 1. In addition, RxLR effector genes were found to be mainly distributed in gene-sparse, repeat-rich regions of the P. nicotianae genome. Conclusions: These results provide not only high quality reference genomes of P. nicotianae, but also insights into the infection mechanisms of P. nicotianae and its co-evolution with the host plant. They also reveal insights into the difference in virulence between the two physiological races.
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