title: Genomes and virulence difference between two physiological races of Phytophthora nicotianae.
abstract: 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.
  
  
  RESULTS
  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.
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China ; University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: Yunnan Agricultural University, Kunming, 650100 China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ma
authors.affiliation: Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China.
authors.forename: Haiqin
authors.initials: H
authors.lastname: Yu
authors.affiliation: Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China.
authors.forename: Dunhuang
authors.initials: D
authors.lastname: Fang
authors.affiliation: Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China.
authors.forename: Yongping
authors.initials: Y
authors.lastname: Li
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China ; University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wang
authors.affiliation: CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500 China ; Yunnan Agricultural University, Kunming, 650100 China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China.
authors.forename: Bingguang
authors.initials: B
authors.lastname: Xiao
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics*; D000595:Amino Acid Sequence; D016000:Cluster Analysis; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D016681:Genome, Fungal / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D054884:Host-Pathogen Interactions; D008969:Molecular Sequence Data; D010838:Phytophthora / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D013045:Species Specificity; D014026:Nicotiana / Q000235:genetics / Q000382:microbiology; D014774:Virulence / Q000235:genetics
chemical_list: D018528:ATP-Binding Cassette Transporters; D005656:Fungal Proteins
keywords: Black shank; Genomes; Hybrid assembly; Phytophthora nicotianae; RxLR effector
references.citation: New Phytol. 2008;177(2):480-492
references.pmid: 18028297
references.citation: Science. 2010 Dec 10;330(6010):1549-1551
references.pmid: 21148394
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3417-24
references.pmid: 23966565
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Bioinformatics. 2007 May 1;23(9):1061-7
references.pmid: 17332020
references.citation: Annu Rev Cell Biol. 1992;8:67-113
references.pmid: 1282354
references.citation: J Comput Biol. 2012 May;19(5):455-77
references.pmid: 22506599
references.citation: Mol Plant Microbe Interact. 2011 Jul;24(7):827-38
references.pmid: 21361788
references.citation: J Mol Biol. 1997 Apr 25;268(1):78-94
references.pmid: 9149143
references.citation: New Phytol. 2010 Jan;185(1):248-57
references.pmid: 19807870
references.citation: Science. 2000 Mar 24;287(5461):2196-204
references.pmid: 10731133
references.citation: Genome Biol. 2010;11(7):R73
references.pmid: 20626842
references.citation: Genome Res. 2008 Feb;18(2):324-30
references.pmid: 18083777
references.citation: PLoS One. 2012;7(10):e46679
references.pmid: 23056399
references.citation: Genomics Proteomics Bioinformatics. 2010 Mar;8(1):77-80
references.pmid: 20451164
references.citation: Gigascience. 2012 Dec 27;1(1):18
references.pmid: 23587118
references.citation: Plant Cell. 2014 Mar;26(3):1345-59
references.pmid: 24632534
references.citation: Fungal Genet Biol. 2000 Jun;30(1):1-15
references.pmid: 10955904
references.citation: Genome Biol. 2004;5(2):R12
references.pmid: 14759262
references.citation: Plant Physiol. 2011 Feb;155(2):628-44
references.pmid: 21119047
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: Plant Cell. 2007 Aug;19(8):2349-69
references.pmid: 17675403
references.citation: PLoS Pathog. 2014 Apr 24;10(4):e1004057
references.pmid: 24763622
references.citation: Proc Natl Acad Sci U S A. 2015 May 5;112(18):5850-5
references.pmid: 25902521
references.citation: Plant Dis. 2005 Nov;89(11):1220-1228
references.pmid: 30786447
references.citation: Science. 2006 Sep 1;313(5791):1261-6
references.pmid: 16946064
references.citation: Fungal Genet Biol. 2005 Jul;42(7):611-23
references.pmid: 15950158
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):45-8
references.pmid: 10592178
references.citation: Bioinformatics. 2000 Nov;16(11):1040-1
references.pmid: 11159316
references.citation: PLoS One. 2013 Oct 04;8(10):e75072
references.pmid: 24124466
references.citation: Plant Cell. 1998 Sep;10(9):1413-26
references.pmid: 9724689
references.citation: Genome Res. 2003 Sep;13(9):2178-89
references.pmid: 12952885
references.citation: Nature. 2009 Sep 17;461(7262):393-8
references.pmid: 19741609
references.citation: Fungal Genet Biol. 2004 Mar;41(3):369-80
references.pmid: 14761797
references.citation: Bioinformatics. 2006 May 15;22(10):1269-71
references.pmid: 16543274
references.citation: BMC Genomics. 2015 Oct 05;16:741
references.pmid: 26438312
references.citation: Nat Biotechnol. 2012 Jul 01;30(7):693-700
references.pmid: 22750884
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):27-30
references.pmid: 10592173
references.citation: Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8
references.pmid: 21400694
references.citation: Genome Res. 2003 Jul;13(7):1675-85
references.pmid: 12840044
references.citation: Genome Res. 2009 Jun;19(6):1117-23
references.pmid: 19251739
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12
references.pmid: 15215400
references.citation: Bioinformatics. 2004 Nov 1;20(16):2878-9
references.pmid: 15145805
references.citation: Trends Microbiol. 2003 Oct;11(10):462-9
references.pmid: 14557029
references.citation: PLoS One. 2013;8(3):e59517
references.pmid: 23536880