| Literature DB >> 22679601 |
The inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in Phytophthora.
Fabian Runge1, Sabine Telle, Sebastian Ploch, Elizabeth Savory, Brad Day, Rahul Sharma, Marco Thines.
Abstract
Pathogens belonging to the Oomycota, a group of heterokont, fungal-like organisms, are amongst the most notorious pathogens in agriculture. In particular, the obligate biotrophic downy mildews and the hemibiotrophic members of the genus Phytophthora are responsible for a huge variety of destructive diseases, including sudden oak death caused by P. ramorum, potato late blight caused by P. infestans, cucurbit downy mildew caused by Pseudoperonospora cubensis, and grape downy mildew caused by Plasmopara viticola. About 800 species of downy mildews and roughly 100 species of Phytophthora are currently accepted, and recent studies have revealed that these groups are closely related. However, the degree to which Phytophthora is paraphyletic and where exactly the downy mildews insert into this genus in relation to other clades could not be inferred with certainty to date. Here we present a molecular phylogeny encompassing all clades of Phytophthora as represented in a multi-locus dataset and two representatives of the monophyletic downy mildews from divergent genera. Our results demonstrate that Phytophthora is at least six times paraphyletic with respect to the downy mildews. The downy mildew representatives are consistently nested within clade 4 (contains Phytophthora palmivora), which is placed sister to clade 1 (contains Phytophthora infestans). This finding would either necessitate placing all downy mildews and Phytopthora species in a single genus, either under the oldest generic name Peronospora or by conservation the later name Phytophthora, or the description of at least six new genera within Phytophthora. The complications of both options are discussed, and it is concluded that the latter is preferable, as it warrants fewer name changes and is more practical.Entities:
Keywords: AU test; Peronosporaceae; Phytophthora; downy mildews; multigene phylogeny; taxonomy
Year: 2011 PMID： 22679601 PMCID： PMC3359814 DOI： 10.5598/imafungus.2011.02.02.07
Source DB: PubMed Journal: IMA Fungus ISSN： 2210-6340 Impact factor: 3.515
INTRODUCTION
MATERIALS AND METHODS
Table S1. GenBank accession numbers for the sequences used in the present study.
| P10568 | EU080605.1 | EU080606.1 | EU080607.1 | EU080608.1 | EU080609.1 | EU080610.1 | EU080611.1 | |
| P13365 | EU080182.1 | EU080183.1 | EU080184.1 | EU080185.1 | EU080186.1 | EU080187.1 | EU080188.1 | |
| P10213 | EU080809.1 | EU080810.1 | EU080811.1 | EU080812.1 | EU080813.1 | EU080814.1 | EU080815.1 | |
| P10690 | EU080564.1 | EU080565.1 | EU080566.1 | EU080567.1 | EU080568.1 | EU080569.1 | EU080570.1 | |
| P10705 | EU080644.1 | EU080645.1 | EU080646.1 | EU080647.1 | EU080648.1 | EU080649.1 | EU080650.1 | |
| P1620 | EU080612.1 | EU080613.1 | EU080614.1 | EU080615.1 | EU080616.1 | EU080617.1 | EU080618.1 | |
| P10117 | EU080741.1 | EU080742.1 | EU080743.1 | EU080744.1 | EU080745.1 | EU080746.1 | EU080747.1 | |
| P6950 | EU080161.1 | EU080162.1 | EU080163.1 | EU080164.1 | EU080165.1 | EU080166.1 | EU080167.1 | |
| P6945 | EU079934.1 | EU079935.1 | EU079936.1 | EU079937.1 | EU079938.1 | EU079939.1 | EU079940.1 | |
| P10414 | EU080523.1 | EU080524.1 | EU080525.1 | EU080526.1 | EU080527.1 | EU080528.1 | EU080529.1 | |
| P10153 | EU080768.1 | EU080769.1 | EU080770.1 | EU080771.1 | EU080772.1 | EU080773.1 | EU080774.1 | |
| P10154 | EU080782.1 | EU080783.1 | EU080784.1 | EU080785.1 | EU080786.1 | EU080787.1 | EU080788.1 | |
| P0714 | EU080277.1 | EU080278.1 | EU080279.1 | EU080280.1 | EU080281.1 | EU080282.1 | EU080283.1 | |
| P0715 | EU080284.1 | EU080285.1 | EU080286.1 | EU080287.1 | EU080288.1 | EU080289.1 | EU080290.1 | |
| P3105 | EU080100.1 | EU080101.1 | EU080102.1 | EU080103.1 | EU080104.1 | EU080105.1 | EU080106.1 | |
| P0592 | EU080550.1 | EU080551.1 | EU080552.1 | EU080553.1 | EU080554.1 | EU080555.1 | EU080556.1 | |
| P0253 | EU080851.1 | EU080852.1 | EU080853.1 | EU080854.1 | EU080855.1 | EU080856.1 | EU080857.1 | |
| P10735 | EU079618.1 | EU079619.1 | EU079620.1 | EU079621.1 | EU079622.1 | EU079623.1 | EU079624.1 | |
| P1314 | EU080405.1 | EU080406.1 | EU080407.1 | EU080408.1 | EU080409.1 | EU080410.1 | EU080411.1 | |
| P0630 | EU080419.1 | EU080420.1 | EU080421.1 | EU080422.1 | EU080423.1 | EU080424.1 | EU080425.1 | |
| P10452 | EU080619.1 | EU080620.1 | EU080621.1 | EU080622.1 | EU080623.1 | EU080624.1 | EU080625.1 | |
| P10386 | EU079543.1 | EU079544.1 | EU079545.1 | EU079546.1 | EU079547.1 | EU079548.1 | EU079549.1 | |
| P1319 | EU079736.1 | EU079737.1 | EU079738.1 | EU079739.1 | EU079740.1 | EU079741.1 | EU079742.1 | |
| P10719 | EU079658.1 | EU079659.1 | EU079660.1 | EU079661.1 | EU079662.1 | EU079663.1 | EU079664.1 | |
| P2159 | EU079756.1 | EU079757.1 | EU079758.1 | EU079759.1 | EU079760.1 | EU079761.1 | EU079762.1 | |
| P8495 | EU079948.1 | EU079949.1 | EU079950.1 | EU079951.1 | EU079952.1 | EU079953.1 | EU079954.1 | |
| P7902 | EU080235.1 | EU080236.1 | EU080237.1 | EU080238.1 | EU080239.1 | EU080240.1 | EU080241.1 | |
| P6310 | EU080537.1 | EU080538.1 | EU080539.1 | EU080540.1 | EU080541.1 | EU080542.1 | EU080543.1 | |
| P3942 | EU079866.1 | EU079867.1 | EU079868.1 | EU079869.1 | EU079870.1 | EU079871.1 | EU079872.1 | |
| P6317 | EU079906.1 | EU079907.1 | EU079908.1 | EU079909.1 | EU079910.1 | EU079911.1 | EU079912.1 | |
| P1088 | EU080446.1 | EU080447.1 | EU080448.1 | EU080449.1 | EU080450.1 | EU080451.1 | EU080452.1 | |
| P8218 | EU080351.1 | EU080352.1 | EU080353.1 | EU080354.1 | EU080355.1 | EU080356.1 | EU080357.1 | |
| P8224 | EU080371.1 | EU080372.1 | EU080373.1 | EU080374.1 | EU080375.1 | EU080376.1 | EU080377.1 | |
| P10331 | EU079506.1 | EU079507.1 | EU079508.1 | EU079509.1 | EU079510.1 | EU079511.1 | EU079512.1 | |
| P10382 | EU080775.1 | EU080776.1 | EU080777.1 | EU080778.1 | EU080779.1 | EU080780.1 | EU080781.1 | |
| P1699 | EU079827.1 | EU079828.1 | EU079829.1 | EU079830.1 | EU079831.1 | EU079832.1 | EU079833.1 | |
| P10385 | EU080433.1 | EU080434.1 | EU080435.1 | EU080436.1 | EU080437.1 | EU080438.1 | EU080439.1 | |
| P10324 | EU079481.1 | EU079482.1 | EU079483.1 | EU079484.1 | EU079485.1 | EU079486.1 | EU079487.1 | |
| P10725 | EU080034.1 | EU080035.1 | EU080036.1 | EU080037.1 | EU080038.1 | EU080039.1 | EU080040.1 | |
| P10969 | EU079679.1 | EU079680.1 | EU079681.1 | EU079682.1 | EU079683.1 | EU079684.1 | EU079685.1 | |
| P3821 | EU080651.1 | EU080652.1 | EU080653.1 | EU080654.1 | EU080655.1 | EU080656.1 | EU080657.1 | |
| P10619 | EU080222.1 | EU080223.1 | EU080224.1 | EU080225.1 | EU080226.1 | EU080227.1 | EU080228.1 | |
| P10337 | EU080530.1 | EU080531.1 | EU080532.1 | EU080533.1 | EU080534.1 | EU080535.1 | EU080536.1 | |
| P11056 | EU080072.1 | EU080073.1 | EU080074.1 | EU080075.1 | EU080076.1 | EU080077.1 | EU080078.1 | |
| P10167 | EU080795.1 | EU080796.1 | EU080797.1 | EU080798.1 | EU080799.1 | EU080800.1 | EU080801.1 | |
| P3822 | EU079513.1 | EU079514.1 | EU079515.1 | EU079516.1 | EU079517.1 | EU079518.1 | EU079519.1 | |
| P3826 | EU080168.1 | EU080169.1 | EU080170.1 | EU080171.1 | EU080172.1 | EU080173.1 | EU080174.1 | |
| P6767 | EU080129.1 | EU080130.1 | EU080131.1 | EU080132.1 | EU080133.1 | EU080134.1 | EU080135.1 | |
| P3939 | EU079859.1 | EU079860.1 | EU079861.1 | EU079862.1 | EU079863.1 | EU079864.1 | EU079865.1 | |
| P10650 | EU079625.1 | EU079626.1 | EU079627.1 | EU079628.1 | EU079629.1 | EU079630.1 | EU079631.1 | |
| P10651 | EU079632.1 | EU079633.1 | EU079634.1 | EU079635.1 | EU079636.1 | EU079637.1 | EU079638.1 | |
| P10341 | EU080384.1 | EU080385.1 | EU080386.1 | EU080387.1 | EU080388.1 | EU080389.1 | EU080390.1 | |
| P6195 | EU080175.1 | EU080176.1 | EU080177.1 | EU080178.1 | EU080179.1 | EU080180.1 | EU080181.1 | |
| P6703 | EU080209.1 | EU080210.1 | EU080211.1 | EU080212.1 | EU080213.1 | EU080214.1 | EU080215.1 | |
| P8478 | EU079941.1 | EU079942.1 | EU079943.1 | EU079944.1 | EU079945.1 | EU079946.1 | EU079947.1 | |
| P10225 | EU080830.1 | EU080831.1 | EU080832.1 | EU080833.1 | EU080834.1 | EU080835.1 | EU080836.1 | |
| P10226 | EU080837.1 | EU080838.1 | EU080839.1 | EU080840.1 | EU080841.1 | EU080842.1 | EU080843.1 | |
| P10227 | EU080844.1 | EU080845.1 | EU080846.1 | EU080847.1 | EU080848.1 | EU080849.1 | EU080850.1 | |
| P3882 | EU080111.1 | EU080112.1 | EU080113.1 | EU080114.1 | EU080115.1 | EU080116.1 | EU080117.1 | |
| P10187 | EU080802.1 | EU080803.1 | EU080804.1 | EU080805.1 | EU080806.1 | EU080807.1 | EU080808.1 | |
| P3389 | EU079814.1 | EU079815.1 | EU079816.1 | EU079817.1 | EU079818.1 | EU079819.1 | EU079820.1 | |
| P10613 | EU079605.1 | EU079606.1 | EU079607.1 | EU079608.1 | EU079609.1 | EU079610.1 | EU079611.1 | |
| P10681 | EU079645.1 | EU079646.1 | EU079647.1 | EU079648.1 | EU079649.1 | EU079650.1 | EU079651.1 | |
| P8223 | EU080364.1 | EU080365.1 | EU080366.1 | EU080367.1 | EU080368.1 | EU080369.1 | EU080370.1 | |
| P8618 | EU080195.1 | EU080196.1 | EU080197.1 | EU080198.1 | EU080199.1 | EU080200.1 | EU080201.1 | |
| P3888 | EU079852.1 | EU079853.1 | EU079854.1 | EU079855.1 | EU079856.1 | EU079857.1 | EU079858.1 | |
| P10267 | EU080004.1 | EU080005.1 | EU080006.1 | EU080007.1 | EU080008.1 | EU080009.1 | EU080010.1 | |
| P6128 | EU079873.1 | EU079874.1 | EU079875.1 | EU079876.1 | EU079877.1 | EU079878.1 | EU079879.1 | |
| P10683 | EU079899.1 | EU079900.1 | EU079901.1 | EU079902.1 | EU079903.1 | EU079904.1 | EU079905.1 | |
| P8516 | EU079969.1 | EU079970.1 | EU079971.1 | EU079972.1 | EU079973.1 | EU079974.1 | EU079975.1 | |
| P3136 | EU080058.1 | EU080059.1 | EU080060.1 | EU080061.1 | EU080062.1 | EU080063.1 | EU080064.1 | |
| P10994 | EU079711.1 | EU079712.1 | EU079713.1 | EU079714.1 | EU079715.1 | EU079716.1 | EU079717.1 | |
| P0646 | EU080702.1 | EU080703.1 | EU080704.1 | EU080705.1 | EU080706.1 | EU080707.1 | EU080708.1 | |
| P3005 | EU079775.1 | EU079776.1 | EU079777.1 | EU079778.1 | EU079779.1 | EU079780.1 | EU079781.1 | |
| P10410 | EU080065.1 | EU080066.1 | EU080067.1 | EU080068.1 | EU080069.1 | EU080070.1 | EU080071.1 | |
| P10327 | EU079499.1 | EU079500.1 | EU079501.1 | EU079502.1 | EU079503.1 | EU079504.1 | EU079505.1 | |
| P10288 | EU079474.1 | EU079475.1 | EU079476.1 | EU079477.1 | EU079478.1 | EU079479.1 | EU079480.1 | |
| P6303 | EU080598.1 | EU080599.1 | EU080600.1 | EU080601.1 | EU080602.1 | EU080603.1 | EU080604.1 | |
| P10802 | EU080715.1 | EU080716.1 | EU080717.1 | EU080718.1 | EU080719.1 | EU080720.1 | EU080721.1 | |
| P10116 | EU079962.1 | EU079963.1 | EU079964.1 | EU079965.1 | EU079966.1 | EU079967.1 | EU079968.1 | |
| P1452 | EU080503.1 | EU080504.1 | EU080505.1 | EU080506.1 | EU080507.1 | EU080508.1 | EU080509.1 | |
| P7146 | EU079555.1 | EU079556.1 | EU079557.1 | EU079558.1 | EU079559.1 | EU079560.1 | EU079561.1 | |
| P10318 | EU080676.1 | EU080677.1 | EU080678.1 | EU080679.1 | EU080680.1 | EU080681.1 | EU080682.1 | |
| P10617 | EU080242.1 | EU080243.1 | EU080244.1 | EU080245.1 | EU080246.1 | EU080247.1 | EU080248.1 | |
| P0255 | EU080338.1 | EU080339.1 | EU080340.1 | EU080341.1 | EU080342.1 | EU080343.1 | EU080344.1 | |
| P0113 | EU080464.1 | EU080465.1 | EU080466.1 | EU080467.1 | EU080468.1 | EU080469.1 | EU080470.1 | |
| P10145 | EU080748.1 | EU080749.1 | EU080750.1 | EU080751.1 | EU080752.1 | EU080753.1 | EU080754.1 | |
| P10150 | EU080761.1 | EU080762.1 | EU080763.1 | EU080764.1 | EU080765.1 | EU080766.1 | EU080767.1 | |
| P15001 | EU080249.1 | EU080250.1 | EU080251.1 | EU080252.1 | EU080253.1 | EU080254.1 | EU080255.1 | |
| P15005 | EU080256.1 | EU080257.1 | EU080258.1 | EU080259.1 | EU080260.1 | EU080261.1 | EU080262.1 | |
| P15004 | EU080263.1 | EU080264.1 | EU080265.1 | EU080266.1 | EU080267.1 | EU080268.1 | EU080269.1 | |
| P10728 | EU079672.1 | EU079673.1 | EU079674.1 | EU079675.1 | EU079676.1 | EU079677.1 | EU079678.1 | |
| P6207 | EU079880.1 | EU079881.1 | EU079882.1 | EU079883.1 | EU079884.1 | EU079885.1 | EU079886.1 | |
| P10333 | EU080398.1 | EU080399.1 | EU080400.1 | EU080401.1 | EU080402.1 | EU080403.1 | EU080404.1 | |
| P10220 | EU080816.1 | EU080817.1 | EU080818.1 | EU080819.1 | EU080820.1 | EU080821.1 | EU080822.1 | |
| P10224 | EU080823.1 | EU080824.1 | EU080825.1 | EU080826.1 | EU080827.1 | EU080828.1 | EU080829.1 | |
| P10437 | EU079562.1 | EU079563.1 | EU079564.1 | EU079565.1 | EU079566.1 | EU079567.1 | EU079568.1 | |
| P10339 | EU080426.1 | EU080427.1 | EU080428.1 | EU080429.1 | EU080430.1 | EU080431.1 | EU080432.1 | |
| P10433 | EU080516.1 | EU080517.1 | EU080518.1 | EU080519.1 | EU080520.1 | EU080521.1 | EU080522.1 | |
| MD9-2 | EU080900.1 | EU080901.1 | EU080902.1 | EU080903.1 | EU080904.1 | EU080905.1 | EU080906.1 | |
| P10334 | EU080489.1 | EU080490.1 | EU080491.1 | EU080492.1 | EU080493.1 | EU080494.1 | EU080495.1 | |
| P10441 | EU080591.1 | EU080592.1 | EU080593.1 | EU080594.1 | EU080595.1 | EU080596.1 | EU080597.1 | |
| P10301 | EU080683.1 | EU080684.1 | EU080685.1 | EU080686.1 | EU080687.1 | EU080688.1 | EU080689.1 | |
| P10811 | EU080496.1 | EU080497.1 | EU080498.1 | EU080499.1 | EU080500.1 | EU080501.1 | EU080502.1 | |
| P10359 | EU080571.1 | EU080572.1 | EU080573.1 | EU080574.1 | EU080575.1 | EU080576.1 | EU080577.1 | |
| P10355 | EU080578.1 | EU080579.1 | EU080580.1 | EU080581.1 | EU080582.1 | EU080583.1 | EU080584.1 | |
| P7788 | EU080637.1 | EU080638.1 | EU080639.1 | EU080640.1 | EU080641.1 | EU080642.1 | EU080643.1 | |
| P3163 | EU080270.1 | EU080271.1 | EU080272.1 | EU080273.1 | EU080274.1 | EU080275.1 | EU080276.1 | |
| P1475 | EU079749.1 | EU079750.1 | EU079751.1 | EU079752.1 | EU079753.1 | EU079754.1 | EU079755.1 | |
| P3114 | EU079789.1 | EU079790.1 | EU079791.1 | EU079792.1 | EU079793.1 | EU079794.1 | EU079795.1 | |
| P10417 | EU080391.1 | EU080392.1 | EU080393.1 | EU080394.1 | EU080395.1 | EU080396.1 | EU080397.1 | |
| P10672 | EU080412.1 | EU080413.1 | EU080414.1 | EU080415.1 | EU080416.1 | EU080417.1 | EU080418.1 | |
| P8619 | EU080202.1 | EU080203.1 | EU080204.1 | EU080205.1 | EU080206.1 | EU080207.1 | EU080208.1 | |
| P10330 | EU080557.1 | EU080558.1 | EU080559.1 | EU080560.1 | EU080561.1 | EU080562.1 | EU080563.1 | |
| P8497 | EU079955.1 | EU079956.1 | EU079957.1 | EU079958.1 | EU079959.1 | EU079960.1 | EU079961.1 | |
| P7010 | EU080141.1 | EU080142.1 | EU080143.1 | EU080144.1 | EU080145.1 | EU080146.1 | EU080147.1 | |
| P10329 | EU080305.1 | EU080306.1 | EU080307.1 | EU080308.1 | EU080309.1 | EU080310.1 | EU080311.1 | |
| P10328 | EU079692.1 | EU079693.1 | EU079694.1 | EU079695.1 | EU079696.1 | EU079697.1 | EU079698.1 | |
| P3019 | EU079782.1 | EU079783.1 | EU079784.1 | EU079785.1 | EU079786.1 | EU079787.1 | EU079788.1 | |
| P10342 | EU080440.1 | EU080441.1 | EU080442.1 | - | EU080443.1 | EU080444.1 | EU080445.1 | |
| P3980 | EU080483.1 | EU080484.1 | EU080485.1 | - | EU080486.1 | EU080487.1 | EU080488.1 | |
| Genome | ||||||||
| Genome | AY035496.1 |
a Local identification numbers from the World Phytophthora Genetic Resource Collection (P) and West Virginia University (MD).
Fig. 1.Phylogenetic reconstruction for Phytophthora and the downy mildews (Bayesian Analysis), with support values in Minimum Evolution, Maximum Likelihood, and Bayesian Analysis, in the respective order, on the branches, and Bremer support below the branches. Small Asterisks denote maximum support in a single analysis, big asterisks denote maximum support in all three phylogenetic analyses. Clade designations are those of Blair , with some additional differentiation corresponding to the statistical testing of the tree topology as given in Table 1. Predominantly caducous and papillate clades are highlighted in blue, the clade containing downy mildews is highlighted in green and the clades with predominantly non-caducous, non-papillate or semi-papillate members are highlighted in brown. For Phytophthora, the highlighted areas are divided into blocks representing groups that lead to paraphyly of Phytophthora and could potentially serve as a basis for the description of new genera.
Table 1. Results of the site-wise log-likelihoods generated under possible associations of species in base edges. The first column gives the possible associations for which the site-wise log-likelihoods were produced. Columns show the support values for the approximately unbiased (AU) test, the observed log-likelihood differences of the edges (OBS), Bootstrap probability tests (NP, BP; and PP), Kishino-Hasegawa (KH) test, Shimodaira-Hasegawa (SH) test, weighted Kishino-Hasegawa (WKH) test, and the weighted Shimodaira-Hasegawa (WSH) test.
| (4.2, DM) | 0,983 | −106,9 | 0,992 | 0,993 | 1,000 | 0,966 | 0,992 | 0,974 | 0,989 |
| (1, 4, DM) | 0,983 | −106,9 | 0,992 | 0,993 | 1,000 | 0,966 | 0,992 | 0,974 | 0,989 |
| (1, 2, 4, DM) | 0,983 | −106,9 | 0,992 | 0,993 | 1,000 | 0,966 | 0,992 | 0,974 | 0,989 |
| (4, DM) | 0,979 | −39,4 | 0,985 | 0,985 | 1,000 | 0,901 | 0,988 | 0,94 | 0,996 |
| (1c,1b) | 0,882 | −32,7 | 0,981 | 0,981 | 1,000 | 0,860 | 0,925 | 0,925 | 0,925 |
| (3, 6) | 0,713 | −28,2 | 0,918 | 0,919 | 1,000 | 0,753 | 0,753 | 0,753 | 0,753 |
| (1–8, 9.1, DM) | 0,679 | −14,1 | 0,648 | 0,646 | 1,000 | 0,721 | 0,909 | 0,666 | 0,916 |
| (1–4, 6, DM) | 0,670 | −5,6 | 0,47 | 0,467 | 0,997 | 0,592 | 0,967 | 0,592 | 0,967 |
| (2b, 2.2) | 0,644 | −5,1 | 0,407 | 0,399 | 0,973 | 0,593 | 0,911 | 0,593 | 0,927 |
| (5, 7) | 0,617 | −14,7 | 0,741 | 0,742 | 1,000 | 0,653 | 0,807 | 0,653 | 0,831 |
| (1, 2, 4, 5, 7, DM) | 0,555 | 5,6 | 0,104 | 0,103 | 0,002 | 0,408 | 0,949 | 0,408 | 0,951 |
| (1, 2, 4, 5, DM) | 0,440 | 14,7 | 0,251 | 0,252 | 0,000 | 0,347 | 0,815 | 0,347 | 0,806 |
| (1–6, DM) | 0,383 | 14,7 | 0,259 | 0,258 | 0,000 | 0,347 | 0,678 | 0,347 | 0,676 |
| (2.1, 2b) | 0,356 | 5,1 | 0,593 | 0,601 | 0,027 | 0,407 | 0,585 | 0,407 | 0,569 |
| (9.1,9.2) | 0,321 | 14,1 | 0,352 | 0,354 | 0,000 | 0,279 | 0,678 | 0,334 | 0,668 |
| (3,5–7) | 0,302 | 5,8 | 0,093 | 0,091 | 0,000 | 0,232 | 0,911 | 0,232 | 0,821 |
| (1–5, 7, DM) | 0,287 | 28,2 | 0,082 | 0,081 | 0,000 | 0,247 | 0,636 | 0,247 | 0,645 |
| (1–4, DM) | 0,287 | 28,2 | 0,082 | 0,081 | 0,000 | 0,247 | 0,636 | 0,247 | 0,645 |
| (1b,1.1) | 0,118 | 32,7 | 0,019 | 0,019 | 0,000 | 0,140 | 0,596 | 0,075 | 0,330 |
| (3, 6, DM) | 0,022 | 106,9 | 0,007 | 0,006 | 0,000 | 0,034 | 0,093 | 0,015 | 0,065 |
| (1, 4.1) | 0,021 | 39,4 | 0,015 | 0,015 | 0,000 | 0,099 | 0,406 | 0,031 | 0,156 |
| (1, 4) | 0,017 | 106,9 | 0,008 | 0,007 | 0,000 | 0,034 | 0,093 | 0,015 | 0,051 |
| (1, 2, 4, 5) | 0,017 | 106,9 | 0,008 | 0,007 | 0,000 | 0,034 | 0,093 | 0,015 | 0,051 |
| (1, 2, 4) | 0,017 | 106,9 | 0,008 | 0,007 | 0,000 | 0,034 | 0,093 | 0,015 | 0,051 |
The following species were randomly chosen as representatives for the corresponding clades and subclades in the statistical analysis – 1c, Phytophthora cactorum ; 1b, P. nicotianae; 1c, P. iranica; 1.1, P. infestans; 2ab, P. capsici; 2.1, P. bisheria; 2.2, P. multivesiculata; 3, P. nemorosa; 4.1, P. quercina; 4.2, P. palmivora; 5, P. katsurae; 6, P. humicola; 7, P. europaea; 8, P. ramorum; 9.1, P. polonica; 9.2, P. captiosa; 10, P. boehmeriae; DM, Pseudoperonospora cubensis.
RESULTS
Fig. S1.Bayesian analysis of the clade representatives used for the statistical tests for the topology of the grouping of the individual clades with posterior probability values.
DISCUSSION
28 in total
1. MRBAYES: Bayesian inference of phylogenetic trees.
Journal: Bioinformatics Date: 2001-08 Impact factor: 6.937
2. CONSEL: for assessing the confidence of phylogenetic tree selection.
Journal: Bioinformatics Date: 2001-12 Impact factor: 6.937
3. A molecular phylogeny of Phytophthora and related oomycetes.
Journal: Fungal Genet Biol Date: 2000-06 Impact factor: 3.495
4. An approximately unbiased test of phylogenetic tree selection.
Journal: Syst Biol Date: 2002-06 Impact factor: 15.683
5. PRAP-computation of Bremer support for large data sets.
Journal: Mol Phylogenet Evol Date: 2004-05 Impact factor: 4.286
6. Phytophthora kernoviae sp. nov., an invasive pathogen causing bleeding stem lesions on forest trees and foliar necrosis of ornamentals in the UK.
Journal: Mycol Res Date: 2005-08
7. Phytophthora polonica, a new species isolated from declining Alnus glutinosa stands in Poland.
Journal: FEMS Microbiol Lett Date: 2006-08 Impact factor: 2.742
8. Phytophthora captiosa sp. nov. and P. fallax sp. nov. causing crown dieback of Eucalyptus in New Zealand.
Journal: Mycol Res Date: 2006-04
9. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.
Journal: Science Date: 2006-09-01 Impact factor: 47.728
10. MAFFT version 5: improvement in accuracy of multiple sequence alignment.
Journal: Nucleic Acids Res Date: 2005-01-20 Impact factor: 16.971
15 in total
Review 1. Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands.
Journal: Persoonia Date: 2018-04-30 Impact factor: 11.051
Review 2. Dynamics and innovations within oomycete genomes: insights into biology, pathology, and evolution.
Journal: Eukaryot Cell Date: 2012-08-24
3. Phytophthora: an ancient, historic, biologically and structurally cohesive and evolutionarily successful generic concept in need of preservation.
Journal: IMA Fungus Date: 2022-06-27 Impact factor: 8.044
4. Dinoflagellate phylogeny revisited: using ribosomal proteins to resolve deep branching dinoflagellate clades.
Journal: Mol Phylogenet Evol Date: 2013-10-14 Impact factor: 4.286
5. Which morphological characteristics are most influenced by the host matrix in downy mildews? A case study in Pseudoperonospora cubensis.
Journal: PLoS One Date: 2012-11-15 Impact factor: 3.240
6. Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present-day large gene families.
Journal: Genome Biol Evol Date: 2012-01-09 Impact factor: 3.416
7. Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.
Journal: BMC Genomics Date: 2015-10-05 Impact factor: 3.969
8. Decay of genes encoding the oomycete flagellar proteome in the downy mildew Hyaloperonospora arabidopsidis.
Journal: PLoS One Date: 2012-10-15 Impact factor: 3.240
9. Baobabopsis, a new genus of graminicolous downy mildews from tropical Australia, with an updated key to the genera of downy mildews.
Journal: IMA Fungus Date: 2015-11-25 Impact factor: 3.515
10. Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes.
Journal: mSphere Date: 2017-04-12 Impact factor: 4.389