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Table 1 The 95 genomes validated after selection based on PCA (see text). Column ‘Status’ states whether genome is complete or gives number of contigs if not

From: Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses

Strain Isolation Host Taxonomy Lineage Location Reference Source Accession/Project Status*
bilvae_NCPPB3213_India 1980 Rosids:Sapindales:Rutaceae outgroup India [14] NCBI CDHI01 60
glycines_CFBP2526_Sudan 1956 Rosids:Fabales:Fabaceae outgroup Sudan [23] NCBI AUWO01 complete
glycines_CFBP7119_Brazil 1981 Rosids:Fabales:Fabaceae outgroup Brazil [23] NCBI NZ_CM002264.1 complete
malv_X20_Burkina ? Rosids:Malvales:Malvaceae outgroup Burkina Faso [24] NCBI NZ_CM002029.1 complete
mang_LG81-27_Reunion 2009 Rosids:Sapindales:Anacardiaceae outgroup Reunion [25] NCBI PEBZ01 6
P._cissicola_LMG21719 1974 Rosids:Vitales:Vitaceae outgroup Japan [21] NCBI LOJT01 313
X._axon._bauhiniae_LMG548 1961 Rosids:Fabales:Fabaceae outgroup India [21] NCBI LOKR 192
X._axon._cajani_LMG558 1950 Rosids:Fabales:Fabaceae outgroup India [21] NCBI LOKQ01 312
X._axon._clitoriae_LMG9045 1974 Rosids:Fabales:Fabaceae outgroup India [21] NCBI LOKA01 91
X._axon._khayae_LMG753 1957 Rosids:Sapindales:Meliaceae outgroup Sudan [21] NCBI LOKN01 354
X._axon._martyniicola_LMG9049 1958 Asterids:Lamiales:Martyniaceae outgroup India [21] NCBI LOJX01 76
X._axon._melhusii_LMG9050 1961 Asterids:Lamiales:Lamiaceae outgroup India [21] NCBI LOJW01 101
X._axon._punicae_LMG_859 1959 Rosids:Myrtales:Lythraceae outgroup India [21] NCBI CAGJ01 217
X._camp._azadirachtae_LMG543 1971 Rosids:Sapindales:Meliaceae outgroup India [21] NCBI LOKS01 236
X._camp._centellae_LMG9044 1979 Asterids:Apiales:Apiaceae outgroup India [21] NCBI LOJR01 315
X._camp._durantae_LMG696 1956 Asterids:Lamiales:Verbenaceae outgroup India [21] NCBI LOKP01 187
X._camp._leeana_LMG9048 1967 Rosids:Vitales:Vitaceae outgroup India [21] NCBI LOJY01 92
X._camp._thespesiae_LMG9057 1978 Rosids:Malvales:Malvaceae outgroup India [21] NCBI LOJU01 93
X._camp._viticola 1972 Rosids:Vitales:Vitaceae outgroup India [21] NCBI CBZT01 50
X._camp._vitiscarnosae_LMG939 1962 Rosids:Vitales:Vitaceae outgroup India [21] NCBI LOKI01 105
X._camp._vitistrifoliae_LMG940 1961 Rosids:Vitales:Vitaceae outgroup India [21] NCBI LOKH01 184
X._camp._vitiswoodrowii_LMG954 1961 Rosids:Vitales:Vitaceae outgroup India [21] NCBI LOKG01 102
Xc_03-1638-1-1_Argentina_A 2003 Rosids:Sapindales:Rutaceae A Argentina [26] NCBI GCA_002952295.1 complete
Xc_306_Brazil_A 1997 Rosids:Sapindales:Rutaceae A Brazil [9] NCBI NC_003919.1 complete
Xc_5208_USA_A 2002 Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP009028.1 complete
Xc_AS270_Saudi_Arabia_As 1988 Rosids:Sapindales:Rutaceae A* Saudi Arabia [13] NW GCA_000950845.1 29
Xc_AS8_Saudi_Arabia_As ? Rosids:Sapindales:Rutaceae A* Saudi Arabia [13] NW GCA_000950875.1 32
Xc_AS9_Saudi_Arabia_As ? Rosids:Sapindales:Rutaceae A* Saudi Arabia [13] NW GCA_000950855.1 31
Xc_Aw12879_USA_Aw 2000 Rosids:Sapindales:Rutaceae Aw USA [27] NCBI NC_020815.1 complete
Xc_AW13_USA_Aw 2003 Rosids:Sapindales:Rutaceae Aw USA [13] NW NZ_CP009031.1 complete
Xc_AW14_USA_Aw 2005 Rosids:Sapindales:Rutaceae Aw USA [13] NW NZ_CP009034.1 complete
Xc_AW15_USA_Aw 2005 Rosids:Sapindales:Rutaceae Aw USA [13] NW NZ_CP009037.1 complete
Xc_AW16_USA_Aw 2005 Rosids:Sapindales:Rutaceae Aw USA [13] NW NZ_CP009040.1 complete
Xc_BL18_USA_A 2011 Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP009025.1 complete
Xc_C40_Reunion_A 1988 Rosids:Sapindales:Rutaceae A Reunion [14] Pruvost CCWX01 complete
Xc_CFBP2852_India_A ? Rosids:Sapindales:Rutaceae A India [14] Pruvost CCWI01 57
Xc_CFBP2911_Pakistan_As 1984 Rosids:Sapindales:Rutaceae A* Pakistan [14] Pruvost CCWD01 87
Xc_FB19_USA_A 2011 Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP009022.1 complete
Xc_FDC1083_Brazil_A 1980 Rosids:Sapindales:Rutaceae A Brazil [14] Pruvost CCVZ01 42
Xc_FDC1662_Brazil_A 2011 Rosids:Sapindales:Rutaceae A Brazil This study BIGA LAUN00000000 85
Xc_FDC1682_Oman_As 1986 Rosids:Sapindales:Rutaceae A* Oman This study BIGA LAUG00000000 168
Xc_FDC217_Brazil_A 2003 Rosids:Sapindales:Rutaceae A Brazil [14] Pruvost CCWY01 41
Xc_FDC628_Brazil_A 2001 Rosids:Sapindales:Rutaceae A Brazil This study BIGA LAUE00000000 101
Xc_FDC636_Brazil_A 1996 Rosids:Sapindales:Rutaceae A Brazil This study BIGA LAUQ00000000 127
Xc_FDC654_Brazil_A 1999 Rosids:Sapindales:Rutaceae A Brazil This study BIGA LAUF00000000 114
Xc_FDC828_Brazil_A 1997 Rosids:Sapindales:Rutaceae A Brazil This study BIGA LAUP00000000 121
Xc_gd2_China_A 2011 Rosids:Sapindales:Rutaceae A China [13] NW NZ_CP009019.1 complete
Xc_gd3_China_A 2011 Rosids:Sapindales:Rutaceae A China [13] NW NZ_CP009016.1 complete
Xc_JF90-2_Oman_As 1986 Rosids:Sapindales:Rutaceae A* Oman [14] Pruvost CCWA01 85
Xc_JF90-8_Oman_Aw 2002 Rosids:Sapindales:Rutaceae Aw Oman [14] Pruvost CCWB01 30
Xc_JJ10-1_Mauritius_A 1985 Rosids:Sapindales:Rutaceae A Mauritius [14] Pruvost CDDV01 258
Xc_JJ238-10_Maldives_A 1987 Rosids:Sapindales:Rutaceae A Maldives [14] Pruvost CCWC01 56
Xc_JJ238-24_Thailand_As 1989 Rosids:Sapindales:Rutaceae A* Thailand [14] Pruvost CCVX01 52
Xc_JK2-10_Saudi_Arabia_As 1988 Rosids:Sapindales:Rutaceae A* Saudi Arabia [14] NCBI CCWV01 complete
Xc_JK4-1_China_A 1985 Rosids:Sapindales:Rutaceae A China [14] Pruvost CDMR01 320
Xc_JM35-2_Saudi_Arabia_As 1992 Rosids:Sapindales:Rutaceae A* Saudi Arabia [14] Pruvost CDMS01 339
Xc_JS581_Iran_As 1997 Rosids:Sapindales:Rutaceae A* Iran [14] Pruvost CDAW01 358
Xc_JS584_Iran_As 1997 Rosids:Sapindales:Rutaceae A* Iran [14] Pruvost CCWF01 61
Xc_JW160-1_Bangladesh_A 2000 Rosids:Sapindales:Rutaceae A Bangladesh [14] Pruvost CCWH01 88
Xc_jx4_China_A 2011 Rosids:Sapindales:Rutaceae A China [13] NW NZ_CP009013.1 complete
Xc_jx5_China_A 2011 Rosids:Sapindales:Rutaceae A China [13] NW NZ_CP009010.1 complete
Xc_jx-6_China_A 2014 Rosids:Sapindales:Rutaceae A China Chen et al. (unpublished) NCBI NZ_CP011827.2 complete
Xc_LB100-1_Seychelles_A 2005 Rosids:Sapindales:Rutaceae A Seychelles [14] Pruvost CDAV01 299
Xc_LC80_Mali_A 2006 Rosids:Sapindales:Rutaceae A Mali [14] Pruvost CCWJ01 51
Xc_LD71a_Cambodia_As 2007 Rosids:Sapindales:Rutaceae A* Cambodia [14] Pruvost CCWE01 49
Xc_LE20-1_Ethiopia_As 2008 Rosids:Sapindales:Rutaceae A* Ethiopia [14] Pruvost CCWK01 41
Xc_LG115_India_Aw 2007 Rosids:Sapindales:Rutaceae Aw India [14] Pruvost CDAY01 377
Xc_LG117_Bangladesh_A 2009 Rosids:Sapindales:Rutaceae A Bangladesh [14] Pruvost CDAX01 338
Xc_LG98_Bangladesh_A 2006 Rosids:Sapindales:Rutaceae A Bangladesh [14] Pruvost CDBA01 323
Xc_LH201_Reunion_A 2010 Rosids:Sapindales:Rutaceae A Reunion [26] NCBI GCA_001922105.1 complete
Xc_LH276_Reunion_A 2010 Rosids:Sapindales:Rutaceae A Reunion [26] NCBI GCA_001922065.1 complete
Xc_LH37-1_Senegal_A2 2010 Rosids:Sapindales:Rutaceae A Senegal [14] Pruvost CDAS01 417
Xc_LJ207-7_Reunion_A 2012 Rosids:Sapindales:Rutaceae A Reunion [26] NCBI GCA_001922085.1 complete
Xc_LL074-4_Martinique_A 2014 Rosids:Sapindales:Rutaceae A Martinique [26] NCBI GCA_001922045.1 complete
Xc_LM180_Argentina_A 2003 Rosids:Sapindales:Rutaceae A Argentina [28] NCBI GCA_001939985.1 complete
Xc_LM199_Argentina_A 2015 Rosids:Sapindales:Rutaceae A Argentina [28] NCBI GCA_001939965.1 complete
Xc_LMG9322_USA_A 1986 Rosids:Sapindales:Rutaceae A USA [14] Pruvost CCVY01 46
Xc_mf20_USA_A 2011 Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP009007.1 complete
Xc_MN10_USA_A 2005 Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP009004.1 complete
Xc_MN11_USA_A ? Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP009001.1 complete
Xc_MN12_USA_A 1997 Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP008998.1 complete
Xc_NCPPB3562_India_A2 1988 Rosids:Sapindales:Rutaceae A India [14] Pruvost CCXZ01 98
Xc_NCPPB3607_India_As 1988 Rosids:Sapindales:Rutaceae A* India [14] Pruvost CDAT01 432
Xc_NCPPB3608_India_Aw 1988 Rosids:Sapindales:Rutaceae Aw India [14] Pruvost CCWG01 55
Xc_NCPPB3612_India_A2 1988 Rosids:Sapindales:Rutaceae A India [14] Pruvost CDAQ01 426
Xc_NIGEB-386_Iran_As 2009 Rosids:Sapindales:Rutaceae A* Iran [29] NCBI JRON01 183
Xc_NIGEB-88_Iran_As 2009 Rosids:Sapindales:Rutaceae A* Iran [30] NCBI LJGA01 18
Xc_NT17_USA_A 2011 Rosids:Sapindales:Rutaceae A USA [13] NW NZ_CP008995.1 complete
Xc_TX160042_USA_Aw 2015 Rosids:Sapindales:Rutaceae Aw USA [31] NCBI GCA_002139975.1 complete
Xc_TX160149_USA_Aw 2015 Rosids:Sapindales:Rutaceae Aw USA [31] NCBI GCA_002139975.1 complete
Xc_TX160197_USA_Aw 2015 Rosids:Sapindales:Rutaceae Aw USA [31] NCBI TX160197 complete
Xc_UI6_China_A 2011 Rosids:Sapindales:Rutaceae A China [13] NW NZ_CP008992.1 complete
Xc_UI7_China_A 2011 Rosids:Sapindales:Rutaceae A China [13] NW NZ_CP008989.1 complete
Xc_X2003-3218_USA_Aw 2003 Rosids:Sapindales:Rutaceae Aw USA [14] Pruvost CCWL01 52
Xc_Xac29-1_China_A ? Rosids:Sapindales:Rutaceae A China NCBI NCBI GCA_000348585.1 complete