Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Genome Sequencing and Assembly
3.2. Phylogenomic Reconstruction
3.3. Species Delineation Based on Average Nucleotide Identity
Pathovar and NCPPB Number | X. euvesicatoria LMG 27970 T | X. campestris ATCC 33913 | X. citri LMG 9322 | X. phaseoli 49119 |
---|---|---|---|---|
X. campestris pv. aberrans 2986 | 85.80 | 98.66 | 85.65 | 85.88 |
X. campestris pv. armoraciae 347 | 85.74 | 98.16 | 85.79 | 85.88 |
X. campestris pv. barbareae 983 | 85.79 | 97.31 | 85.84 | 85.95 |
X. campestris pv. incanae 937 | 85.78 | 97.29 | 85.79 | 85.89 |
X. campestris pv. papavericola 2970 | 85.66 | 96.49 | 85.60 | 85.78 |
X. campestris pv. plantaginis 1061 | 85.88 | 96.45 | 85.78 | 85.79 |
X. campestris pv. raphani 1946 | 85.83 | 97.23 | 85.72 | 85.80 |
X. phaseoli pv. passiflorae 2346 | 93.86 | 85.96 | 93.65 | 98.16 |
X. citri pv. merremiae 3114 | 93.85 | 85.81 | 96.20 | 93.91 |
X. citri pv. trichodesmae 585 | 93.77 | 85.83 | 96.16 | 93.82 |
X. euvesicatoria pv. alangii 1336 | 98.01 | 85.86 | 94.33 | 94.18 |
[X. campestris] pv. blepharidis 1757 | 97.90 | 85.86 | 94.45 | 94.11 |
[X. campestris] pv. carissae 2373 | 97.54 | 85.80 | 94.73 | 94.12 |
[X. campestris] pv. clerodendri 575 | 97.98 | 85.85 | 94.31 | 94.08 |
[X. campestris] pv. convolvuli 2498 | 98.13 | 85.93 | 94.50 | 94.14 |
[X. campestris] pv. coriandri 1758 | 97.98 | 85.89 | 94.47 | 94.10 |
[X. campestris] pv. daturae 2932 | 98.73 | 85.85 | 94.27 | 94.01 |
[X. campestris] pv. euphorbiae 1828 | 97.57 | 85.91 | 94.41 | 94.10 |
[X. campestris] pv. fici 2372 | 98.00 | 85.91 | 94.40 | 94.19 |
[X. campestris] pv. heliotropii 2057 | 97.53 | 85.97 | 94.31 | 94.06 |
[X. campestris] pv. ionidii 1334 | 97.92 | 85.88 | 94.38 | 94.08 |
[X. campestris] pv. lawsoniae 579 | 98.04 | 85.90 | 94.45 | 94.12 |
[X. campestris] pv. mirabilis 4348 | 98.00 | 85.84 | 94.36 | 94.17 |
[X. campestris] pv. obscurae 3759 | 98.42 | 85.93 | 94.37 | 94.11 |
[X. campestris] pv. paulliniae 3079 | 97.69 | 85.85 | 94.36 | 94.37 |
[X. campestris] pv. pennamericanum 4349 | 97.45 | 85.80 | 94.27 | 94.04 |
X. euvesicatoria pv. physalidis 1756 | 98.74 | 85.92 | 94.31 | 94.10 |
[X. campestris] pv. spermacoces 1760 | 97.83 | 85.86 | 94.50 | 94.10 |
[X. campestris] pv. uppalii 586 | 98.38 | 85.95 | 94.37 | 94.09 |
[X. campestris] pv. vernoniae 1787 | 98.10 | 85.95 | 94.41 | 94.18 |
[X. campestris] pv. viegasii 4351 | 98.05 | 85.94 | 94.31 | 94.18 |
[X. campestris] pv. zingibericola 4352 | 98.10 | 85.88 | 94.47 | 94.23 |
4. Discussion
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
GenBank Accession | Taxon | Reference |
---|---|---|
GCA_019201075.1 | [X. axonopodis] pv. passiflorae NCPPB 2346 | This study |
GCA_019201485.1 | [X. campestris] pv. blepharidis NCPPB 1757 | This study |
GCA_019201365.1 | [X. campestris] pv. carissae NCPPB 2373 | This study |
GCA_019201225.1 | [X. campestris] pv. clerodendri NCPPB 575 | This study |
GCA_019201245.1 | [X. campestris] pv. convolvuli NCPPB 2498 | This study |
GCA_019201305.1 | [X. campestris] pv. coriandri NCPPB 1758 | This study |
GCA_019201325.1 | [X. campestris] pv. daturae NCPPB 2932 | This study |
GCA_019201425.1 | [X. campestris] pv. euphorbiae NCPPB 1828 | This study |
GCA_019201375.1 | [X. campestris] pv. fici NCPPB 2372 | This study |
GCA_019201405.1 | [X. campestris] pv. heliotropii NCPPB 2057 | This study |
GCA_019201465.1 | [X. campestris] pv. ionidii NCPPB 1334 | This study |
GCA_019201185.1 | [X. campestris] pv. lawsoniae NCPPB 579 | This study |
GCA_019201545.1 | [X. campestris] pv. merremiae NCPPB 3114 | This study |
GCA_019201145.1 | [X. campestris] pv. mirabilis NCPPB 4348 | This study |
GCA_019201105.1 | [X. campestris] pv. obscurae NCPPB 3759 | This study |
GCA_019201285.1 | [X. campestris] pv. paulliniae NCPPB 3079 | This study |
GCA_019201165.1 | [X. campestris] pv. pennamericanum NCPPB 4349 | This study |
GCA_019201445.1 | [X. campestris] pv. spermacoces NCPPB 1760 | This study |
GCA_019201525.1 | [X. campestris] pv. trichodesmae NCPPB 585 | This study |
GCA_019201115.1 | [X. campestris] pv. uppalii NCPPB 586 | This study |
GCA_019201345.1 | [X. campestris] pv. vernoniae NCPPB 1787 | This study |
GCA_019201265.1 | [X. campestris] pv. viegasii NCPPB 4351 | This study |
GCA_019201205.1 | [X. campestris] pv. zingibericola NCPPB 4352 | This study |
GCA_002939705.1 | X. albilineans CFBP 2523 T | - |
GCA_001013475.1 | X. arboricola CFBP 2528 T | [81] |
GCA_001401595.1 | X. axonopodis LMG 982 T | - |
GCA_017163705.1 | X. bonasiae FX4 T | [82] |
GCA_002939755.1 | X. bromi CFBP 1976 T | [83] |
GCA_020813115.1 | X. campestris pv. aberrans NCPPB 2986 | This study |
GCA_020731405.1 | X. campestris pv. armoraciae NCPPB 347 | This study |
GCA_020813315.1 | X. campestris pv. barbareae NCPPB 983 | This study |
GCA_000007145.1 | X. campestris pv. campestris ATCC 33913 T | [62] |
GCA_020813295.1 | X. campestris pv. incanae NCPPB 937 | This study |
GCA_020813015.1 | X. campestris pv. papavericola NCPPB 2970 | This study |
GCA_020813005.1 | X. campestris pv. plantaginis NCPPB 1061 | This study |
GCA_020813075.1 | X. campestris pv. raphani NCPPB 1946 | This study |
GCA_000454545.1 | X. cassavae CFBP 4642 T | [84] |
GCA_002019225.1 | X. cissicola LMG 21719 T | [11] |
GCA_002018575.1 | X. citri LMG 9322 T | [85] |
GCA_002939885.1 | X. cucurbitae CFBP 2542 T | - |
GCA_002939865.1 | X. dyei CFBP 7245 T | - |
GCA_900476395.1 | X. euroxanthea CPBF 424 T | [86] |
GCA_019193005.1 | X. euvesicatoria pv. alangii NCPPB 1336 | This study |
GCA_017724035.1 | X. euvesicatoria pv. alfalfae CFBP3836 | [87] |
GCA_000730305.1 | X. euvesicatoria pv. allii CFBP6369 | [88] |
GCA_001401555.1 | X. euvesicatoria pv. euvesicatoria LMG 27970 T | - |
GCA_019192985.1 | X. euvesicatoria pv. physalidis NCPPB1756 | This study |
GCA_001642575.1 | X. floridensis WHRI 8848 T | [89] |
GCA_900380235.1 | X. fragariae PD 885 T | [90] |
GCA_003064105.1 | X. hortorum NCPPB 939 T | [91] |
GCA_009769165.1 | X. hyacinthi CFBP 1156 T | [92] |
GCA_905142475.1 | X. hydrangeae LMG 31884 T | [93] |
GCA_022669045.1 | X. indica PPL560 T | [94] |
GCA_009192945.1 | X. maliensis LMG 27592 T | [95] |
GCA_900018785.1 | X. massiliensis SN8 T | [96] |
GCA_020783655.1 | X. melonis NCPPB 3434 T | - |
GCA_001660815.1 | X. nasturtii WHRI 8853 T | [89] |
GCA_004136375.1 | X. oryzae ICMP 3125 T | [97] |
GCA_013112235.1 | X. perforans DSM 18975 T | - |
GCA_022749655.1 | X. phaseoli ATCC 49119 T | - |
GCA_001010415.1 | X. pisi DSM 18956 T | [98] |
GCA_002940065.1 | X. populi CFBP 1817 T | - |
GCA_002846205.1 | X. prunicola CFBP 8353 T | [99] |
GCA_002940085.1 | X. sacchari CFBP 4641 T | - |
GCA_008119715.1 | X. sontii PPL1 T | [100] |
GCA_014836395.1 | X. surreyensis Sa3BUA13 T | [101] |
GCA_014236795.1 | X. theicola CFBP 4691 T | [102] |
GCA_020880735.1 | X. translucens ATCC 19319 T | [103] |
GCA_000772705.2 | X. vasicola NCPPB 2417 T | [12] |
GCA_001908725.1 | X. vesicatoria ATCC 35937 T | [104] |
Appendix B
GenBank Accession | Pathovar | Completeness (%) | Contamination (%) |
---|---|---|---|
GCA_020813115.1 | aberrans | 99.89 | 0.03 |
GCA_019193005.1 | alangii | 99.94 | 0.61 |
GCA_020731405.1 | armoraciae | 99.89 | 0.03 |
GCA_020813315.1 | barbareae | 99.85 | 0.03 |
GCA_019201485.1 | blepharidis | 99.89 | 0.03 |
GCA_020813135.1 | campestris | 99.77 | 0 |
GCA_019201365.1 | carissae | 99.94 | 0.41 |
GCA_019201225.1 | clerodendri | 99.94 | 0.36 |
GCA_019201245.1 | convolvuli | 99.94 | 0.03 |
GCA_019201305.1 | coriandri | 99.89 | 0.3 |
GCA_019201325.1 | daturae | 99.87 | 0.53 |
GCA_019201425.1 | euphorbiae | 99.89 | 0.03 |
GCA_019201375.1 | fici | 99.94 | 0.68 |
GCA_019201405.1 | heliotropii | 99.82 | 0.32 |
GCA_020813295.1 | incanae | 99.64 | 0.53 |
GCA_019201465.1 | ionidii | 99.89 | 0.15 |
GCA_019201185.1 | lawsoniae | 99.64 | 0.03 |
GCA_019201545.1 | merremiae | 99.81 | 0.34 |
GCA_019201145.1 | mirabilis | 99.94 | 0.22 |
GCA_019201105.1 | obscurae | 99.94 | 0.07 |
GCA_020813015.1 | papavericola | 99.89 | 1.71 |
GCA_019201075.1 | passiflorae | 99.89 | 0.42 |
GCA_019201285.1 | paulliniae | 99.89 | 0.03 |
GCA_019201165.1 | pennamericanum | 99.89 | 0 |
GCA_019192985.1 | physalidis | 99.94 | 0.03 |
GCA_020813005.1 | plantaginis | 99.89 | 0.53 |
GCA_020813075.1 | raphani | 99.89 | 0.11 |
GCA_019201445.1 | spermacoces | 99.89 | 0.03 |
GCA_019201525.1 | trichodesmae | 99.76 | 0.93 |
GCA_019201115.1 | uppalii | 99.62 | 0.25 |
GCA_019201345.1 | veroniae | 99.89 | 0.37 |
GCA_019201265.1 | viegasii | 99.94 | 0.03 |
GCA_019201205.1 | zingibericola | 99.89 | 0.18 |
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Pathovar | Strain NCPPB Number | Host | FAME Cluster | References |
---|---|---|---|---|
Controls: X. campestris | ||||
aberrans | 2986 | Brassica oleracea var. capitata | 2 | [14] |
armoraciae | 347 | Iberis sp. | 1 | [15,16,17] |
barbareae | 983 | Barbarea vulgaris | 7 | [18] |
incanae | 937 | Matthiola sp. | 2 | [19] |
papavericola | 2970 | Papaver rhoeas | 2 | [20] |
plantaginis | 1061 | Plantago lanceolata | 3 | [21] |
raphani | 1946 | Raphanus sativus | 2 | [22] |
Controls: X. euvesicatoria | ||||
alangii | 1336 | Alangium lamarckii | 1 | [10,23] |
physalidis | 1756 | Physalis minima | 1 | [10,24] |
Controls: X. citri | ||||
merremiae | 3114 | Merremia gangetica | 1 | [11,25] |
trichodesmae | 585 | Trichodesma zeylanicum | 1 | [11,26] |
Control: X. phaseoli | ||||
passiflorae | 2346 | Passiflora edulis | 1 | [27] |
Transfer to Xanthomonas euvesicatoria | ||||
blepharidis | 1757 | Blepharis boarhaavifolia | 1 | [28] |
carissae | 2373 | Carissa carandas | 1 | [29] |
clerodendri | 575 | Clerodendron sp. | 1 | [30] |
convolvuli | 2498 | Convolvulus arvensis | (1) | [31] |
coriandri | 1758 | Coriandrum sativum | 1 | [32] |
daturae | 2932 | Datura metel | N.d. | [33] |
euphorbiae | 1828 | Euphorbia acalyphoides | 1 | [34] |
fici | 2372 | Ficus religiosa | (1) | [35] |
heliotropii | 2057 | Heliotropium sudanicum | [1] | [34] |
ionidii | 1334 | Ionidium heterophyllum | 1 | [36] |
lawsoniae | 579 | Lawsonia inermis | [1] | [37] |
mirabilis | 4348 | Mirabilis jalapa | N.d. | [38] |
obscurae | 3759 | Ipomea obscura | N.d. | [39] |
paulliniae | 3079 | Paullinia cupana | (1) | [40] |
pennamericanum | 4349 | Pennisetum americanum | N.d. | [41] |
spermacoces | 1760 | Spermacoce hispida | 14 | [28] |
uppalii | 586 | Ipomoea muricata | (1) | [42] |
vernoniae | 1787 | Vernonia cinerea | (1) | [43] |
viegasii | 4351 | Pachystachys lutea | N.d. | [44] |
zingibericola | 4352 | Zingiber officinale | (1) | [45] |
Assembly Accession | Strain (NCPPB Number) | Length (b.p.) | Number of Contigs | N50 Length (b.p.) |
---|---|---|---|---|
GCA_020813115.1 | aberrans 2986 | 5,136,506 | 75 | 145,536 |
GCA_020731405.1 | armoraciae 347 | 5,063,577 | 72 | 149,552 |
GCA_020813315.1 | barbareae 983 | 4,982,365 | 62 | 208,499 |
GCA_020813295.1 | incanae 937 | 4,916,318 | 50 | 191,313 |
GCA_020813015.1 | papavericola 2970 | 5,509,044 | 46 | 220,536 |
GCA_020813005.1 | plantaginis 1061 | 5,214,263 | 76 | 153,285 |
GCA_020813075.1 | raphani 1946 | 4,898,270 | 53 | 196,893 |
GCA_019193005.1 | alangii 1336 | 4,984,130 | 20 | 399,322 |
GCA_019192985.1 | physalidis 1756 | 5,125,394 | 37 | 354,850 |
GCA_019201545.1 | merremiae 3114 | 5,092,415 | 53 | 310,143 |
GCA_019201525.1 | trichodesmae 585 | 5,572,310 | 82 | 194,166 |
GCA_019201075.1 | passiflorae 2346 | 5,022,320 | 68 | 164,613 |
GCA_019201485.1 | blepharidis 1757 | 4,969,587 | 58 | 167,765 |
GCA_019201365.1 | carissae 2373 | 5,089,141 | 136 | 93,135 |
GCA_019201225.1 | clerodendri 575 | 5,097,109 | 39 | 312,137 |
GCA_019201245.1 | convolvuli 2498 | 4,982,289 | 54 | 201,220 |
GCA_019201305.1 | coriandri 1758 | 5,049,250 | 34 | 522,126 |
GCA_019201325.1 | daturae 2932 | 5,173,277 | 46 | 333,897 |
GCA_019201425.1 | euphorbiae 1828 | 4,926,792 | 26 | 995,918 |
GCA_019201375.1 | fici 2372 | 4,880,201 | 87 | 109,976 |
GCA_019201405.1 | heliotropii 2057 | 5,161,499 | 120 | 107,075 |
GCA_019201465.1 | ionidii 1334 | 4,974,037 | 50 | 264,595 |
GCA_019201185.1 | lawsoniae 579 | 5,050,397 | 112 | 114,657 |
GCA_019201145.1 | mirabilis 4348 | 5,091,739 | 25 | 745,972 |
GCA_019201105.1 | obscurae 3759 | 5,007,609 | 61 | 242,019 |
GCA_019201285.1 | paulliniae 3079 | 4,806,543 | 18 | 540,544 |
GCA_019201165.1 | pennamericanum 4349 | 5,014,174 | 87 | 133,002 |
GCA_019201445.1 | spermacoces 1760 | 5,070,626 | 45 | 344,807 |
GCA_019201115.1 | uppalii 586 | 4,954,104 | 37 | 305,235 |
GCA_019201345.1 | vernoniae 1787 | 4,961,493 | 98 | 150,860 |
GCA_019201265.1 | viegasii 4351 PT | 5,007,865 | 38 | 232,093 |
GCA_019201205.1 | zingibericola 4352 | 4,926,474 | 31 | 267,819 |
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Harrison, J.; Hussain, R.M.F.; Aspin, A.; Grant, M.R.; Vicente, J.G.; Studholme, D.J. Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. Taxonomy 2023, 3, 29-45. https://doi.org/10.3390/taxonomy3010003
Harrison J, Hussain RMF, Aspin A, Grant MR, Vicente JG, Studholme DJ. Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. Taxonomy. 2023; 3(1):29-45. https://doi.org/10.3390/taxonomy3010003
Chicago/Turabian StyleHarrison, Jamie, Rana M. F. Hussain, Andrew Aspin, Murray R. Grant, Joana G. Vicente, and David J. Studholme. 2023. "Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria" Taxonomy 3, no. 1: 29-45. https://doi.org/10.3390/taxonomy3010003
APA StyleHarrison, J., Hussain, R. M. F., Aspin, A., Grant, M. R., Vicente, J. G., & Studholme, D. J. (2023). Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. Taxonomy, 3(1), 29-45. https://doi.org/10.3390/taxonomy3010003