Table 1
List of the samples, gene sequence length (bp), and sequence accessions provided to Genbank in this study.
| ITS rDNA | D2D3 28S rRNA | SSU 18S rDNA | Hsp90 | |||||
|---|---|---|---|---|---|---|---|---|
| Sample | Length (bp) | Accessions | Length (bp) | Accessions | Length (bp) | Accessions | Length (bp) | Accessions |
| PG-(33-AB) | (615) | MG386845 | (562), (568), (569) | MG551892, MG551897, MG551898 | (811), (812) | MG383943, MG383943 | 920 | MG674309 |
| PG-(44-SK) | ND | (570) | MG693783 | ND | ND | |||
| PG-(58-AB) | (619), (672), (730), (142), (705d) | MG386846, MG386861, MG386871, MG386827, MG386867 | (561) | MG551891 | (822), (814) | MG383953, MG383945 | (905) | MG676342 |
| PG-(76-SK) | (675) | MG386862 | ND | (807) | MG383941 | ND | ||
| PG-(81-MB) | (635) | MG386853 | (564) | MG551894 | ND | (921) | MG674310 | |
| PG-(84-MB) | (629) | MG386850 | (566) | MG551895 | (813) | MG383944 | ND | |
| CT-(81-MB) | (631) | MG386852 | ND | ND | ND | |||
| aCT-(84-MB) | (645) | MG386855 | (558) | MG551888 | (818), (821) | MG383949, MG383952 | (917), (913) | MG674307, MG676342 |
| CT-(B-MB) | (630) | MG386851 | (557) | MG551887 | (806) | ND | ||
| CT-(C-MB) | (743), (745), (726) | MG386876, MG386877, MG386869 | (567) | MG551896 | (815) | MG383946 | ND | |
| CT-(Road side1-MB) | (646),(647),(648) | MG386856, MG386857, MG386858 | (556) | MG551886 | (819), (820) | MG383950, MG383951 | ND | |
| CT-(Road side2-MB) | (733) | MG386874 | (574) | MG551900 | (817) | MG383948 | ND | |
| CT-(C11F7-SK) | (725), (732), (746), (731) | MG386868, MG386873, MG386878, MG386872 | ND | (816) | MG383947 | ND | ||
| CT-(C11F11-MB) | (145) | MG386828 | (560) | MG551890 | ND | (918) | MG674308 | |
| CT-(C11F17-MB) | (146) | MG386829 | ND | ND | ND | |||
| CT-(C11F18-SK) | ND | ND | 809 | (914) | MG676343 | |||
| CT-(C11F19-SK) | (729), (620), (751) | MG386870, MG386847, MG386879 | (563) | MG551893 | ND | (907) | MG674306 | |
| CT-(GL1-MB) | (13) | MG386825 | (٭580) | MG551899 | ND | ND | ||
| CT-(GL 2-MB) | (128) | MG386826 | ND | ND | ND | |||
| CT-(GL3-MB) | (601) | MG386831 | ND | ND | ND | |||
| CT-(GL4-MB) | (603), (604) | MG386832, MG386833 | ND | ND | ND | |||
| CT-(GL5-MB) | (605) | MG386834 | (594) | MG551909 | (803) | MG383938 | ND | |
| CT-(GL6-MB) | (606) | MG386835 | (555) | MG551885 | (804) | MG383939 | (901) | KJ817197 |
| CT-(GL7-MB) | (607) | MG386836 | (595) | MG551910 | (805) | MG383940 | (902) | MG655239 |
| CT-(GL8-MB) | (608) | MG386837 | (584) | MG551904 | ND | (903) | MG662121 | |
| CT-(GL9-MB) | (609) | MG386838 | (582) | MG551902 | ND | ND | ||
| CT-(GL10-MB) | (610) | MG386839 | (593) | MG551908 | ND | (904) | MG662122 | |
| CT-(GL11-MB) | (611) | MG386840 | ND | ND | ND | |||
| CT-(GL12-MB) | (612), (613) | MG386841, MG386842 | (581) | MG551901 | ND | ND | ||
| CT-(GL13-MB) | (614) | MG386843 | (583) | MG551903 | ND | ND | ||
| CT-(GL14-MB) | (621) | MG386848 | ND | ND | ND | |||
| CT-(GL15-MB) | (622) | MG386849 | ND | ND | ND | |||
| CT-(GL16-MB) | (644) | MG386854 | ND | ND | ND | |||
| CT-(GL17-MB) | (665) | MG386860 | ND | ND | ND | |||
| CT-(GL18-MB) | (676) | MG386863 | ND | ND | ND | |||
| CT-(GL19-MB) | (687) | MG386864 | (590) | MG551905 | ND | ND | ||
| CT-(GL20-MB) | (688) | MG386865 | (591) | MG551906 | ND | ND | ||
| CT-(GL21-MB) | (689) | MG386866 | (592) | MG551907 | ND | ND | ||
| CT-(GL22-MB) | (148) | MG386830 | ND | ND | ND | |||
| CT-(GL23-MB) | (650) | MG386859 | ND | ND | ND | |||
| CT-(RU) | (127), (692), (691) | MG384317, MG384319 MG384318 | (559) | MG551889 | (825), (824) | MG383955, MG383954 | (931) | |
| G-( Guelph -ON) | (659), (660), (732d), (147), (143), (144) | MG384718, MG384719, MG384731 MG384717 | ND | (802) | MG434349 | (916), (915) | MG711914,MG676344, | |
| G-(C58-ON) | (669), (710d), (711d) | MG384725, MG384729, MG384730 | ND | (801) | MG434348 | (930) | MG711917 | |
| G-(PQ-GLG) | (694), (695), (696),(661), (662) | MG384726, MG384727, MG384728, MG384720, MG384721 | ND | ND | (928) | MG711916 | ||
| G-(PQ-D77) | (663), (664), (668) | MG384722, MG384723, MG384724 | ND | ND | (926) | MG711915 | ||
| Total | 74 | 27 | 22 | 18 |
[i] Note: Sample origin coding is; CT = from creeping thistle in yellow pea fields, PG = from yellow pea grain with creeping thistle seeds, R = creeping thistle from roadsides, AB = Alberta, SK = Saskatchewan, and MB = Manitoba for Canadian Provinces plant material collected from, G-PQ = garlic from Quebec, G-ON = garlic from Ontario and RU = is creeping thistle root from Russia.
Table 2
Accession codes for sequences of the four genes in this study and plant host of Ditylenchus species retrieved from GenBank.
| Species | Host plant | ITS rDNA | LSU D2D3 28S rRNA | SSU 18S rDNA | Hsp90 |
|---|---|---|---|---|---|
| D. weischeri | Cirsium arvense, | AF396322 | — | — | HM778133.1, HM778133.3, HM778134 |
| D. dipsaci | Allium sativum | AY574298, JX123258, HQ219249 | aJX123259, aJX123259, aFJ707362, JF327761, HQ219225 | HQ219249 | — |
| D. dipsaci | Allium cepa | AY574289, AY574290 | HQ219226, HQ219223) | HQ219210 | HM778138, HM778140 |
| D. dipsaci | Vicia faba | AF396323, AY574286, AY574284, HQ219246, HQ219248, HQ219244, HQ219244 | — | — | HQ219229 |
| D. dipsaci | Trifolium pratense | AF396319, AY574300 | — | — | — |
| D. dipsaci | Medicago sativa | AY574297, AF396320 | — | — | — |
| D. dipsaci | Pisum sativum | HQ219247 | FJ707364 | HQ219247 | — |
| D. dipsaci | Fragaria sp | AF396321, HQ219241 | HQ219219 | — | HQ219230, HM778139, HM778137 |
| D. dipsaci | Beta vulgaris | AY574299 | — | — | — |
| D. dipsaci | Plantago lanceolata | AY574301 | — | — | — |
| D.dipsaci | Tulipa gesneriana | — | JF327765 | — | — |
| D. dipsaci | Digitalis lutea | AY574292 | — | — | — |
| D. dipsaci | Avena sativa | AY574293 | — | — | — |
| D. dipsaci | Veronica gentianoides | AY574295 | — | — | — |
| D. dipsaci | Lysimachia vulgaris | AY574296 | — | — | |
| D. dipsaci | Host? | aJN376069 | — | — | — |
| D. dipsaci | Zea mays | AY574294 | — | — | — |
| D. dipsaci | Phlox drummondi | AY574291 | — | — | — |
| D. dipsaci | Beta vulgaris | HQ219243 | — | — | — |
| D. dipsaci | Un known | — | — | AY593908, EU669931, AY284636 | — |
| D.dipsaci | Narcissus sp | — | aFJ707361 | — | — |
| D.dipsaci | Cichorium sp | — | ٭FJ707360 | — | — |
| D.dipsaci | Lucerne sp | — | FJ707363, | — | — |
| D. gigas | Vicia faba | HQ219232, HQ219235, HQ219236, HQ219231, HQ219240, HQ219234, HQ219237, HQ219238, HQ219239 | HQ219216, HQ219217 | HQ219211 | HQ219227, HQ219228 |
| D. gigas | Unknown | aJN376074 | — | — | — |
| Ditylenchus . sp B | Vicia faba | AY574285 | — | — | — |
| Ditylenchus . sp | Arachis sp | — | JX145345 | — | — |
| Ditylenchus . sp | Pilosella officinarum | AY574302, AY574305, AY574304 | — | — | — |
| Ditylenchus . sp | Crepis praemorsa | AY574303 | — | — | — |
| Ditylenchus . sp | Leontodon autumnalis | AY574306 | — | — | — |
| Ditylenchus. sp | Plantago maritima | AY574287, AY574288 | — | — | HM778135, HM778136 |
| Ditylenchus . sp | Turfgrass | — | — | — | AY603512 |
| D. destructor | Solanum tuberosum | HQ235675, HQ235694, HQ235692, GQ469492, HQ235682, JN376068 JN66693 | HQ235698, EU400642, EU400625, DQ328727, FJ707365 | — | — |
| D. destructor | Ipomoea batatas | JX145343, AY987007 | EU400638, EU400634, EU400628, EU400626, EU400622, EU400629, EU400629 (China) | — | — |
| D. myceliophagous | Agaricus sp | DQ151458, AM232236 | — | — | — |
| D. halictus | Halictus sexcinctus | AY589364 |
Table 3
Nucleotide position and composition on 631 bp of internal transcribed spacer (ITS1, 5.8S, ITS2 rDNA), comparison among samples from this study (Table 1) and those derived from the GenBank database (Table 2) after multiple sequence alignments. Only positions with nucleotide differences are presented. Only one sequence result for multiple individuals from the same sample shown because of lack of intra-sample differences. Sample sequences generated in this study are in bold. W = (A or T), Y = (C or T).
Table 4
Nucleotide position and composition, comparison sequences obtained in this study and accessions from GenBank. The LSU D2D3 28S rDNA sequence trimmed to 637 bp used for the analysis. Only one sequence result for multiple individuals from the same sample shown because of lack of intra-sample differences.
| Nucleotide Position | 47 | 76 | 82 | 89 | 92 | 100-1 | 106-7 | 160 | 178 | 234 | 244 | 249 | 257 | 279 | 281 | 304 | 308 | 320 | 336 | 341 | 457 | 483 | 500 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample/isolate | |||||||||||||||||||||||
| CT-(GL8-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| CT-(RU) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| CT-(Road side-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| CT-(C11F11-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| CT-(C11F19-SK) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| CT-(B-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| CT-(C-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| CT-(84-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| PG-(33-SK) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| PG-(58-SK) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| PG-(81-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| PG-(84-MB) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| D. dipsaci (a FJ707364) | A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
| D. gigas (HQ219217) | A | T | A | T | T | AT | TA | C | — | A | T | A | A | A | T | T | G | T | A | T | A | T | A |
| D. gigas (HQ219216) | A | T | A | T | T | AT | TA | C | — | A | T | A | A | A | T | T | G | T | A | T | A | T | A |
| D. sp (JX145345) | T | T | G | C | A | GG | TA | A | — | A | A | A | A | T | T | A | G | T | A | T | A | T | A |
| D. dipsaci (HQ219223) | G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
| D. dipsaci (HQ219219) | G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
| D. dipsaci (JF327765) | G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
| D. dipsaci (JF327761) | G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
| D. dipsaci (JF327763) | G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
| D. dipsaci ( JF327760) | G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
[ii] aSequence deosted by Douda et al. (2013).
Figure 1:
Phylogenetic relationships of Ditylenchus weischeri with related Ditylenchus species based on ITS rDNA sequences using MrBayes 3.2.6. jModelTest 2.1.7, and the Akaike Information Criterion were used to select TVM + G as the best model (−ln L = 2956.2229; gamma shape = 0.5380; G = 0.2537; R = 0.7816) and the figure created using Tree View 1.6.6. Posterior probability support values are given above the branches. Sequences generated in this study are given in bold.
Figure 2:
Phylogenetic relationships of Ditylenchus weischeri with related Ditylenchus species from the LSU D2D3 28S rDNA using MrBayes 3.2.6. jModelTest 2.1.7, and the Akaike Information Criterion were used to select GTR+I as the best model (−lnL = 2342.5725; gamma shape = 4.2350; K=102; G = 0.3040; R = 0.7030) and the figure created using Tree View 1.6.6. Posterior probability support values are given above the branches. Sequences generated in this study are given in bold. aSequence deposited in GenBank by Douda et al. (2013).
Figure 3:
Phylogenetic relationships of Ditylenchus weischeri with related Ditylenchus species using MrBayes 3.2.6. jModelTest 2.1.7, and the Akaike Information Criterion were used to select HKY + G as the best models (−ln L = 917.5224; gamma shape = 0.5040; K = 63; G = 0.2154) and figure created using Tree View 1.6.6. Posterior probability support values are given above the branches. Sequences generated in this study are given in bold.