Molecular Characterization and Phylogeny of Ditylenchus weischeri from Cirsium arvense in the Prairie Provinces of Canada
e | 03 giu 2018
INFORMAZIONI SU QUESTO ARTICOLO
Article Category: research-article
Pubblicato online: 03 giu 2018
Pagine: 163 - 182
DOI: https://doi.org/10.21307/jofnem-2018-011
Parole chiave
© 2018 Mehrdad Madani et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Figure 1:
Figure 2:
Figure 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).
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | G | T | T | AT | TA | G | — | A | C | A | G | A | T | T | T | C | A | T | A | T | A |
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A | T | A | T | T | AT | TA | C | — | A | T | A | A | A | T | T | G | T | A | T | A | T | A |
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A | T | A | T | T | AT | TA | C | — | A | T | A | A | A | T | T | G | T | A | T | A | T | A |
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T | T | G | C | A | GG | TA | A | — | A | A | A | A | T | T | A | G | T | A | T | A | T | A |
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G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
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G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
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G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
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G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
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G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
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G | C | A | C | A | GC | CG | T | A | G | T | G | A | G | C | C | G | T | G | A | G | C | G |
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 |
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|---|---|---|---|---|---|---|---|---|
| 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 |
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 |
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AF396322 | — | — | HM778133.1, HM778133.3, HM778134 |
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AY574298, JX123258, HQ219249 | aJX123259, aJX123259, aFJ707362, JF327761, HQ219225 | HQ219249 | — |
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AY574289, AY574290 | HQ219226, HQ219223) | HQ219210 | HM778138, HM778140 |
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AF396323, AY574286, AY574284, HQ219246, HQ219248, HQ219244, HQ219244 | — | — | HQ219229 |
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AF396319, AY574300 | — | — | — |
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AY574297, AF396320 | — | — | — |
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HQ219247 | FJ707364 | HQ219247 | — |
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AF396321, HQ219241 | HQ219219 | — | HQ219230, HM778139, HM778137 |
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AY574299 | — | — | — |
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AY574301 | — | — | — |
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— | JF327765 | — | — |
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AY574292 | — | — | — |
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AY574293 | — | — | — |
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AY574295 | — | — | — |
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AY574296 | — | — | |
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Host? | aJN376069 | — | — | — |
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AY574294 | — | — | — |
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AY574291 | — | — | — |
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HQ219243 | — | — | — |
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Un known | — | — | AY593908, EU669931, AY284636 | — |
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Narcissus sp | — | aFJ707361 | — | — |
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— | ٭FJ707360 | — | — |
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Lucerne sp | — | FJ707363, | — | — |
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HQ219232, HQ219235, HQ219236, HQ219231, HQ219240, HQ219234, HQ219237, HQ219238, HQ219239 | HQ219216, HQ219217 | HQ219211 | HQ219227, HQ219228 |
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Unknown | aJN376074 | — | — | — |
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AY574285 | — | — | — |
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— | JX145345 | — | — |
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AY574302, AY574305, AY574304 | — | — | — |
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AY574303 | — | — | — |
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AY574306 | — | — | — |
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AY574287, AY574288 | — | — | HM778135, HM778136 |
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Turfgrass | — | — | — | AY603512 |
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HQ235675, HQ235694, HQ235692, GQ469492, HQ235682, JN376068 JN66693 | HQ235698, EU400642, EU400625, DQ328727, FJ707365 | — | — |
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JX145343, AY987007 | EU400638, EU400634, EU400628, EU400626, EU400622, EU400629, EU400629 (China) | — | — |
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DQ151458, AM232236 | — | — | — |
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AY589364 |