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Discovery and Identification of Meloidogyne Species Using COI DNA Barcoding Cover

Discovery and Identification of Meloidogyne Species Using COI DNA Barcoding

Journal of Nematology
Volume 50 (2018): Issue 3 (January 2018)
By: Thomas Powers,  Timothy Harris,  Rebecca Higgins,  Peter Mullin and  Kirsten Powers  
Open Access
|Oct 2018

Figures & Tables

Fig. 1

Maximum likelihood tree of 322 Meloidogyne COI sequences created in MEGA 6.06 using GTR+G substitution model, with 200 bootstraps and a gap treatment of use all sites. Support values that designate clades and haplotype groups are circled. Clades that correspond to named and unnamed species or haplotype groups are numbered. Clades that include specimens with a single amino acid deletion are denoted by (Δ721 bp). Group 1 has been reduced to a box of species names. Sequences within Group 1 are presented in Table 2. A list of GenBank accession numbers for specimens included in Group 1 are found in supplementary Table 1.
Maximum likelihood tree of 322 Meloidogyne COI sequences created in MEGA 6.06 using GTR+G substitution model, with 200 bootstraps and a gap treatment of use all sites. Support values that designate clades and haplotype groups are circled. Clades that correspond to named and unnamed species or haplotype groups are numbered. Clades that include specimens with a single amino acid deletion are denoted by (Δ721 bp). Group 1 has been reduced to a box of species names. Sequences within Group 1 are presented in Table 2. A list of GenBank accession numbers for specimens included in Group 1 are found in supplementary Table 1.

Fig. 2

Selected Meloidogyne juveniles from unnamed groups. A, Entire body of NID 8084 in Group 12, from chestnut in Great Smoky Mountains National Park (GRSM); B, Anterior region of NID 8012 in Group 12 from chestnut in GRSM; C, Anterior region of NID 8283 from Group 9 from Mt. St. Hilaire, Quebec; D, Anterior region of NID 4379 in Group 5 from chestnut in GRSM.
Selected Meloidogyne juveniles from unnamed groups. A, Entire body of NID 8084 in Group 12, from chestnut in Great Smoky Mountains National Park (GRSM); B, Anterior region of NID 8012 in Group 12 from chestnut in GRSM; C, Anterior region of NID 8283 from Group 9 from Mt. St. Hilaire, Quebec; D, Anterior region of NID 4379 in Group 5 from chestnut in GRSM.

COI sequences included in group 1_

NIDSpeciesLocalityHost/HabitatGenBank accession #
N137 M. konaensis HawaiiPineapplesMH128384
N138 M. konaensis HawaiiPineapplesMH128385
N7067 Meloidogyne sp.Charleston, MissouriSoybeanMH128414
N7066 Meloidogyne sp.Charleston, MissouriSoybeanMH128413
N7065 Meloidogyne sp.Charleston, MissouriSoybeanMH128412
N5777 Meloidogyne sp.NebraskaConservatoryMH128410
N5775 Meloidogyne sp.NebraskaConservatoryMH128409
N5771 Meloidogyne sp.Nebraska Phoenix dactylifera MH128408
N3836 Meloidogyne sp.NebraskaBananaMH128407
N2668 Meloidogyne sp.Sonora, MexicoGrapevineMH128406
N2667 Meloidogyne sp.Sonora, MexicoGrapevineMH128405
N2666 Meloidogyne sp.Sonora, MexicoGrapevineMH128404
N2665 Meloidogyne sp.Sonora, MexicoGrapevineMH128403
N2664 Meloidogyne sp.Sonora, MexicoGrapevineMH128402
N2663 Meloidogyne sp.Sonora, MexicoGrapevineMH128401
N2662 Meloidogyne sp.Sonora, MexicoGrapevineMH128400
N2661 Meloidogyne sp.Sonora, MexicoGrapevineMH128399
N2659 Meloidogyne sp.FloridaPeanutsMH128397
N7068 Meloidogyne sp.Clarkton, MissouriSoybeanMH128415
N7069 Meloidogyne sp.Clarkton, MissouriSoybeanMH128416
N7070 Meloidogyne sp.Clarkton, MissouriSoybeanMH128417
N7072 Meloidogyne sp.Clarkton, MissouriSoybeanMH128418
N7073 Meloidogyne sp.Clarkton, MissouriSoybeanMH128419
N7075 Meloidogyne sp.Clarkton, MissouriSoybeanMH128420
N8309 Meloidogyne sp.Charleston, MissouriSoybeanMH128421
P118094 Meloidogyne incognita MissouriPotatoMH128424
P120058 M. incognita ArizonaCultureMH128425
P120059 M. incognita ArizonaCultureMH128426
P121032 M. incognita MississippiPotatoMH128427
P121058 M. incognita Gasconade County, MissouriDaylilyMH128428
P121060 M. incognita Moniteau County, MissouriDaylilyMH128429
P156046 Meloidogyne floridensis FloridaGH cultureMH128430
P156048 M. floridensis FloridaGH cultureMH128431
P158036 Meloidogyne arenaria Alachua County, Florida–MH128432
P158037 M. arenaria Alachua County, Florida–MH128433
P160024 Meloidogyne sp.Alachua County, Florida–MH128434
P160025 Meloidogyne sp.Alachua County, Florida–MH128435
P160075 M. arenaria Alachua County, Florida–MH128437
P167014 Meloidogyne javanica ––MH128438
P167019 M. arenaria ––MH128439
P167020 M. arenaria ––MH128440
P167021 M. arenaria ––MH128441
P176014 Meloidogyne sp.MissouriCultureMH128443
P178075 M. arenaria TexasPotatoMH128444
P195088 M. javanica ––MH128445
P195089 M. javanica ––MH128446
P196023 M. javanica ––MH128447
P196024 M. javanica ––MH128448
P196025 M. javanica ––MH128449
P202009 Meloidogyne sp.IsraelCultureMH128450
P229051 Meloidogyne sp.FloridaCultureMH128451
P229053 Meloidogyne sp.FloridaCultureMH128452
P229056 Meloidogyne sp.FloridaCultureMH128453
P233011 Meloidogyne sp.–CoffeeMH128457
P233014 Meloidogyne sp.–CoffeeMH128458
P234004 Meloidogyne sp.Morocco–MH128459
P234005 Meloidogyne sp.Morocco–MH128460
P234006 Meloidogyne sp.Morocco–MH128461
P234007 Meloidogyne sp.Morocco–MH128462
P73085 Meloidogyne incognita Bonita, ArizonaPinto beansMH128422
P73088 M. incognita Bonita, ArizonaPinto beansMH128423
N5796 Meloidogyne sp.Ash Meadows NWR, Nevada–MH128411
P230069 Meloidogyne incognita grahami West VirginiaCultureMH128454
P230095 M. incognita grahami West VirginiaCultureMH128456
P230070 M. incognita grahami West VirginiaCultureMH128455
N2660 Meloidogyne sp.FloridaPeanutMH128398
P167027 M. arenaria ––MH128442
N329 Meloidogyne sp.North DakotaPotatoMH128386
N330 Meloidogyne sp.North DakotaPotatoMH128387
N331 Meloidogyne sp.North DakotaPotatoMH128388
N332 Meloidogyne sp.North DakotaPotatoMH128389
N333 Meloidogyne sp.North DakotaPotatoMH128390
N334 Meloidogyne sp.North DakotaPotatoMH128391
N335 Meloidogyne sp.North DakotaPotatoMH128392
N336 Meloidogyne sp.North DakotaPotatoMH128393
N337 Meloidogyne sp.North DakotaPotatoMH128394
N348 Meloidogyne sp.North DakotaPotatoMH128395
N351 Meloidogyne sp.North DakotaPotatoMH128396
P160071 M. arenaria Alachua, FloridaCultureMH128436

COI sequence collection data for groups 2 to 19_

NIDGroupSpeciesLocalityHost/habitatGenBank accession #
P2030603 Meloidogyne enterolobii FloridaOrnamentals-NurseryMH128522
P1790693 M. enterolobii FloridaOrnamentals-NurseryMH128519
P1790703 M. enterolobii FloridaOrnamentals-NurseryMH128520
P1960903 M. enterolobii FloridaOrnamentals-NurseryMH128521
P2100133 M. enterolobii FloridaOrnamentals-NurseryMH128523
P2100143 M. enterolobii FloridaOrnamentals-NurseryMH128524
P2100713 M. enterolobii FloridaOrnamentals-urseryMH128529
P2100593 M. enterolobii FloridaOrnamentals-NurseryMH128527
P2100573 M. enterolobii FloridaOrnamentals-NurseryMH128525
P2100583 M. enterolobii FloridaOrnamentals-NurseryMH128526
P2100723 M. enterolobii FloridaOrnamentals-NurseryMH128530
P2100653 M. enterolobii FloridaOrnamentals-NurseryMH128528
N43144 Meloidogyne sp.Lance Rosier Unit, BITHa Loblolly pineMH128531
N43214 Meloidogyne sp.Lance Rosier Unit, BITHa Loblolly pineMH128532
N43795 Meloidogyne sp.Cove Mtn. Trail, GRSMb ChestnutMH128537
N43885 Meloidogyne sp.Cove Mtn. Trail, GRSMb ChestnutMH128538
N21105 Meloidogyne sp.GWMPc Fort Marcy earthworksMH128533
N39525 Meloidogyne sp.Turkey Creek, BITHa Baygall communityMH128534
N42855 Meloidogyne sp.Canyonlands South, BITHa MagnoliaMH128535
N42915 Meloidogyne sp.Canyonlands South, BITHa MagnoliaMH128536
P2140086 Meloidogyne partityla Dona Ana County, New MexicoPecanMH128540
P2140106 M. partityla Dona Ana County, New MexicoPecanMH128542
P2140096 M. partityla Dona Ana County, New MexicoPecanMH128541
N23386 M. partityla Neches Bottoms Unit, BITHa SandbarMH128539
P1210547 Meloidogyne hapla Gasconade County, MissouriPeonyMH128568
P2000317 M. hapla Cass County, NebraskaNurseryMH128577
N1637 M. hapla NebraskaWheatMH128543
P2000187 M. hapla Daggett County, UtahGrass pastureMH128575
P2000197 M. hapla Daggett County, UtahGrass pastureMH128576
P1780647 M. hapla OregonPotatoMH128570
P2000327 M. hapla Colfax County, NebraskaNurseryMH128578
N13767 M. hapla Fremont County, WyomingRed beanMH128558
N13777 M. hapla Fremont County, WyomingRed beanMH128559
P1790687 M. hapla New YorkGHMH128572
P1780637 M. hapla OregonPotatoMH128569
P2220837 M. hapla Portales, New MexicoGH cultureMH128579
P2220847 M. hapla Portales, New MexicoGH cultureMH128580
N14487 M. hapla GWMPc Waterfowl sanctuaryMH128560
N8577 M. hapla Goshen County, WyomingPotatoMH128554
N8597 M. hapla Goshen County, WyomingPotatoMH128555
N8607 M. hapla Goshen County, WyomingPotatoMH128556
N8617 M. hapla Goshen County, WyomingPotatoMH128557
P2000017 M. hapla Hot Springs County, WyomingAlfalfaMH128573
P2000027 M. hapla Hot Springs County, WyomingAlfalfaMH128574
N41247 M. hapla Wyoming–MH128561
N3187 M. hapla IdahoPotatoMH128544
N4977 M. hapla California–MH128551
N4897 M. hapla California–MH128550
N4987 M. hapla California–MH128552
P1790547 M. hapla Rhode IslandGH cultureMH128571
N3207 M. hapla IdahoPotatoMH128545
N3587 M. hapla IdahoPotatoMH128546
N3597 M. hapla IdahoPotatoMH128547
N4217 M. hapla Carbon County, MontanaAlfalfaMH128548
N4227 M. hapla Carbon County, MontanaAlfalfaMH128549
N8567 M. hapla Goshen County, WyomingPotatoMH128553
N70977 M. hapla NebraskaAlfalfaMH128562
N70987 M. hapla NebraskaAlfalfaMH128563
N71007 M. hapla NebraskaAlfalfaMH128565
N70997 M. hapla NebraskaAlfalfaMH128564
N85957 M. hapla Chalti, NepalPine forestMH128566
N86127 M. hapla Chalti, NepalPine forestMH128567
N42229 Meloidogyne sp.Canyonlands South, BITHa BeechMH128581
N42299 Meloidogyne sp.Canyonlands South, BITHa BeechMH128582
N84319 Meloidogyne sp.Canyonlands South, BITHa BeechMH128584
N84339 Meloidogyne sp.Canyonlands South, BITHa BeechMH128585
N82839 Meloidogyne sp.Mt. St. Hilaire, Quebec, CanadaHardwood forestMH128583
N443110 Meloidogyne sp.Cove Mtn. Trail, GRSMb ChestnutMH128463
N449610 Meloidogyne sp.Cove Mtn. Trail, GRSMb ChestnutMH128464
N449711 Meloidogyne sp.Cove Mtn. Trail, GRSMb ChestnutMH128465
N808412 Meloidogyne sp.Purchase Knob, GRSMb ChestnutMH128468
N812112 Meloidogyne sp.Cataloochee, GRSMb OakMH128470
N805812 Meloidogyne sp.Cataloochee, GRSMb ChestnutMH128467
N801212 Meloidogyne sp.Cataloochee, GRSMb ChestnutMH128466
N811112 Meloidogyne sp.Cataloochee, GRSMb OakMH128469
N147913 Meloidogyne sp.Roy E. Larsen Sandylands, BITHa Baygall communityMH128471
N396913 Meloidogyne sp.Turkey Creek, BITHa Baygall communityMH128472
P12905214 Meloidogyne oryzae Costa RicaRiceMH128473
P12905414 M. oryzae Costa RicaRiceMH128474
P16901114 Meloidogyne graminicola FloridaPurple nutsedgeMH128475
N21415 Meloidogyne exigua NicaraguaCoffeeMH128477
N21515 M. exigua NicaraguaCoffeeMH128478
N21315 M. exigua NicaraguaCoffeeMH128476
P19906916 Meloidogyne naasi Sanpete County, UtahGrassMH128480
P19907116 M. naasi Sanpete County, UtahGrassMH128481
P19907216 M. naasi Sanpete County, UtahGrassMH128482
N32616 M. naasi IdahoPotatoMH128479
P19208417 Meloidogyne fallax ScotlandGenomic DNAMH128507
P11903217 Meloidogyne chitwoodi New MexicoCultureMH128488
P11502617 M. chitwoodi Fort Garland, ColoradoSoil sampleMH128487
P12201017 M. chitwoodi ColoradoSoil sampleMH128489
P12204717 M. chitwoodi ColoradoSoil sampleMH128490
P12405617 M. chitwoodi CommercialPotatoMH128491
P12405717 M. chitwoodi CommercialPotatoMH128492
P12405917 M. chitwoodi CommercialPotatoMH128493
N714517 M. chitwoodi Elko County, NevadaPotatoMH128483
N714717 M. chitwoodi Elko County, NevadaPotatoMH128484
N714817 M. chitwoodi Elko County, NevadaPotatoMH128485
N714917 M. chitwoodi Elko County, NevadaPotatoMH128486
P17310017 M. chitwoodi CommercialPotatoMH128494
P17400117 M. chitwoodi CommercialPotatoMH128495
P17506817 M. chitwoodi IdahoPotatoMH128496
P17506917 M. chitwoodi IdahoPotatoMH128497
P17507017 M. chitwoodi IdahoPotatoMH128498
P17507117 M. chitwoodi IdahoPotatoMH128499
P17709217 M. chitwoodi TexasPotatoMH128500
P17709417 M. chitwoodi TexasPotatoMH128501
P17709817 M. chitwoodi TexasPotatoMH128502
P19201117 M. chitwoodi CommercialPotatoMH128504
P19201217 M. chitwoodi CommercialPotatoMH128505
P19201317 M. chitwoodi CommercialPotatoMH128506
P21108817 M. chitwoodi OregonPotatoMH128508
P21108917 M. chitwoodi OregonPotatoMH128509
P21201317 M. chitwoodi CaliforniaPotatoMH128510
P21201417 M. chitwoodi CaliforniaPotatoMH128511
P21201517 M. chitwoodi CaliforniaPotatoMH128512
P21201617 M. chitwoodi CaliforniaPotatoMH128513
P21303917 M. chitwoodi WashingtonPotatoMH128514
P21304017 M. chitwoodi WashingtonPotatoMH128515
P22108717 M. chitwoodi New MexicoPotatoMH128518
P21503217 M. chitwoodi WashingtonPotatoMH128517
P17802817 M. chitwoodi CommercialPotatoMH128503
P21503117 M. chitwoodi WashingtonPotatoMH128516

Accession numbers of specimens from Group 1 acquired from GenBank_

GenBank accession #Species
KU372176.1 Meloidogyne sp.
KM491194.1 Meloidogyne incognita
KU372162.1 Meloidogyne ethiopica
KU360142.1 M. incognita
KM491204.1 Meloidogyne arenaria
KU372172.1 Meloidogyne luci
KU372173.1 M. luci
KM491195.1 M. incognita
KM491192.1 M. incognita
KM491191.1 M. incognita
KM491196.1 M. incognita
KM491188.1 M. incognita
KM491203.1 M. arenaria
KM491201.1 M. arenaria
KM491207.1 M. incognita
KM491199.1 M. arenaria
KM491202.1 M. arenaria
KM491200.1 M. arenaria
KM491190.1 M. incognita
KM491189.1 M. incognita
NC_026556.1 Meloidogyne javanica
NC_026554.1 M. arenaria
KP202352.1 M. javanica
KP202350.1 M. arenaria
NC_024097.1 M. incognita
KJ476151.1 M. incognita
KU372158.1 M. arenaria
KU372165.1 M. incognita
KU372167.1 Meloidogyne inornata
KU372159.1 M. arenaria
KU372166.1 M. incognita
KU372169.1 M. javanica
KU372170.1 M. javanica
KU372171.1 M. luci
KU372174.1 Meloidogyne sp.
KU372168.1 M. inornata
KU372175.1 Meloidogyne sp.
KU372164.1 M. incognita
KU372163.1 M. incognita
KU517167.1 M. incognita
KU360143.1 M. arenaria
JX683704.1 M. arenaria
KU360144.1 M. javanica
JX683696.1 M. incognita
JX683698.1 M. incognita
JX683699.1 M. incognita
JX683700.1 M. incognita
JX683706.1 M. javanica
JX683701.1 M. arenaria
JX683702.1 M. arenaria
JX683703.1 M. arenaria
JX683705.1 M. arenaria
JX683707.1 M. javanica
JX683708.1 M. javanica
JX683709.1 M. javanica
JX683711.1 M. javanica
JX683710.1 M. javanica
JX683712.1 Meloidogyne hispanica
JX683713.1 M. hispanica
KM887153.1 M. arenaria
KM887152.1 M. incognita
KM887155.1 M. arenaria
KM887154.1 M. incognita
JX683697.1 M. incognita
KM887156.1 M. javanica
KU517172.1 M. javanica
KU517176.1 M. arenaria
KU372160.1 M. arenaria
KM491193.1 M. incognita
KM491206.1 M. incognita

Measurements of j2 Meloidogyne specimens from unnamed COI haplotype groups and reference species_

Haplotype group/species N LengthTail lengthStylet length a b c
Unnamed 42441 (430–452)421724.3 (22.7–25.9)3.8 (3.7–3.9)10.5 (10.3–10.8)
Unnamed 55431 (406–460)47 (40–53)14 (13–1525.4 914.4–30.8)3.9 (3.0–4.8)9.3 (8.0–10.1)
Unnamed 95393 (380–405)40 (38–44)15 (15–16)26.0 (25.5–26.7)4.0 (3.3–4.4)9.7 (9.2–10.1)
Unnamed 11 (Singleton A)1384421527.53.59.1
Unnamed 125353 (339–379)41 (38–43)15 (14–15)22.7 (21.2–25.0)3.5 (3.3–4.0)8.6 (8.0–8.9)
Unnamed 132490 (439–541)59 (57–62)1430.7 (30.4–31)3.9 (3.8–4.0)8.2 (7.7–8.6)
Meloidogyne ovalis 10370 (350–430)––22 (21–24)–8 (8–9)
Meloidogyne pini 30434 (376–493)44 (37–53)12.8 (11.4–14.1)25.7 (21.8–29.1)–9.8 (7.5–11.8)
Meloidogyne camelliae 70501 (443–576)47 (40–56)11.6 (11.2–12)26 (21–30)3.110.7 (9.5–12
Meloidogyne querciana 70467 (411–541)46 (39–52)11.1 (10.2–11.6)30 (23–39)2.610 (7–13)
Meloidogyne megatyla 23416 (392–457)39.7 (31.6–45.1)14.6 (13.8–16.6)26 (22–29)7.1 (6.7–7.8)10.5 (9.5–13.5)
DOI: https://doi.org/10.21307/jofnem-2018-029 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X
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Language: English
Page range: 399 - 412
Published on: Oct 17, 2018
Published by: Society of Nematologists, Inc.
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
Keywords:
COI,
DNA barcoding,
Plant parasitic nematodes,
Root-knot nematodes,
Taxonomy
Related subjects:
Life sciences,
Life sciences, other

© 2018 Thomas Powers, Timothy Harris, Rebecca Higgins, Peter Mullin, Kirsten Powers, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

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