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Discovery and Identification of Meloidogyne Species Using COI DNA Barcoding

Thomas Powers
Thomas Powers
, 
Timothy Harris
Timothy Harris
, 
Rebecca Higgins
Rebecca Higgins
, 
Peter Mullin
Peter Mullin
 et 
Kirsten Powers
Kirsten Powers
   | 17 oct. 2018
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Publié en ligne: 17 oct. 2018
Pages: 399 - 412
DOI: https://doi.org/10.21307/jofnem-2018-029
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© 2018 Thomas Powers et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.

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.

NID Species Locality Host/Habitat GenBank accession #
N137 M. konaensis Hawaii Pineapples MH128384
N138 M. konaensis Hawaii Pineapples MH128385
N7067 Meloidogyne sp. Charleston, Missouri Soybean MH128414
N7066 Meloidogyne sp. Charleston, Missouri Soybean MH128413
N7065 Meloidogyne sp. Charleston, Missouri Soybean MH128412
N5777 Meloidogyne sp. Nebraska Conservatory MH128410
N5775 Meloidogyne sp. Nebraska Conservatory MH128409
N5771 Meloidogyne sp. Nebraska Phoenix dactylifera MH128408
N3836 Meloidogyne sp. Nebraska Banana MH128407
N2668 Meloidogyne sp. Sonora, Mexico Grapevine MH128406
N2667 Meloidogyne sp. Sonora, Mexico Grapevine MH128405
N2666 Meloidogyne sp. Sonora, Mexico Grapevine MH128404
N2665 Meloidogyne sp. Sonora, Mexico Grapevine MH128403
N2664 Meloidogyne sp. Sonora, Mexico Grapevine MH128402
N2663 Meloidogyne sp. Sonora, Mexico Grapevine MH128401
N2662 Meloidogyne sp. Sonora, Mexico Grapevine MH128400
N2661 Meloidogyne sp. Sonora, Mexico Grapevine MH128399
N2659 Meloidogyne sp. Florida Peanuts MH128397
N7068 Meloidogyne sp. Clarkton, Missouri Soybean MH128415
N7069 Meloidogyne sp. Clarkton, Missouri Soybean MH128416
N7070 Meloidogyne sp. Clarkton, Missouri Soybean MH128417
N7072 Meloidogyne sp. Clarkton, Missouri Soybean MH128418
N7073 Meloidogyne sp. Clarkton, Missouri Soybean MH128419
N7075 Meloidogyne sp. Clarkton, Missouri Soybean MH128420
N8309 Meloidogyne sp. Charleston, Missouri Soybean MH128421
P118094 Meloidogyne incognita Missouri Potato MH128424
P120058 M. incognita Arizona Culture MH128425
P120059 M. incognita Arizona Culture MH128426
P121032 M. incognita Mississippi Potato MH128427
P121058 M. incognita Gasconade County, Missouri Daylily MH128428
P121060 M. incognita Moniteau County, Missouri Daylily MH128429
P156046 Meloidogyne floridensis Florida GH culture MH128430
P156048 M. floridensis Florida GH culture MH128431
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. Missouri Culture MH128443
P178075 M. arenaria Texas Potato MH128444
P195088 M. javanica – – MH128445
P195089 M. javanica – – MH128446
P196023 M. javanica – – MH128447
P196024 M. javanica – – MH128448
P196025 M. javanica – – MH128449
P202009 Meloidogyne sp. Israel Culture MH128450
P229051 Meloidogyne sp. Florida Culture MH128451
P229053 Meloidogyne sp. Florida Culture MH128452
P229056 Meloidogyne sp. Florida Culture MH128453
P233011 Meloidogyne sp. – Coffee MH128457
P233014 Meloidogyne sp. – Coffee MH128458
P234004 Meloidogyne sp. Morocco – MH128459
P234005 Meloidogyne sp. Morocco – MH128460
P234006 Meloidogyne sp. Morocco – MH128461
P234007 Meloidogyne sp. Morocco – MH128462
P73085 Meloidogyne incognita Bonita, Arizona Pinto beans MH128422
P73088 M. incognita Bonita, Arizona Pinto beans MH128423
N5796 Meloidogyne sp. Ash Meadows NWR, Nevada – MH128411
P230069 Meloidogyne incognita grahami West Virginia Culture MH128454
P230095 M. incognita grahami West Virginia Culture MH128456
P230070 M. incognita grahami West Virginia Culture MH128455
N2660 Meloidogyne sp. Florida Peanut MH128398
P167027 M. arenaria – – MH128442
N329 Meloidogyne sp. North Dakota Potato MH128386
N330 Meloidogyne sp. North Dakota Potato MH128387
N331 Meloidogyne sp. North Dakota Potato MH128388
N332 Meloidogyne sp. North Dakota Potato MH128389
N333 Meloidogyne sp. North Dakota Potato MH128390
N334 Meloidogyne sp. North Dakota Potato MH128391
N335 Meloidogyne sp. North Dakota Potato MH128392
N336 Meloidogyne sp. North Dakota Potato MH128393
N337 Meloidogyne sp. North Dakota Potato MH128394
N348 Meloidogyne sp. North Dakota Potato MH128395
N351 Meloidogyne sp. North Dakota Potato MH128396
P160071 M. arenaria Alachua, Florida Culture MH128436

COI sequence collection data for groups 2 to 19.

NID Group Species Locality Host/habitat GenBank accession #
P203060 3 Meloidogyne enterolobii Florida Ornamentals-Nursery MH128522
P179069 3 M. enterolobii Florida Ornamentals-Nursery MH128519
P179070 3 M. enterolobii Florida Ornamentals-Nursery MH128520
P196090 3 M. enterolobii Florida Ornamentals-Nursery MH128521
P210013 3 M. enterolobii Florida Ornamentals-Nursery MH128523
P210014 3 M. enterolobii Florida Ornamentals-Nursery MH128524
P210071 3 M. enterolobii Florida Ornamentals-ursery MH128529
P210059 3 M. enterolobii Florida Ornamentals-Nursery MH128527
P210057 3 M. enterolobii Florida Ornamentals-Nursery MH128525
P210058 3 M. enterolobii Florida Ornamentals-Nursery MH128526
P210072 3 M. enterolobii Florida Ornamentals-Nursery MH128530
P210065 3 M. enterolobii Florida Ornamentals-Nursery MH128528
N4314 4 Meloidogyne sp. Lance Rosier Unit, BITHa Loblolly pine MH128531
N4321 4 Meloidogyne sp. Lance Rosier Unit, BITHa Loblolly pine MH128532
N4379 5 Meloidogyne sp. Cove Mtn. Trail, GRSMb Chestnut MH128537
N4388 5 Meloidogyne sp. Cove Mtn. Trail, GRSMb Chestnut MH128538
N2110 5 Meloidogyne sp. GWMPc Fort Marcy earthworks MH128533
N3952 5 Meloidogyne sp. Turkey Creek, BITHa Baygall community MH128534
N4285 5 Meloidogyne sp. Canyonlands South, BITHa Magnolia MH128535
N4291 5 Meloidogyne sp. Canyonlands South, BITHa Magnolia MH128536
P214008 6 Meloidogyne partityla Dona Ana County, New Mexico Pecan MH128540
P214010 6 M. partityla Dona Ana County, New Mexico Pecan MH128542
P214009 6 M. partityla Dona Ana County, New Mexico Pecan MH128541
N2338 6 M. partityla Neches Bottoms Unit, BITHa Sandbar MH128539
P121054 7 Meloidogyne hapla Gasconade County, Missouri Peony MH128568
P200031 7 M. hapla Cass County, Nebraska Nursery MH128577
N163 7 M. hapla Nebraska Wheat MH128543
P200018 7 M. hapla Daggett County, Utah Grass pasture MH128575
P200019 7 M. hapla Daggett County, Utah Grass pasture MH128576
P178064 7 M. hapla Oregon Potato MH128570
P200032 7 M. hapla Colfax County, Nebraska Nursery MH128578
N1376 7 M. hapla Fremont County, Wyoming Red bean MH128558
N1377 7 M. hapla Fremont County, Wyoming Red bean MH128559
P179068 7 M. hapla New York GH MH128572
P178063 7 M. hapla Oregon Potato MH128569
P222083 7 M. hapla Portales, New Mexico GH culture MH128579
P222084 7 M. hapla Portales, New Mexico GH culture MH128580
N1448 7 M. hapla GWMPc Waterfowl sanctuary MH128560
N857 7 M. hapla Goshen County, Wyoming Potato MH128554
N859 7 M. hapla Goshen County, Wyoming Potato MH128555
N860 7 M. hapla Goshen County, Wyoming Potato MH128556
N861 7 M. hapla Goshen County, Wyoming Potato MH128557
P200001 7 M. hapla Hot Springs County, Wyoming Alfalfa MH128573
P200002 7 M. hapla Hot Springs County, Wyoming Alfalfa MH128574
N4124 7 M. hapla Wyoming – MH128561
N318 7 M. hapla Idaho Potato MH128544
N497 7 M. hapla California – MH128551
N489 7 M. hapla California – MH128550
N498 7 M. hapla California – MH128552
P179054 7 M. hapla Rhode Island GH culture MH128571
N320 7 M. hapla Idaho Potato MH128545
N358 7 M. hapla Idaho Potato MH128546
N359 7 M. hapla Idaho Potato MH128547
N421 7 M. hapla Carbon County, Montana Alfalfa MH128548
N422 7 M. hapla Carbon County, Montana Alfalfa MH128549
N856 7 M. hapla Goshen County, Wyoming Potato MH128553
N7097 7 M. hapla Nebraska Alfalfa MH128562
N7098 7 M. hapla Nebraska Alfalfa MH128563
N7100 7 M. hapla Nebraska Alfalfa MH128565
N7099 7 M. hapla Nebraska Alfalfa MH128564
N8595 7 M. hapla Chalti, Nepal Pine forest MH128566
N8612 7 M. hapla Chalti, Nepal Pine forest MH128567
N4222 9 Meloidogyne sp. Canyonlands South, BITHa Beech MH128581
N4229 9 Meloidogyne sp. Canyonlands South, BITHa Beech MH128582
N8431 9 Meloidogyne sp. Canyonlands South, BITHa Beech MH128584
N8433 9 Meloidogyne sp. Canyonlands South, BITHa Beech MH128585
N8283 9 Meloidogyne sp. Mt. St. Hilaire, Quebec, Canada Hardwood forest MH128583
N4431 10 Meloidogyne sp. Cove Mtn. Trail, GRSMb Chestnut MH128463
N4496 10 Meloidogyne sp. Cove Mtn. Trail, GRSMb Chestnut MH128464
N4497 11 Meloidogyne sp. Cove Mtn. Trail, GRSMb Chestnut MH128465
N8084 12 Meloidogyne sp. Purchase Knob, GRSMb Chestnut MH128468
N8121 12 Meloidogyne sp. Cataloochee, GRSMb Oak MH128470
N8058 12 Meloidogyne sp. Cataloochee, GRSMb Chestnut MH128467
N8012 12 Meloidogyne sp. Cataloochee, GRSMb Chestnut MH128466
N8111 12 Meloidogyne sp. Cataloochee, GRSMb Oak MH128469
N1479 13 Meloidogyne sp. Roy E. Larsen Sandylands, BITHa Baygall community MH128471
N3969 13 Meloidogyne sp. Turkey Creek, BITHa Baygall community MH128472
P129052 14 Meloidogyne oryzae Costa Rica Rice MH128473
P129054 14 M. oryzae Costa Rica Rice MH128474
P169011 14 Meloidogyne graminicola Florida Purple nutsedge MH128475
N214 15 Meloidogyne exigua Nicaragua Coffee MH128477
N215 15 M. exigua Nicaragua Coffee MH128478
N213 15 M. exigua Nicaragua Coffee MH128476
P199069 16 Meloidogyne naasi Sanpete County, Utah Grass MH128480
P199071 16 M. naasi Sanpete County, Utah Grass MH128481
P199072 16 M. naasi Sanpete County, Utah Grass MH128482
N326 16 M. naasi Idaho Potato MH128479
P192084 17 Meloidogyne fallax Scotland Genomic DNA MH128507
P119032 17 Meloidogyne chitwoodi New Mexico Culture MH128488
P115026 17 M. chitwoodi Fort Garland, Colorado Soil sample MH128487
P122010 17 M. chitwoodi Colorado Soil sample MH128489
P122047 17 M. chitwoodi Colorado Soil sample MH128490
P124056 17 M. chitwoodi Commercial Potato MH128491
P124057 17 M. chitwoodi Commercial Potato MH128492
P124059 17 M. chitwoodi Commercial Potato MH128493
N7145 17 M. chitwoodi Elko County, Nevada Potato MH128483
N7147 17 M. chitwoodi Elko County, Nevada Potato MH128484
N7148 17 M. chitwoodi Elko County, Nevada Potato MH128485
N7149 17 M. chitwoodi Elko County, Nevada Potato MH128486
P173100 17 M. chitwoodi Commercial Potato MH128494
P174001 17 M. chitwoodi Commercial Potato MH128495
P175068 17 M. chitwoodi Idaho Potato MH128496
P175069 17 M. chitwoodi Idaho Potato MH128497
P175070 17 M. chitwoodi Idaho Potato MH128498
P175071 17 M. chitwoodi Idaho Potato MH128499
P177092 17 M. chitwoodi Texas Potato MH128500
P177094 17 M. chitwoodi Texas Potato MH128501
P177098 17 M. chitwoodi Texas Potato MH128502
P192011 17 M. chitwoodi Commercial Potato MH128504
P192012 17 M. chitwoodi Commercial Potato MH128505
P192013 17 M. chitwoodi Commercial Potato MH128506
P211088 17 M. chitwoodi Oregon Potato MH128508
P211089 17 M. chitwoodi Oregon Potato MH128509
P212013 17 M. chitwoodi California Potato MH128510
P212014 17 M. chitwoodi California Potato MH128511
P212015 17 M. chitwoodi California Potato MH128512
P212016 17 M. chitwoodi California Potato MH128513
P213039 17 M. chitwoodi Washington Potato MH128514
P213040 17 M. chitwoodi Washington Potato MH128515
P221087 17 M. chitwoodi New Mexico Potato MH128518
P215032 17 M. chitwoodi Washington Potato MH128517
P178028 17 M. chitwoodi Commercial Potato MH128503
P215031 17 M. chitwoodi Washington Potato MH128516

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 Length Tail length Stylet length a b c
Unnamed 4 2 441 (430–452) 42 17 24.3 (22.7–25.9) 3.8 (3.7–3.9) 10.5 (10.3–10.8)
Unnamed 5 5 431 (406–460) 47 (40–53) 14 (13–15 25.4 914.4–30.8) 3.9 (3.0–4.8) 9.3 (8.0–10.1)
Unnamed 9 5 393 (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) 1 384 42 15 27.5 3.5 9.1
Unnamed 12 5 353 (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 13 2 490 (439–541) 59 (57–62) 14 30.7 (30.4–31) 3.9 (3.8–4.0) 8.2 (7.7–8.6)
Meloidogyne ovalis 10 370 (350–430) – – 22 (21–24) – 8 (8–9)
Meloidogyne pini 30 434 (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 70 501 (443–576) 47 (40–56) 11.6 (11.2–12) 26 (21–30) 3.1 10.7 (9.5–12
Meloidogyne querciana 70 467 (411–541) 46 (39–52) 11.1 (10.2–11.6) 30 (23–39) 2.6 10 (7–13)
Meloidogyne megatyla 23 416 (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)
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