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Reliability and Utility of Standard Gene Sequence Barcodes for the Identification and Differentiation of Cyst Nematodes of the Genus Heterodera Cover

Reliability and Utility of Standard Gene Sequence Barcodes for the Identification and Differentiation of Cyst Nematodes of the Genus Heterodera

Open Access
|Jul 2022

Figures & Tables

Table 1

Numbers of species of Heterodera for which one or more gene sequences of one or more molecular markers (18S, ITS, 28S, and coxI) are available on GenBank.

Species of Heterodera18SITS28ScoxIAll
Species with at least one sequence1855363813
Species with more than one sequence1338222911
Table 2

Species pairs of Heterodera which are inadequately or poorly distinguished from one another using one or more of the standard molecular markers evaluated (18S, ITS, 28S, coxI), including minimum base pair differences observed between sequences of problematic species pairs.

Species groupSpecies pairGene regionMinimum base pair differenceDelineation powerNotes
AvenaeH. avenae–H. filipjevi18S1Inadequate
AvenaeH. avenae–H. hordecalis18S4WeakH. hordecalis not monophyletic
in NJ/ML analyses; potentially
distinguishable from closely
related species in isolated
analyses.
AvenaeH. avenae–H. mani18S1Inadequate
AvenaeH. filipjevi–H. hordecalis18S1Inadequate
AvenaeH. filipjevi–H. mani18S2Inadequate
AvenaeH. hordecalis–H. mani18S3WeakSee above note.
AvenaeH. arenaria–H. avenaeITS0Inadequate
AvenaeH. avenae–H. pratensisITS0Inadequate
AvenaeH. avenae–H. australisITS2WeakAlthough only two bp different,
sequences of H. australis form
clade with some sequences
of “H. avenae” which have
been shown to be H. australis
(see Subbotin et al., 2018).
AvenaeH. avenae–H. maniITS2WeakDespite only two bp difference,
sequences of H. mani form
monophyletic clade to
exclusion of other closely
related sequences.
AvenaeH. aucklandica–H.28S1InadequateOnly one 28S sequence of
avenaeH. aucklandica available for
comparison.
AvenaeH. aucklandica–H.28S1InadequateTwo 28S sequences of
hordecalisH. hordecalis 9 bp different
AvenaeH. aucklandica–H.28S1InadequateOnly one 28S sequence of
pratensisH. pratensis available for
comparison.
AvenaeH. avenae–H. pratensis28S0inadequateSee above note.
AvenaeH. avenae–H. hordecalis28S0InadequateTwo 28S sequences of
H. hordecalis 9 bp different
AvenaeH. arenaria–H. avenaecox12WeakDespite only two bp
difference, H. arenaria forms
monophyletic clade within
H. avenae group.
CyperiH. elachista–H. oryzaeITS1Inadequate
CyperiH. elachista–H. oryzae28S0Inadequate
GoettingianaH. carotae–H. cruciferaeITS1Inadequate
GoettingianaH. goettingiana–H.28S0InadequateTwo 28S sequences of
microulaeH. goettingiana are 19 bp
different from one another; one
potentially misidentified
GoettingianaH. carotae–H. urticae28S2WeakOnly one 28S sequence
of H. urticae available for
comparison.
GoettingianaH. carotae–H. cruciferae28S2WeakOnly one 28S sequence of
H. cruciferae available for
comparison (two on GenBank
but one appears to actually be
H. schachtii).
GoettingianaH. carotae–H. cruciferaecox11InadequateThree cox1 sequences
available for H. cruciferae, one
15 bp different from others.
SchachtiiH. betae–H. glycines18S2WeakH. glycines forms
monophyletic clade to
exclusion of H. betae,
H. schachtii & H. trifolii in ML,
but not NJ, analyses.
SchachtiiH. betae–H. schachtii18S0Inadequate
SchachtiiH. betae–H. trifolii18S0Inadequate
SchachtiiH. schachtii–H. glycines18S2WeakSee above note.
SchachtiiH. schachtii–H. trifolii18S0Inadequate
SchachtiiH. trifolii–H. glycines18S2WeakSee above note.
SchachtiiH. betae–H. davertiITS0Inadequate
SchachtiiH. betae–H. schachtiiITS0Inadequate
SchachtiiH. betae–H. trifoliiITS0Inadequate
SchachtiiH. ciceri–H. schachtiiITS2Inadequate
SchachtiiH. ciceri–H. trifoliiITS1Inadequate
SchachtiiH. daverti–H. schacthiiITS0Inadequate
SchachtiiH. daverti–H. trifoliiITS0Inadequate
SchachtiiH. glycines–H.ITS1Inadequate
medicaginis
SchachtiiH. schachtii–H. trifoliiITS0Inadequate
SchachtiiH. betae–H. daverti28S1Inadequate
SchachtiiH. betae–H. schachtii28S2Inadequate
SchachtiiH. betae–H. trifolii28S1Inadequate
SchachtiiH. daverti–H. schachtii28S3Weak
SchachtiiH. daverti–H. trifolii28S1Inadequate
SchachtiiH. schachtii–H. trifolii28S1Inadequate
Figure 1

Geographic origin of 18S, ITS, 28S, and coxI gene sequences analyzed in the present study. The size of the circle reflects the total number of sequences of all markers centered on the country of origin.

Figure 2

Neighbor-joining tree based on coxI sequences of Heterodera avenae from the NCBI database GenBank showing a clade of mislabeled sequences.

Table 3

Intraspecific differences observed in the 18S, ITS, 28S, and coxl gene regions for those species of Heterodera for which more than one sequence of one or more of the respective gene regions are available, excluding problematic sequences.

18SITS28Scox1
Speciesnbp (%)nbp (%)nbp (%)nbp (%)
Heterodera arenaria40–1; 0.50 (0–0.29; 0.15)60–2; 2 (0–0.48; 0.48)
Heterodera aucklandica30(0)50–1; 0 (0–0.24; 0)
Heterodera australis180–9; 3 (0–0.93; 0.31)50(0)
Heterodera avenae170–11; 1 (0–1.09; 0.06)5420–80; 8 (0–11.89; 0.89)760–5; 0 (0–0.67; 0)910–34; 9 (0–8.17; 2.40)
Heterodera betae21 (0.06)70–12; 3 (0–1.29; 0.37)20(0)20(0)
Heterodera bifenestra32–10; 8 (0.20–1.02; 0.81)
Heterodera cajani120–12; 4 (0–1.18; 0.39)130–11; 2 (0–1.46; 0.26)
Heterodera carotae130–13; 6 (0–1.35; 0.62)80–6; 3 (0–0.83; 0.41)170–20; 3 (0–4.77; 0.82)
Heterodera ciceri37–14; 11 (0.74–1.49; 1.18)
Heterodera cruciferae110–10; 3 (0–1.21; 0.36)252 (9.49)31–16; 16 (0.24–4.01; 3.77)
Heterodera cyperi20(0)
Heterodera daverti50–2; 1 (0–0.24; 0.11)30–2; 2 (0–0.51; 0.51)
Heterodera dunensis30(0)30(0)30(0)80–1; 0 (0–0.28; 0)
Heterodera elachista33–4; 3 (0.25–0.36; 0.36)430–48; 11 (0–4.52; 1.05)180–4; 1 (0–0.54; 0.15)20(0)
Heterodera fici22 (0.34)80–3; 1 (0–0.31; 0.10)90–2; 1 (0–0.47; 0.24)
Heterodera filipjevi31–2; 1 (0.12–0.17; 0.17)2560–43; 2 (0–4.46; 0.21)100–2; 1 (0–0.30; 0.13)750–44; 10 (0–10.58; 2.42)
Heterodera glycines60–1; 0 (0–0.16; 0)3190–112; 3 (0–11.89; 0.32)560–43; 2 (0–5.79; 0.26)810–9; 0 (0–1.04; 0)
Heterodera goettingiana40–10; 5 (0–1.21; 0.59)150–81; 37 (0–11.34; 5.08)219 (2.92)30–17; 17 (0–4.84; 4.84)
Heterodera goldeni50–6; 2 (0–0.59; 0.23)
Heterodera guangdongensis30–3; 3 (0–0.26; 0.26)71–6; 4 (0.15–0.91; 0.58)
Heterodera hordecalis25 (0.31)370–68; 7 (0–8.89; 0.84)29 (1.33)100–47; 14 (0–11.4; 3.37)
Heterodera humuli130–4; 1 (0–0.57; 0.17)190–9; 2 (0–5.92; 0.59)
Heterodera koreana31–22; 2 (0.17–1.27; 0.34)290–28; 7 (0–3.08; 0.73)480–21; 2 (0–2.88; 0.27)440–18; 5 (0–4.57; 1.27)
Heterodera latipons1540–122; 13 (0–13.32; 1.46)21 (0.15)160–50; 27 (0–12.05; 6.52)
Heterodera litoralis40(0)
Heterodera mani61–9; 3 (0.10–0.93; 0.31)60–1; 1 (0–0.27; 0.24)
Heterodera medicaginis140–9; 3 (0–0.95; 0.42)140–2; 0 (0–0.49; 0)
Heterodera mediterranea21 (0.17)61–9; 7 (0.11–0.95; 0.74)23 (0.38)
Heterodera mothi23 (0.30)22 (0.44)
Heterodera orientalis56–18; 12 (0.66–1.94; 1.28)
Heterodera pratensis130–10; 6 (0–1.08; 0.62)200–8; 2 (0–1.93; 0.53)
Heterodera ripae50–4; 2 (0–0.46; 0.22)190–11; 1 (0–2.59; 0.24)
Heterodera sacchari30–1; 1 (0–0.09; 0.09)
Heterodera salixophila50–20; 15 (0–2.10; 1.58)21 (0.15)160–18; 2 (0–4.57; 0.51)
Heterodera schachtii91–9; 4 (0.06–0.99; 0.31)640–31; 12 (0–3.04; 1.29)200–4; 1 (0–0.58; 0.13)380–7; 1 (0–1.88; 0.12)
Heterodera sojae50–12; 4.5 (0–1.36; 1.03)100–8; 4 (0–1.06; 0.53)120–6; 1 (0–1.59; 0.24)
Heterodera sturhani70–3; 0 (0–0.72; 0)
Heterodera trifolii50–8; 3 (0–0.47; 0.29)230–14; 3 (0–1.48; 0.43)190–1; 0 (0–0.15; 0)260–5; 0 (0–1.24; 0)
Heterodera ustinovi51–8; 3.5 (0.10–0.88; 0.36)50–1; 1 (0–0.24; 0.24)
Heterodera zeae160–39; 14 (0–5.65; 2.19)40–2; 1 (0–0.31; 0.15)

[i] Intraspecific differences are presented in the format “base pair difference range; median of base pair difference range (percent difference range; median of percent difference range).” Medians indicated only in cases of three or more comparisons; n = the number of sequences compared.

Figure 3

Neighbor joining (A) and maximum likelihood (B) trees derived from analyses of ITS gene sequences for the Schachtii species group showing multiple instances where species cannot be differentiated.

Table S1

Total number of sequences of species of Heterodera per country available on the NCBI database GenBank, up to 10 August 2021.

ITS18S28ScoxITotal
Afghanistan11
Algeria627877
Australia111618
Azerbaijan36137
Belgium21121438
Canada1917532
Chile11
China7611613121937
Costa Rica1113
Cyprus2121
Czech Republic77721
Egypt7310
Estonia22
France11920
Georgia112
Germany3512864
Ghana22
Greece611715
Guatemala22
India2615142
Iran411651108
Iraq3811
Ireland123
Israel77
Italy19681245
Ivory Coast11
Japan476450161
Jordan235
Kazakhstan5353
Kyrgyzstan32133
Madagascar22
Mexico336
Morocco34539
Myanmar22
Netherlands1623728
New Zealand22711
Norway44
Pakistan213
Poland123
Portugal112
Qatar11
Russia122335
Saudi Arabia231125
Serbia7310
Slovak Republic347
South Africa3115
South Korea303836104
Spain10331329
Sweden4228
Switzerland33
Syria1512137
Tajikistan134
Tunisia412613
Turkey21953272
Ukraine31711
United Kingdom111921
USA71718158254
Vietnam213
Unknown2211125
Total1724773465922739
Table S2

Species of Heterodera, and associated number of sequences, recorded from 59 countries based on data from the NCBI database GenBank, up to 10 August 2021.

SpeciesCountry18SITS28ScoxI
Heterodera arenariaItaly13
Netherlands2
United Kingdom31
Heterodera aucklandicaBelgium1
New Zealand113
United Kingdom12
Heterodera australisAustralia75
China11
Heterodera avenaeAlgeria46
Australia1
Azerbaijan9
China4359574
Czech Republic777
Egypt53
France97
Germany34
India41
Iran214
Iraq3
Israel34
Morocco275
Norway4
Pakistan1
Saudi Arabia2311
Serbia11
South Korea121
Spain33
Switzerland1
Syria36
Tunisia16
Turkey3926
United Kingdom1
USA110314
Unknown4
Heterodera betaeBelgium1
Germany3
Netherlands322
Unknown2
Heterodera bifenestraBelgium2
Sweden11
Heterodera cajaniIndia1213
Heterodera cardiolataPakistan11
United Kingdom1
Heterodera carotaeBelgium1
Algeria2
Canada565
France12
Italy315
Mexico21
South Africa111
Switzerland1
Heterodera ciceriSyria31
Heterodera circeaeGermany1
Heterodera cruciferaeAlgeria5
Iran11
Italy11
Netherlands1
Russia11
Serbia1
USA12
Heterodera cyperiSpain1
USA11
Heterodera davertiGermany32
Italy111
Netherlands11
Heterodera dunensisSpain3338
Heterodera elachistaChina12710
Iran211
Italy2442
Japan113
Heterodera ficiCanada2
Georgia11
Greece4
Iran13
Italy21
Qatar1
USA211
Heterodera filipjeviAlgeria2
Azerbaijan20
China5872
Germany21
Greece1
India1
Iran519
Italy1
Kazakhstan25
Kyrgyzstan31
Russia37
Serbia12
Slovakia1
Spain12
Sweden11
Syria6
Tajikistan13
Turkey8020
Ukraine3
United Kingdom13
USA315
Unknown2
Heterodera glycinesCanada1121
Chile1
China527529
Iran21
Japan610
South Korea USA14 217 781
Unknown11
Heterodera goettingianaChina11013
Germany21
Iran1
Ireland1
Italy2
Netherlands4
USA1
Heterodera goldeniEgypt2
Iran2
Israel1
Heterodera graminisIndia1
Heterodera graminophilaUSA1
Heterodera guangdongensisChina33
Myanmar2
Vietnam21
Heterodera hainanensisChina11
Heterodera hordecalisAlgeria2212
Estonia1
Germany12
Iran43
Israel32
Italy2
Netherlands12
Slovakia12
Sweden11
Tunisia1
United Kingdom1
Heterodera humuliBelgium1
Germany12
Iran318
Kyrgyzstan11
Portugal1
Russia12
USA65
Heterodera koreanaChina122
Iran11
Japan204141
South Korea333
USA231
Heterodera latiponsCyprus21
Iran33
Israel2
Jordan23
Kazakhstan28
Morocco3
Russia11
Syria917
Turkey873
Heterodera litoralisNew Zealand114
Heterodera maniGermany41
United Kingdom1
USA14
Unknown1
Heterodera medicaginisRussia1
USA13114
Heterodera mediterraneaItaly22
Spain2
Tunisia122
Heterodera microulaeChina111
Heterodera mothiAzerbaijan11
Iran11
Heterodera orientalisGuatemala2
Russia1
USA21
Heterodera oryzaeSouth Korea111
Heterodera oryzicolaIndia11
Heterodera persicaIran1
Heterodera pratensisBelgium1
Germany88
Iran5
Netherlands11
Russia12
South Korea212
USA11
Heterodera ripaeBelgium Germany15 4
Greece12
Russia Serbia1 14
Slovakia2
Sweden1
United Kingdom2
Heterodera sacchariGhana2
Ivory Coast1
Heterodera salixophilaBelgium113
Germany4
Iran11
Russia5
Ukraine34
Heterodera schachtiiAlgeria1
Australia4
Belgium115
China1183
France13
Germany4
Iran21
Ireland2
Japan111
Mexico12
Morocco3
Netherlands811
Poland11
Serbia3
South Africa1
South Korea347
Turkey12
USA2322
Unknown61
Heterodera scutellariaeGermany1
Heterodera sinensisChina1
Heterodera skohensisIndia1
Heterodera sojaeChina11
Japan11
South Korea3812
Heterodera sorghiIndia1
Heterodera sturhaniChina7
Heterodera trifoliiCosta Rica111
Estonia1
Iran112
Italy1
Japan888
South Korea889
United Kingdom121
USA25
Unknown4
Heterodera turcomanicaIran11
Heterodera urticaeBelgium113
Heterodera ustinoviBelgium1
Germany1
Slovakia1
United Kingdom1
USA12
Heterodera vallicolaRussia11
Heterodera zeaeAfghanistan1
China5
Greece151
India4
Portugal1
USA21
DOI: https://doi.org/10.2478/jofnem-2022-0024 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X
Language: English
Submitted on: Dec 13, 2021
Published on: Jul 29, 2022
Published by: Society of Nematologists, Inc.
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2022 Daniel C. Huston, Manda Khudhir, Mike Hodda, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.