Discovery and Identification of <italic>Meloidogyne</italic> Species Using COI DNA Barcoding

Thomas Powers; Timothy Harris; Rebecca Higgins; Peter Mullin; Kirsten Powers

doi:10.21307/jofnem-2018-029

VOLUME 50 , ISSUE 3 (September 2018) > List of articles

Discovery and Identification of Meloidogyne Species Using COI DNA Barcoding

Thomas Powers / Timothy Harris / Rebecca Higgins / Peter Mullin / Kirsten Powers ^*

Keywords : COI, DNA barcoding, Meloidogyne, Plant parasitic nematodes, Root-knot nematodes, Taxonomy

Citation Information : Journal of Nematology. Volume 50, Issue 3, Pages 399-412, DOI: https://doi.org/10.21307/jofnem-2018-029

License : (PUBLISHER)

Published Online: 17-October-2018

ARTICLE
FIGURES & TABLES
REFERENCES
EXTRA FILES
COMMENTS

ARTICLE

ABSTRACT

DNA barcoding with a new cytochrome oxidase c subunit 1 primer set generated a 721 to 724 bp fragment used for the identification of 322 Meloidogyne specimens, including 205 new sequences combined with 117 from GenBank. A maximum likelihood analysis grouped the specimens into 19 well-supported clades and four single-specimen lineages. The “major” tropical apomictic species (Meloidogyne arenaria, Meloidogyne incognita, Meloidogyne javanica) were not discriminated by this barcode although some closely related species such as Meloidogyne konaensis were characterized by fixed diagnostic nucleotides. Species that were collected from multiple localities and strongly characterized as discrete lineages or species include Meloidogyne enterolobii, Meloidogyne partityla, Meloidogyne hapla, Meloidogyne graminicola, Meloidogyne naasi, Meloidogyne chitwoodi, and Meloidogyne fallax. Seven unnamed groups illustrate the limitations of DNA barcoding without the benefit of a well-populated reference library. The addition of these DNA sequences to GenBank and the Barcode of Life Database (BOLD) should stimulate and facilitate root-knot nematode identification and provide a first step in new species discovery.

Graphical ABSTRACT

Full Text XML PDF Share

The term DNA-barcoding has multiple definitions. The earliest mention of barcoding in nematology was in 1998 by Dr Mark Blaxter, then of Edinburgh University, referring to the “(d)evelopment of a molecular barcode system for soil nematode identification” in the first volume of the Natural Environment Research Council Soil Biodiversity Newsletter (http://soilbio.nerc.ac.uk/newsletters.htm). The barcode he was referring to was the 18S nuclear (small subunit) ribosomal gene. Other gene regions proposed for DNA-barcoding soon followed, creating a broader definition that generally applied to the use of DNA sequences for species identification (Floyd et al., 2002; Blaxter, 2004; Powers, 2004). In 2003 a widely cited paper by Hebert et al. (2003) proposed a standardization of the barcode definition linked to the amplification of a 658 bp gene region within the cytochrome oxidase subunit 1 mitochondrial gene. The goal of this conceptual paper was the development of a global bioidentification system for animals. Considerable controversy immediately followed this publication with criticism ranging from theoretical concerns about the use of a single gene, the ability of an organelle gene to track species boundaries, and barcoding’s impact on the process of taxonomic investigation (DeSalle et al., 2005; Will et al., 2005). Practical concerns were expressed about lack of amplification with some groups, the designation of types, taxonomic resolution, and economic cost at the expense of traditional taxonomic approaches (Meyer and Paulay, 2005; Rubinoff et al., 2006; McFadden et al., 2011). Now, 15 years later, DNA-barcoding has become a component within the broader scope of integrated taxonomy and a routine tool for identification (Hodgetts et al., 2016; Janssen et al., 2016). As a diagnostic and discovery enterprise, DNA barcoding has generated thousands of publications, features biennial international conferences, has a dedicated database – BOLD, the Barcode of Life Database – and has multiple administrative structures such as the International Barcode of Life (IBOLD) and its affiliates (www.boldsystems.org/index.php/default).

Nematology was slow to adopt this formalized version of barcoding, perhaps due to poor amplification with the original “Folmer” primer sets (Folmer et al., 1994). Now multiple primer sets for amplification of nematode cytochrome oxidase c subunit 1 (COI) are available (Derycke et al., 2005, 2010; Prosser et al., 2013; Kiewnick et al., 2014; Powers et al., 2014; Janssen et al., 2016). These primer sets typically have limited taxonomic scope with amplifications specific for genera or in some cases extending across families and superfamilies (Powers et al., 2014). The objective of this study is to present a primer set used for the amplification of 721 to 724 bp of COI sequence from Meloidogyne. A maximum likelihood (ML) tree is provided to illustrate the ability of this gene region to discriminate among many described Meloidogyne species. The primers also function as a means to amplify DNA from juvenile stages in community analyses, possibly leading to new species discoveries. Contributions to a COI reference library should aid future taxonomic and ecological research in the genus.

Materials and Methods

Nematode collection

Most of the specimens DNA barcoded in this study were either specimens submitted to the UNL Nematology Diagnostics Clinic, specimens contributed by colleagues, or specimens collected during grant funded surveys (NSF projects DEB-1145440; USDA Multistate Project W3186).

Primer sequences

The primer set for amplification of the COI gene region were:

COI-F5-Mel – 5′-TGATTGATTTAGGTTCTGGAACTKSWTGAAC-3′

COI-R9-Mel – 5′-CATAATGAAAATGGGCAACAACATAATAAGTATC-3′

After removal of the primer sequences, amplification products from the Meloidogyne specimens were either 721 or 724 bp. GenBank sequences used in this study generally were 100 to 300 nucleotides shorter than sequences generated with the new primer set.

Amplification conditions

Nematodes amplified at the UNL Nematology Laboratory were individually smashed in 18 ul of sterile H20 with a transparent microfuge micropipette tip on a coverslip and added to a 0.5 ml microfuge tube. Nematode lysate was either amplified immediately or stored at −20°C. Amplification conditions were as follows: denaturation at 94°C for 5 min, followed by 45 cycles of denaturation at 94°C for 30 sec, annealing at 48.0°C for 30 sec, and extension at 72°C for 90 sec with a 0.5° per second ramp rate to 72°C. A final extension was performed at 72 °C for 5 min as described by Powers et al. (2014) and Olson et al. (2017). Polymerase chain reaction (PCR) products were separated and visualized on 1% agarose using 0.5XTBE and stained with ethidium bromide. PCR products of sufficiently high quality were cleaned and sent for sequencing of both strands by University of California–Davis DNA sequencing facility.

Data storage

Nucleotide sequences have been submitted to GenBank (accession numbers MH128384–MH128585) and the Barcode of Life Database (BOLD).

Phylogenetic analysis

Phylogenetic trees were constructed under ML and Neighbor Joining (NJ) criteria in MEGA version 6. Sequences were edited using CodonCode Aligner version 7.1 (www.codoncode.com/) and aligned using Muscle within MEGA version 6 (Tamura et al., 2013). Gap opening penalty was set at –400 with a gap extension penalty of –200. The General Time Reversible Model with Gamma distributed rates (GTR+G) was determined to be the best substitution model by Bayesian Information Criterion using the Best Fit Substitution Model tool in MEGA 6.0. ML trees used a use all sites option for gaps and 200 bootstrap replications to assess clade support.

Results

Figure 1 displays a ML tree of 322 Meloidogyne sequences including 117 sequences from GenBank and 205 sequences from the University of Nebraska–Lincoln Nematology Laboratory. ML partitions these sequences into 19 groups with bootstrap support values from 93 to 100 (Tables 1, 2, Fig. 1). Three unique GenBank sequences represent Meloidogyne haplanaria Eisenback et al., 2004, Meloidogyne duytsi Karssen et al., 1998, and Meloidogyne artiellia Franklin, 1961 as distinct from other sequences in the dataset, but without additional supporting sequences.

Table 1

COI sequence collection data for groups 2 to 19.

Table 2

COI sequences included in group 1.

Groups 1 to 3 form a clade characterized by the loss of a single amino acid (3 bp) resulting in a 721 bp sequenced region. This shared deletion unites M. haplanaria, and M. enterolobii Yang & Eisenback, 1983 with the so-called “major” tropical apomictic species of Meloidogyne (Elling, 2013). Included in this group are sequences representing M. arenaria (Neal, 1889) Chitwood, 1949, M. incognita (Kofoid & White, 1919) Chitwood, 1949, M. javanica (Treub, 1885) Chitwood, 1949, as well as M. hispanica Hirschmann, 1986, M. floridensis Handoo et al., 2004, M. konaensis Eisenback, Bernard & Schnitt, 1995, M. luci Carneiro et al., 2014, and M. inornata Lordello, 1956 (Table 2). The same amino acid deletion is also found in unnamed group 12. Within group 1, the COI sequences are nearly identical with a few notable exceptions. Four substitutions are shared by three specimens identified as M. konaensis, including GenBank accession KU372176, identified as Meloidogyne sp. 2 TJ-2016 T316 on Beta vulgaris from Spain in Janssen et al. (2016). Two substitutions are shared by specimens identified as M. incognita grahami, originally described as M. grahami Golden & Slana, 1978, and considered distinct from M. incognita based on reproduction on NC-95 tobacco, a cultivar with resistance to M. incognita, plus a greater juvenile length and a distinctive perineal pattern (Golden and Slana, 1978).

Outside of clades 1-3 there are 11 other described species represented by a minimum of a single COI sequence. Meloidogyne hapla Chitwood, 1949 is represented by specimens from 10 U.S. states and two specimens from Nepal. There are multiple haplotypes within M. hapla and possibly some population substructure within the species. Group 17 identified as M. chitwoodi Golden, O’Bannon, Santo & Finley, 1980 and M. fallax Karssen, 1996 is virtually homogeneous except for a 5-bp difference between the two species. Within group 6, identified as M. partityla Kleynhans, 1986 one specimen collected from Big Thicket National Preserve, Texas comes from a native lowland plant community, compared with other specimens from New Mexico collected from commercial pecan (Carya illinoinensis (Wangenh.) K. Koch) production.

There are seven groups labeled as unnamed, all with sequence derived from j2 stage specimens except for N4431 and N4496 which were males collected from native chestnut (Castanea dentata (Marshall) Borkh.) in Great Smoky Mountains National Park (GRSM), North Carolina. All specimens in the unnamed groups 4, 5, 9 to 13 were isolated from soil samples within Gulf Coast or Eastern North American forests. Groups 9 and 12 were associated with American beech, (Fagus grandifolia Ehrh.) and chestnut or oak, respectively. Measurements of the unidentified juveniles are presented in Table 3, and Fig. 2 illustrates juveniles from three of the unnamed groups.

Table 3

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

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.

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.

Discussion

The COI gene region used as a diagnostic marker in this study appears to discriminate many of the described species of Meloidogyne. It does not separate the apomictic “major species” and their close relatives, except possibly M. konaensis and M. incognita grahami. Other mitochondrial genes such as NAD 5 may help resolve some of those species boundaries (Janssen et al., 2016). Aside from an inability to discriminate among the tropical clade 1 species, there are advantages to using COI as a DNA barcode. As a protein coding gene, nucleotide alignment is easier compared with non-protein coding genes. Taxonomic resolution is at the population and species level, although for many genera, mutational saturation, lineage extinctions, or inadequate sampling may obscure deeper relationships that aid in the recognition of species groupings. Nonetheless, COI barcodes in combination with an adequately curated sequence database, provide a powerful tool for identification and discovery. The limitation of DNA barcoding without a corresponding database is illustrated by the unnamed groups in the Meloidogyne dataset. For example, there was an expectation that focal samples from soil around individual chestnut and oak trees in GRSM might yield Meloidogyne querciana Golden, 1979 which was described from northern red oak (Quercus rubra L.) and chestnut hosts within the same ecoregion. Indeed Meloidogyne specimens were found in these samples, however, the barcode data demonstrate that multiple COI lineages were associated with chestnut and oaks in the park. Similarly, unnamed lineages were also discovered associated with American beech and baygall plant communities in Big Thicket National Preserve, Texas (www.nps.gov/bith/plant-communities.htm). These results indicate that considerable Meloidogyne diversity exists in the primary and secondary forests of eastern and southern United States. Characterization of this diversity by COI barcoding allows us to rule out described species with representation in the COI database, yet neither COI barcode nor morphometrics of juvenile specimens permits unequivocal assignment of a species name to these specimens. For these unknown specimens a more complete taxonomic analysis that includes obtaining adult stages will be required before a barcode sequence can be linked to a formal Latin binomial.

Acknowledgements

Thanks to the sponsors of nematode surveys, Department of Interior-National Park Service, Discover Life in America, NSF project DEB-1145440, Nebraska Department of Agriculture, Thicket of Diversity, USDA Multistate Project 3186, and University of Nebraska-Lincoln Agricultural Research Division IC-282. Most of all we thank the numerous collaborators and colleagues who have contributed nematode specimens for identification.

Appendices

Appendix

Supplementary Table S1

Supplementary Table S1.

Accession numbers of specimens from Group 1 acquired from GenBank.

References

Blaxter, M.L.. 2004. The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 669-679, doi: 10.1098/rstb.2003.1447.
[CROSSREF] [URL]
Derycke, S., Remerie, T., Vierstraete, A., Backeljau, T., Vanfleteren, J., Vincx, M. and Moens, T.. 2005. Mitochondrial DNA variation and cryptic speciation within the free-living marine nematode Pellioditis marina. Marine Ecology Progress Series 300: 91-103, doi: 10.3354/meps300091.
[CROSSREF] [URL]
Derycke, S., Vanaverbeke, J., Rigaux, A., Backeljau, T. and Moens, T.. 2010. Exploring the use of cytochrome oxidase c subunit 1 (COI) for DNA barcoding of free-living marine nematodes. PLOS ONE 5 10: e13716, doi: 10.1371/journal.pone.0013716.
[CROSSREF] [URL]
DeSalle, R., Egan, M.G. and Siddall, M.. 2005. The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B 360: 1905-1916.
[CROSSREF]
Eisenback, J.D., Bernard, E.C. and Schmitt, D.P.. 1994. Description of the Kona coffee root-knot nematode, Meloidogyne konaensis n.sp. Journal of Nematology 26 4: 363-374.
[PUBMED]
Elling, A.A.. 2013. Major emerging problems with minor Meloidogyne species. Phytopathology 103: 1092-1102, doi: 10.1094/PHYTO-01-13-0019-RVW.PMID:23777404.
[CROSSREF] [URL]
Floyd, R., Abebe, E., Papert, A. and Blaxter, M.. 2002. Molecular barcodes for soil nematode identification. Molecular Ecology 11: 839-850, doi: 10.1046/j.1365-294X.2002.01485.x.
[CROSSREF] [URL]
Folmer, O., Black, M., Hoeh, W., Lutz, R. and Vrijenhoek, R.. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294-299.
[PUBMED]
Hebert, P.D., Ratnasingham, S. and de Waard, J.R.. 2003. Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London B: Biological Sciences 270 Suppl 1: S96-S99, doi: 10.1098/rsbl.2003.0025..
[CROSSREF] [URL]
Hodgetts, J., Ostojá-Starzewski, J.C., Prior, T., Lawson, R., Hall, J. and Boonham, N.. 2016. DNA barcoding for biosecurity: Case studies from the UK plant protection program. Genome 59: 1033-1048, doi: dx.doi.org/10.1139/gen-2016-0010.
[CROSSREF] [URL]
Janssen, T., Karssen, G., Verhaeven, M., Coyne, D. and Bert, W.. 2016. Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution. Scientific Reports 6: 22591, http://doi.org/10.1038/srep22591.
[CROSSREF] [URL]
Kiewnick, S., Holterman, M., van den Elsen, S., van Megen, H., Frey, J.E. and Helder, J.. 2014. Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives. European Journal of Plant Pathology 140: 97-110, http://dx.doi.org/10.1007/s10658-014-0446-1.
[CROSSREF] [URL]
McFadden, C.S., Benayahu, Y., Pante, E., Thoma, J.N., Nevarez, P.A. and France, S.C.. 2011. Limitations of mitochondrial gene barcoding in Octocorallia. Molecular Ecology Resources 11: 19-31, doi: 10.1111/j.1755-0998.2010.02875.x.
[CROSSREF] [URL]
Meyer, C.P. and Paulay, G.. 2005. DNA barcoding: Error rates based on comprehensive sampling. PLOS Biology 3: 2229-2237.
Olson, M., Harris, T., Higgins, R., Mullin, P., Powers, K., Olson, S. and Powers, T.O.. 2017. Species delimitation and description of Mesocriconema nebraskense n. sp. (Nematoda: Criconematidae), a morphologically cryptic, parthenogenetic species from North American grasslands. Journal of Nematology 49 1: 42-68.
[CROSSREF]
Powers, T.O.. 2004. Nematode molecular diagnostics: From bands to barcodes. Annual Review of Phytopathology 42: 367-383.
[CROSSREF]
Powers, T.O., Bernard, E.C., Harris, T., Higgins, R., Olson, M., Lodema, M., Mullin, P., Sutton, L. and Powers, K.S.. 2014. COI haplotype groups in Mesocriconema (Nematoda: Criconematidae) and their morphospecies associations. Zootaxa 3827 2: 101-146, http://dx.doi.org/10.11646/zootaxa.3827.2.1.
[CROSSREF] [URL]
Prosser, S., Velarde-Aguilar, M.G., León-Règagnon, V. and Hebert, P.D.. 2013. Advancing nematode barcoding: a primer cocktail for the cytochrome c oxidase subunit I gene from vertebrate parasitic nematodes. Molecular Ecology Resources 13 6: 1108-1115 DOI:10.1111/1755-0998.12.
[CROSSREF] [URL]
Rubinoff, D., Cameron, S. and Will, K.. 2006. A genomic perspective on the shortcomings of mitochondrial DNA for ‘barcoding’ identification. Journal of Heredity 97: 581-594.
[CROSSREF]
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S.. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729.
[CROSSREF]
Will, K.W., Mishler, B.D. and Wheeler, Q.D.. 2005. The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54: 844-851.
[CROSSREF]

XML PDF Share

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.

Full Size | Slide (.pptx)

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.