A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America
Pratylenchus species are among the most common plant parasitic nematodes in the Great Plains Region of North America. Our goal was to survey Pratylenchus species diversity across the Great Plains region using a mitochondrial COI DNA barcode. The objectives were to (i) determine species boundaries of...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Sciendo
2019-01-01
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| Series: | Journal of Nematology |
| Subjects: | |
| Online Access: | https://doi.org/10.21307/jofnem-2019-081 |
| _version_ | 1811159224205443072 |
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| author | Ozbayrak Mehmet Todd Tim Harris Timothy Higgins Rebecca Powers Kirsten Mullin Peter Sutton Lisa Powers Thomas |
| author_facet | Ozbayrak Mehmet Todd Tim Harris Timothy Higgins Rebecca Powers Kirsten Mullin Peter Sutton Lisa Powers Thomas |
| author_sort | Ozbayrak Mehmet |
| collection | DOAJ |
| description | Pratylenchus species are among the most common plant parasitic nematodes in the Great Plains Region of North America. Our goal was to survey Pratylenchus species diversity across the Great Plains region using a mitochondrial COI DNA barcode. The objectives were to (i) determine species boundaries of the common Pratylenchus species within the region, (ii) assess the host associations of the barcoded Pratylenchus specimens, and (iii) determine Pratylenchus distribution patterns throughout the region. A total of 860 soil samples, primarily associated with eight major crops, were collected from Colorado, Kansas, Montana, Nebraska, North Dakota, and Wyoming. From this total, 246 soil samples provided the majority of 915 individual nematode specimens that were amplified by PCR and sequenced for a 727 to 739 bp region of COI. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic trees all recognized 19 distinct and well-supported haplotype groups. The most common and widespread haplotype group, representing 53% of all specimens was P. neglectus, detected from 178 fields in 100 counties and associated with fields growing wheat, corn, dry beans, barley, alfalfa, sugar beets, potatoes, and a vineyard. The second most prevalent haplotype group was P. scribneri, representing 30% of all specimens and recovered from 104 fields in 45 counties, and most frequently associated with corn. Mixed field populations were encountered in approximately 20% of infested fields, with P. neglectus and P. scribneri most often occurring together in corn-soybean cropping systems. Less frequently encountered from the region were P. hexincisus, P. thornei, P. penetrans, P. alleni, and P. zeae. Eight additional haplotype groups, potentially new Pratylenchus species, were discovered in the survey. |
| first_indexed | 2024-04-10T05:37:29Z |
| format | Article |
| id | doaj.art-1b46b372c6bd45528d88721861718c47 |
| institution | Directory Open Access Journal |
| issn | 2640-396X |
| language | English |
| last_indexed | 2024-04-10T05:37:29Z |
| publishDate | 2019-01-01 |
| publisher | Sciendo |
| record_format | Article |
| series | Journal of Nematology |
| spelling | doaj.art-1b46b372c6bd45528d88721861718c472023-03-06T16:52:21ZengSciendoJournal of Nematology2640-396X2019-01-0151112110.21307/jofnem-2019-081A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North AmericaOzbayrak Mehmet0Todd Tim1Harris Timothy2Higgins Rebecca3Powers Kirsten4Mullin Peter5Sutton Lisa6Powers Thomas7Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722 USADepartment of Plant Pathology, Kansas State University, Manhattan, KS, 66502 USADepartment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722 USADepartment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722 USADepartment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722 USADepartment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722 USADepartment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722 USADepartment of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, 68583-0722 USAPratylenchus species are among the most common plant parasitic nematodes in the Great Plains Region of North America. Our goal was to survey Pratylenchus species diversity across the Great Plains region using a mitochondrial COI DNA barcode. The objectives were to (i) determine species boundaries of the common Pratylenchus species within the region, (ii) assess the host associations of the barcoded Pratylenchus specimens, and (iii) determine Pratylenchus distribution patterns throughout the region. A total of 860 soil samples, primarily associated with eight major crops, were collected from Colorado, Kansas, Montana, Nebraska, North Dakota, and Wyoming. From this total, 246 soil samples provided the majority of 915 individual nematode specimens that were amplified by PCR and sequenced for a 727 to 739 bp region of COI. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic trees all recognized 19 distinct and well-supported haplotype groups. The most common and widespread haplotype group, representing 53% of all specimens was P. neglectus, detected from 178 fields in 100 counties and associated with fields growing wheat, corn, dry beans, barley, alfalfa, sugar beets, potatoes, and a vineyard. The second most prevalent haplotype group was P. scribneri, representing 30% of all specimens and recovered from 104 fields in 45 counties, and most frequently associated with corn. Mixed field populations were encountered in approximately 20% of infested fields, with P. neglectus and P. scribneri most often occurring together in corn-soybean cropping systems. Less frequently encountered from the region were P. hexincisus, P. thornei, P. penetrans, P. alleni, and P. zeae. Eight additional haplotype groups, potentially new Pratylenchus species, were discovered in the survey.https://doi.org/10.21307/jofnem-2019-081coidna barcodingspecies delimitationabgdgmyctcspratylenchusroot lesion nematodetaxonomy |
| spellingShingle | Ozbayrak Mehmet Todd Tim Harris Timothy Higgins Rebecca Powers Kirsten Mullin Peter Sutton Lisa Powers Thomas A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America Journal of Nematology coi dna barcoding species delimitation abgd gmyc tcs pratylenchus root lesion nematode taxonomy |
| title | A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America |
| title_full | A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America |
| title_fullStr | A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America |
| title_full_unstemmed | A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America |
| title_short | A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America |
| title_sort | coi dna barcoding survey of pratylenchus species in the great plains region of north america |
| topic | coi dna barcoding species delimitation abgd gmyc tcs pratylenchus root lesion nematode taxonomy |
| url | https://doi.org/10.21307/jofnem-2019-081 |
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