Prevalence of the root lesion nematode virus (RLNV1) in populations of Pratylenchus penetrans from North America

						Detection and sequencing
Genus	Species	Population	No. of individuals	Host	Origin of population	Helicase	RdRP
Pratylenchus	penetrans	NL 10p RH	Bulk	Corn	Beltsville, Maryland	Yes*	Yes*
Pratylenchus	penetrans	R3605	Bulk	Potato	NA, Michigan	−	−
Pratylenchus	penetrans	R3606	Bulk	Potato	NA, Michigan	Yes	Yes
Pratylenchus	penetrans	Greenhouse	200	Mint	Various locations from OR and WA	Yes	Yes
Pratylenchus	penetrans	Cherry	120	Cherry	Hood River, OR	−	−
Pratylenchus	penetrans	CAR	200	Apple	Kenniwick, WA	Yes	Yes
Pratylenchus	penetrans	Pole Road	200	Raspberry	Lynden, WA	−	−
Pratylenchus	penetrans	R-BDM	Bulk	Raspberry	Lynden, WA	−	−
Pratylenchus	penetrans	82−13	Bulk	Soybean	Calumet Co., WI	−	−
Pratylenchus	penetrans	511−14	Bulk	Soybean	Chippewa Co., WI	−	−
Pratylenchus	penetrans	546−16	Bulk	Soybean	Chippewa Co., WI	Yes	Yes
Pratylenchus	penetrans	736−13	Bulk	Soybean	Grant Co., WI	Yes	Yes
Pratylenchus	penetrans	92−16	Bulk	Soybean	Iowa Co., WI	−	−
Pratylenchus	penetrans	99−16	Bulk	Soybean	Lafayette Co., WI	−	−
Pratylenchus	penetrans	128−16	Bulk	Soybean	Marathon Co., WI	−	−
Pratylenchus	penetrans	551−14	Bulk	Soybean	Marquette Co., WI	−	−
Pratylenchus	penetrans	Malek	Bulk	Potato	Portage CO., WI	Yes	Yes
Pratylenchus	penetrans	P*	Bulk	Potato	Portage CO., WI	Yes	Yes
Pratylenchus	penetrans	PRF	Bulk	Potato	Portage CO., WI	Yes	Yes
Pratylenchus	penetrans	PP6-1	Bulk	Potato	Portage CO., WI	−	−
Pratylenchus	penetrans	469A-13	Bulk	Soybean	Sheboygan Co., WI	Yes	Yes
Pratylenchus	penetrans	Lauer	Bulk	Potato	Waushara Co., WI	Yes	Yes
Pratylenchus	penetrans	422−14	Bulk	Soybean	Wood Co., WI	−	−
Pratylenchus	penetrans	PA	Bulk	Corn	NA	Yes	Yes
Pratylenchus	penetrans	R3784	Bulk	Potato	New Brunswick, CA**	No	Yes
Pratylenchus	penetrans	R3790	Bulk	Potato	New Brunswick, CA**	Yes	Yes
Pratylenchus	penetrans	R3794	Bulk	Potato	New Brunswick, CA**	Yes	Yes
Pratylenchus	penetrans	R3813	Bulk	Potato	New Brunswick, CA**	−	−
Pratylenchus	penetrans	R3816	Bulk	Potato	New Brunswick, CA**	−	−
Pratylenchus	penetrans	R3739	Bulk	Potato	Prince Edward Island, CA**	−	−
Pratylenchus	penetrans	R3771	Bulk	Potato	Prince Edward Island, CA**	−	−
Pratylenchus	penetrans	QCLA	Bulk	Potato	L'Acadie, Quebec, CA**	−	−

1 Notes: NA, not available specific location. *These sequences were original obtained and published in Vieira and Nemchinov (2019); **Canada; the symbol “−” denotes nematode populations with no detection regarding the presence of RLNV1.

Reverse transcription-polymerase chain reaction (RT-PCR) detection of the root lesion nematode virus (RLNV1) from cDNA libraries generated from 21 out of the 31 populations of *Pratylenchus penetrans* collected in North America. PCR amplification was performed using specific primers for the RLNV1 helicase (A) and RdRP (B) regions. The isolate NL 10p RH was used as positive control for the detection of the RNLV1. C: The nematode 18 S rRNA gene was used as a positive control to validate the presence of *P. penetrans* transcripts within each generated cDNA library.

Table S1.

Nucleotide (A) and protein (B) pairwise comparisons of the helicase sequence data of different RLNV1 isolates from Pratylenchus penetrans.

A
	RLNV1	3606	Green house	Car	546-16	736-13	Malele	P*	PRF	469A	Lauer	PA	R3794	R3790
RLNV1		98.65	98.77	99.26	98.53	98.89	96.93	98.89	99.63	98.89	98.65	99.75	98.65	99.63
3606	11		99.39	99.14	99.14	99.51	96.56	99.51	99.02	99.51	99.75	98.89	99.75	99.02
Greenhouse	10	5		99.26	99.26	99.63	96.93	99.63	99.14	99.63	99.39	99.02	99.39	99.14
Car	6	7	6		99.26	99.63	97.17	99.63	99.63	99.63	99.14	99.51	99.14	99.63
546-16	12	7	6	6		99.63	96.44	99.63	98.89	99.63	99.14	98.77	99.14	98.89
736-13	9	4	3	3	3		96.81	100	99.26	100	99.51	99.14	99.51	99.26
Malele	25	28	25	23	29	26		96.81	97.3	96.81	96.56	97.17	96.56	97.3
P*	9	4	3	3	3	0	26		99.26	100	99.51	99.14	99.51	99.26
PRF	3	8	7	3	9	6	22	6		99.26	99.02	99.88	99.02	100
469A	9	4	3	3	3	0	26	0	6		99.51	99.14	99.51	99.26
Lauer	11	2	5	7	7	4	28	4	8	4		98.89	99.75	99.02
PA	2	9	8	4	10	7	23	7	1	7	9		98.89	99.88
R3794	11	2	5	7	7	4	28	4	8	4	2	9		99.02
R3790	3	8	7	3	9	6	22	6	0	6	8	1	8
B
	RLNV1	3606	Green house	Car	546-16	736-13	Malele	P*	PRF	469A	Lauer	PA	R3794	R3790
RLNV1		99.63	100	100	99.26	100	100	100	100	100	100	100	100	100
3606	1		99.63	99.63	98.89	99.63	99.63	99.63	99.63	99.63	99.63	99.63	99.63	99.63
Greenhouse	0	1		100	99.26	100	100	100	100	100	100	100	100	100
Car	0	1	0		99.26	100	100	100	100	100	100	100	100	100
546-16	2	3	2	2		99.26	99.26	99.26	99.26	99.26	99.26	99.26	99.26	99.26
736-13	0	1	0	0	2		100	100	100	100	100	100	100	100
Malele	0	1	0	0	2	0		100	100	100	100	100	100	100
P*	0	1	0	0	2	0	0		100	100	100	100	100	100
PRF	0	1	0	0	2	0	0	0		100	100	100	100	100
469A	0	1	0	0	2	0	0	0	0		100	100	100	100
Lauer	0	1	0	0	2	0	0	0	0	0		100	100	100
PA	0	1	0	0	2	0	0	0	0	0	0		100	100
R3794	0	1	0	0	2	0	0	0	0	0	0	0		100
R3790	0	1	0	0	2	0	0	0	0	0	0	0	0

1 Note: Lower and upper panels represent the number of different nucleotides (counts) and nucleotide sequence similarity (%) within isolates, respectively.

Table S2.

Nucleotide (A) and protein (B) pairwise comparisons of the RdRP sequence data of different RLNV1 isolates from Pratylenchus penetrans.

A
	RLNV1	3606	Green house	Car	546-16	736-13	Malele	P*	PRF	469A	Lauer	PA	R3784	R3790	R3794
RLNV1		99.16	99.16	98.74	98.95	98.85	97.9	98.85	99.69	98.95	99.27	99.79	98.43	98.85	98.64
3606	8		99.58	98.95	99.16	99.06	97.48	99.06	99.48	99.16	99.69	99.16	99.06	98.64	99.27
Greenhouse	8	4		99.37	99.58	99.48	97.48	99.48	99.48	99.58	99.48	99.16	98.85	98.64	99.06
Car	12	10	6		99.79	99.69	97.06	99.69	99.06	99.79	98.85	98.74	98.22	98.22	98.43
546-16	10	8	4	2		99.9	97.27	99.9	99.27	100	99.06	98.95	98.43	98.43	98.64
736-13	11	9	5	3	1		97.17	99.79	99.16	99.9	98.95	98.85	98.32	98.32	98.53
Malele	20	24	24	28	26	27		97.17	98.01	97.27	97.38	97.69	96.75	97.17	96.96
P*	11	9	5	3	1	2	27		99.16	99.9	98.95	98.85	98.32	98.32	98.53
PRF	3	5	5	9	7	8	19	8		99.27	99.37	99.69	98.74	99.16	98.95
469A	10	8	4	2	0	1	26	1	7		99.06	98.95	98.43	98.43	98.64
Lauer	7	3	5	11	9	10	25	10	6	9		99.27	98.95	98.53	99.16
PA	2	8	8	12	10	11	22	11	3	10	7		98.43	98.85	98.64
R3784	15	9	11	17	15	16	31	16	12	15	10	15		99.37	99.79
R3790	11	13	13	17	15	16	27	16	8	15	14	11	6		99.37
R3794	13	7	9	15	13	14	29	14	10	13	8	13	2	6
B
	RLNV1	3606	Green house	Car	546-16	736-13	Malele	P*	PRF	469A	Lauer	PA	R3784	R3790	R3794
RLNV1		99.37	99.68	99.68	99.68	99.68	99.37	99.37	99.68	99.68	100	100	98.42	98.11	98.42
3606	2		99.68	99.68	99.68	99.68	99.37	99.37	99.68	99.68	99.37	99.37	98.42	98.11	98.42
Greenhouse	1	1		100	100	100	99.68	99.68	100	100	99.68	99.68	98.74	98.42	98.74
Car	1	1	0		100	100	99.68	99.68	100	100	99.68	99.68	98.74	98.42	98.74
546-16	1	1	0	0		100	99.68	99.68	100	100	99.68	99.68	98.74	98.42	98.74
736-13	1	1	0	0	0		99.68	99.68	100	100	99.68	99.68	98.74	98.42	98.74
Malele	2	2	1	1	1	1		99.37	99.68	99.68	99.37	99.37	98.42	98.11	98.42
P*	2	2	1	1	1	1	2		99.68	99.68	99.37	99.37	98.42	98.11	98.42
PRF	1	1	0	0	0	0	1	1		100	99.68	99.68	98.74	98.42	98.74
469A	1	1	0	0	0	0	1	1	0		99.68	99.68	98.74	98.42	98.74
Lauer	0	2	1	1	1	1	2	2	1	1		100	98.42	98.11	98.42
PA	0	2	1	1	1	1	2	2	1	1	0		98.42	98.11	98.42
R3784	5	5	4	4	4	4	5	5	4	4	5	5		99.68	100
R3790	6	6	5	5	5	5	6	6	5	5	6	6	1		99.68
R3794	5	5	4	4	4	4	5	5	4	4	5	5	0	1

1 Note: Lower and upper panels represent the number of different nucleotides (counts) and nucleotide sequence similarity (%) within isolates, respectively.

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DOI: https://doi.org/10.21307/jofnem-2020-045 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X

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Language: English

Page range: 1 - 10

Submitted on: Jan 29, 2020

Published on: May 18, 2020

Published by: Society of Nematologists, Inc.

In partnership with: Paradigm Publishing Services

Publication frequency: 1 issue per year

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© 2020 Paulo Vieira, Amy Peetz, Benjamin Mimee, Kanan Saikai, Dimitre Mollov, Ann MacGuidwin, Inga Zasada, Lev G. Nemchinov, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 52 (2020): Issue 1 (January 2020)

Prevalence of the root lesion nematode virus (RLNV1) in populations of Pratylenchus penetrans from North America

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Table 1.

Figure 1:

Table S1.

Table S2.

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