High Mitochondrial Genome Diversity and Intricate Population Structure of Bursaphelenchus xylophilus in Kyushu, Japan

Population	Code	N^a	No. of trees^b	Location	Prefecture
Matsuura	Ma	23	16	33.3°N, 129.7°E	Nagasaki
Karatsu	Ka	27	10	33.5°N, 129.9°E	Saga
Itoshima	It	25	25	33.6°N, 130.2°E	Fukuoka
Yukuhashi	Yu	14	14	33.7°N, 131.0°E	Fukuoka
Chikujo	Ch	12	12	33.7°N, 131.1°E	Fukuoka
Amakusa	Am	28	10	32.6°N, 130.4°E	Kumamoto
Shintomi	Sh	24	20	32.1°N, 131.5°E	Miyazaki
Miyazaki	Mi	26	20	31.9°N, 131.4°E	Miyazaki
North Nichinan	Ni-N	28	4	31.6°N, 131.4°E	Miyazaki
South Nichinan	Ni-S	27	20	31.6°N, 131.4°E	Miyazaki
Sendai	Se	25	20	31.8°N, 130.2°E	Kagoshima
Ibusuki	Ib	26	20	31.2°N, 130.6°E	Kagoshima

[i] ^aNumber of individuals analyzed in each population. Total number of individuals analyzed = 285; ^bThe number of trees in each population that became the source of the sequenced nematodes.

Location of the studied populations of *Bursaphelenchus xylophilus* (black dots) in Kyushu and the group of haplotype distribution of each population. The names of populations are written in code as indicated in Table 1. The classification of haplotypes is presented as in Figure 2.

Phylogentic tree for 33 mitochondrial haplotypes of *Bursaphelenchus xylophilus* containing 30 from Kyushu and 3 from previous studies was inferred by using the Maximum Likelihood (ML) method based on the Kimura 2-parameter model. Numbers under the branches represent support values from bootstrap replications of 1,000. Evolutionary distances greater than 0.0001 are shown above branches. Wide bars indicate the major clades clustering.

Table 2

Sequence polymorphism and substitutions identified in the mitochondrial genome of Bursaphelenchus xylophilus.

						Substitution
			Sequence polymorphism			Nucleotide				Amino acid residue
Gene/region		Length^a (bp)	No. Indels	Indels/bp^b	No. SNPs	SNPs/bp^b	No. Ts^c	No. Tv^c	Ts^c/Tv^c ratio	No. Syns^d	No. Non-syns^d	Syn^d/Non-syn^d ratio
Protein-coding gene	cox1	1,156			39	1/30	35	4	8.8	34	5	6.8
	cox2	690			7	1/99	7	0	–	6	1	6.0
	nad3	342			6	1/57	5	1	5.0	4	2	2.0
	nad5	1,569			40	1/39	30	10	3.0	30	9	3.3
	nad6	435			13	1/33	11	2	5.5	11	2	5.5
	nad4L	234			5	1/47	4	1	4.0	5	0	–
	nad1	873			22	1/40	17	5	3.4	21	1	21.0
	atp6	417			7	1/60	5	2	2.5	7	0	–
	subtotal	5,716			139	1/41	114	25	4.6	118	20	5.9
tRNA	trnC	54			1	1/54	0	1	–
	trnM	54			1	1/54	0	1	–
	trnD	55
	trnG	54
	trnH	55
	trnA	55
	trnP	57
	trnV	57
	trnW	55
	trnE	55
	trnS	55			1	1/55	0	1	–
	trnY	63	1	1/63
	subtotal	669	1	1/669	3	1/223	0	3	–
rRNA	rrnL	937			7	1/134	4	3	1.3
	rrnS	697			6	1/116	3	3	1.0
	subtotal	1,634			13	1/126	7	6	1.2
Non-coding region	cox1-trnC	15	1	1/15	2	1/7.5	0	2	–
	trnC-trnM	7
	trnM-trnD	20
	trnD-trnG	3			1	1/3	1	0	–
	nad3-nad5	1
	rrnS-trnS	4
	subtotal	50	1	1/50	3	1/17	1	2	0.5
Total		8,060^e	2	1/4030	158	1/51	122	36	3.4	118	20	5.9

[i] ^aThe nucleotide sequence length for that gene or region; ^bThe average occurrence of single nucleotide polymorphisms (SNPs) or insertions/deletions (Indels) in that specific part of the sequenced mitochondrial genome; ^cTs, transitions; Tv, transversions; ^dSyn, synonymous substitution; Non-syn, non-synonymous substitution; ^eThe total length contains 9 bp overlapping genes or regions; Blank cells indicate no value; – means the value cannot be calculated.

Table 3

Haplotype distribution within in each population.

	Haplotype
Population	01	02	03	04	05	06	07	08	09	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30	Nh^a	Hd^b
Matsuura	16	3	1	3																											4	0.50
Karatsu			8	3	1	8	2	1	1	3																					8	0.82
Itoshima										1	1		20	3																	4	0.36
Yukuhashi										6			7	1																	3	0.60
Chikujo										3		1	8																		3	0.53
Amakusa													7	4	2	1	1	1	1	9	2										9	0.83
Shintomi	8																			1	14	1									4	0.57
Miyazaki	5																				21										2	0.32
Nichinan-N	4																				21	3									3	0.42
Nichinan-S	10																				15	1	1								4	0.57
Sendai																					21			2	1	1					4	0.30
Ibusuki		9	1	1																	4						7	2	1	1	8	0.80
Total	43	12	10	7	1	8	2	1	1	13	1	1	42	8	2	1	1	1	1	10	98	5	1	2	1	1	7	2	1	1		0.83
Frequency (%)	15.1	4.2	3.5	2.5	0.4	2.8	0.7	0.4	0.4	4.6	0.4	0.4	14.7	2.8	0.7	0.4	0.4	0.4	0.4	3.5	34.4	1.8	0.4	0.7	0.4	0.4	2.5	0.7	0.4	0.4

[i] Numbers indicate the number of individuals present in each haplotype. –indicate that no individual presented the haplotype. ^aNumber of haplotypes detected in the population; ^bHaplotype diversity, Hd = (1−∑xi ²) n/(n−1), where xi is the frequency of the ith haplotype and n is the sample size (Nei and Tajima, 1981).

Table 4.

Pairwise genetic distances between the 12 populations examined based on haplotype frequency.

Population	Ma	Ka	It	Yu	Ch	Am	Sh	Mi	Ni-N	Ni-S	Se
Matsuura (Ma)
Karatsu (Ka)	0.570
Itoshima (It)	0.693	0.665
Yukuhashi (Yu)	0.703	0.738	0.144
Chikujo (Ch)	0.703	0.714	0.367	0.288
Amakusa (Am)	0.773	0.671	0.549	0.598	0.706
Shintomi (Sh)	0.560	0.771	0.693	0.703	0.703	0.465
Miyazaki (Mi)	0.570	0.916	0.752	0.714	0.714	0.752	0.347
North Nichinan (Ni-N)	0.549	0.809	0.703	0.693	0.693	0.673	0.144	0.203
South Nichinan (Ni-S)	0.560	0.752	0.693	0.703	0.703	0.652	0.223	0.347	0.144
Sendai (Se)	0.693	0.752	0.693	0.703	0.703	0.662	0.560	0.570	0.703	0.560
Ibusuki (Ib)	0.464	0.560	0.752	0.809	0.809	0.678	0.665	0.811	0.714	0.665	0.665

Neighbor-joining (NJ) tree diagram showing the genetic relationship that was determined using genetic distances of 12 populations. Numbers next to corresponding nodes indicate the branch lengths in the same units of the genetic distances that are computed based on the haplotype frequency for each population.

Table S1

Nucleotide variations at 160 polymorphic sites in the 30 haplotypes (Ht) detected in Kyushu.

			Haplotype (Ht)
Gene / Region	Nucleotide position^a	Reference position^b	01	02	03	04	05	06	07	08	09	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26	27	28	29	30
cox1	40	447	A	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	43	450	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	61	468	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	A	.	A	.	.
	175	582	C	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	202	609	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	229	636	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	231	638	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	T	.	T	.	.	.	.	.	.	.	.	.	.
	253	660	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	274	681	C	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	289	696	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	G	.	G	.	.
	292	699	T	C	C	.	.	C	.	.	.	C	C	C	C	C	C	C	C	C	C	C	C	.	C	.	C	C	.	C	.	.
	340	747	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	367	774	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	394	801	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	A	.	.	.	A	.	A	.	A	A	.	A	.	.
	472	879	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	490	897	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	511	918	T	C	C	.	.	.	.	.	.	C	.	.	.	.	.	.	C	.	.	.	C	.	C	.	C	.	.	C	.	.
	518	925	G	.	.	.	A	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	544	951	G	A	A	.	.	T	.	.	.	A	.	.	.	.	.	.	A	.	.	.	A	.	A	.	A	.	.	A	.	.
	556	963	T	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	628	1035	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	634	1041	G	.	.	.	.	A	.	.	.	.	A	A	A	A	A	A	A	A	A	A	.	.	.	.	.	.	A	.	.	A
	682	1089	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	703	1110	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	724	1131	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	796	1203	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	823	1230	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	829	1236	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	868	1275	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	.	.	T	.	.
	877	1284	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	919	1326	C	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	.	.	T	.	.
	934	1341	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	940	1347	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	961	1368	G	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	1024	1431	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	1072	1479	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	1099	1506	A	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	1116	1523	A	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.
	1122	1529	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	.	A
cox1-trnC	1160		A	–	–	.	.	.	.	.	.	.	.	.	.	.	.	-	.	.	.	.	–	.	–	.	–	.	.	–	.	.
	1161		T	–	–	.	.	.	.	.	.	.	.	.	.	.	.	-	.	.	.	.	–	.	–	.	–	.	.	–	.	.
	1162		A	–	–	.	.	.	.	.	.	.	.	.	.	.	.	-	.	.	.	.	–	.	–	.	–	.	.	–	.	.
	1163		A	–	–	.	.	.	.	.	.	.	.	.	.	.	.	-	.	.	.	.	–	.	–	.	–	.	.	–	.	.
	1166	1569	T	.	.	.	.	A	.	.	.	.	A	A	A	A	A	A	.	A	A	A	.	.	.	.	.	.	.	.	.	.
	1168	1571	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	.	.	.
trnC	1216	1619	A	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	T	.	.	.	T	.	T	.	T	.	.	T	.	.
trnM	1233	1634	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.
trnD-trnG	1364	1765	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
cox2	1586	1987	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	1688	2089	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	G
	1754	2155	C	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	1825	2226	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	2015	2416	C	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	2021	2422	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	A	.	A	.	.
	2036	2437	C	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
rrnL	2179	2579	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	2182	2582	G	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	2324	2724	T	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	2328	2728	G	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	2411	2812	T	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	A	.	A	A	.
	2450	2851	C	T	T	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	T	.
	2842	3242	T	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
nad3	3152	3552	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	3199	3599	A	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	3221	3621	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	G	.	.	.	G	.	G	.	G	.	.	G	.	.
	3231	3631	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	3242	3642	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	A	.	.	.	A	.	A	.	A	A	.	A	.	.
	3419	3819	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
nad5	3492	3892	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	3507	3907	G	T	T	.	.	.	T	.	.	.	.	.	.	T	T	.	.	T	.	.	T	T	T	.	T	T	.	T	.	T
	3515	3915	A	.	.	.	.	T	.	.	.	.	T	T	T	T	.	T	.	T	.	T	.	.	.	.	.	.	.	.	.	.
	3516	3916	T	.	.	.	.	A	.	.	.	.	.	A	A	A	.	A	.	A	A	A	.	.	.	.	.	.	.	.	.	.
	3549	3949	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	.	.	.	C	.	.
	3643	4043	C	T	T	.	.	T	.	.	.	T	T	T	T	T	T	T	T	T	T	T	T	.	T	.	T	T	T	T	T	T
	3651	4051	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	3706	4106	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	3810	4210	A	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	3864	4264	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	G	.	.	.	G	.	G	.	G	G	.	G	.	.
	3921	4321	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	3972	4372	G	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	A	.	A	.	.
	3975	4375	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	3993	4393	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	4002	4402	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	4041	4441	A	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4140	4540	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	4164	4564	A	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	4197	4597	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4235	4635	G	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4323	4723	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4329	4729	A	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	4374	4774	C	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4416	4816	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4449	4849	C	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	T	.	.	.	T	.	T	.	T	T	.	T	.	.
	4455	4855	G	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	A	.	A	.	.
	4514	4914	A	T	T	.	.	T	.	.	.	T	T	T	T	T	T	T	T	T	T	T	T	.	T	.	T	T	T	T	.	T
	4524	4924	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	A	.	.	.	A	.	A	.	A	A	.	A	.	.
	4587	4987	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	4648	5048	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	4653	5053	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	4716	5116	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4760	5160	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	.	C
	4771	5171	A	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	4776	5176	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	.	.	.
	4785	5185	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	4836	5236	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	.	.	T	.	.
	4937	5337	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	.	T
	4944	5344	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	4962	5362	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
nad6	5238	5638	G	A	A	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	5268	5668	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	5271	5671	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	5293	5693	T	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	5331	5731	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	5373	5773	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	5388	5788	G	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	5389	5789	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	5442	5842	A	.	.	.	.	.	.	.	.	.	G	G	G	G	G	G	.	.	G	.	.	.	.	.	.	.	.	.	.	.
	5451	5851	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	5454	5854	G	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	.	.	.	A	.	.
	5545	5945	G	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	5559	5959	T	.	.	C	C	.	C	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.
nad4L	5651	6051	G	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	.	.	A	.	.
	5738	6138	G	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	5756	6156	C	T	T	.	.	T	.	.	.	T	T	T	T	T	T	T	T	T	T	T	T	.	T	.	T	.	.	T	.	.
	5768	6168	G	.	.	.	.	A	.	.	.	.	A	A	A	A	A	A	A	A	A	A	.	.	.	.	.	.	.	.	.	.
	5774	6174	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
rrnS	6028	6428	G	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	.	.	T	.	.
	6130	6529	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	6188	6588	G	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	.	.	T	.	.
	6343	6743	T	.	.	.	.	A	.	.	.	.	A	A	A	A	A	A	A	A	A	A	.	.	.	.	.	.	.	.	.	.
	6389	6789	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	G
	6557	6956	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
trnS	6665	7064	T	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
trnY	6748	7140	G	.	.	.	.	.	.	.	–	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
nad1	6779	7171	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	6802	7194	A	G	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	6814	7206	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	6847	7239	G	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	6889	7281	G	A	A	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	A	.	A	.	.
	6934	7326	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	6940	7332	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	.	A
	6943	7335	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7009	7401	T	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7108	7500	C	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	7150	7542	A	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	7159	7551	G	A	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A	.	A	.	A	A	.	A	.	.
	7189	7581	T	.	.	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7201	7593	C	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7306	7698	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	7309	7701	A	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
	7359	7751	C	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7399	7791	G	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7435	7827	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	C	.	C	.	.
	7534	7926	A	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	G	.	.	.	G	.	G	.	G	.	.	G	.	.
	7567	7959	C	T	T	.	.	.	.	.	.	T	.	.	.	.	.	.	T	.	.	.	T	.	T	.	T	T	.	T	.	.
	7579	7971	C	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	T	T	.	T	.	.
atp6	7760	8152	C	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7772	8164	T	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	7844	8236	T	C	C	.	.	.	.	.	.	C	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	7850	8242	T	C	C	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	C	.	C	.	C	.	.	C	.	.
	7865	8257	T	G	G	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	G	.	G	.	G	.	.	G	.	.
	7904	8296	A	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
	7985	8377	C	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

[i] Notes: a The position of the SNPs and indels in the total sequence nucleotide in this study; b The position of the SNPs and indels in the reference sequence (GQ332424); Number indicates the position of the SNPs and indels in the total sequence nucleotide in this study; . indicates the same nucleotide with ht-01 at the polymorphic site; – indicates deletion. Blank indicates the position which was not exciting in the reference sequence.

References

Authors

Metrics

Articles in this issue

DOI: https://doi.org/10.21307/jofnem-2018-034 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X

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Language: English

Page range: 281 - 302

Published online: Oct 17, 2018

Published in print: Jan 1, 2018

Published by: Society of Nematologists, Inc.

In partnership with: Paradigm Publishing Services

Publication frequency: 1 issue per year

Keywords:

Bursaphelenchus xylophilus,

Haplotype diversity,

Genomics,

Mitochondrial polymorphism,

Pinewood nematode,

Population structure,

Sequence polymorphism.

Related subjects:

Life sciences,

Life sciences, other

© 2018 Hanyong Zhang, Erika Okii, Eiji Gotoh, Susumu Shiraishi, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 50 (2018): Issue 3 (January 2018)

High Mitochondrial Genome Diversity and Intricate Population Structure of Bursaphelenchus xylophilus in Kyushu, Japan

Figures & Tables

Table 1

Figure 1

Figure 2

Table 2

Table 3

Table 4.

Figure 3

Table S1

Paradigm

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