Genetic Diversity of the Pear Scab Fungus Venturia nashicola in Korea

Figures & data

Figure 1. Typical symptoms of pear scab. Irregular dark sooty spots (A) on leaf vein, (B) petiole, and (C) young fruit in early growing season. Irregular mild sooty spot (D) on magnified leaf surface, (E) along the midrib and major lateral veins on the leaf surface, and (F) on mature fruit in late growing season.

Table 1. Isolates of Venturia nashicola, V. pirina, and V. inaequalis used in this study.

Isolate	Host plant	Origin	Year	ITS	β-tubulin	TEF-1α	References
Venturia nashicola
NJGC1340	Japanese pear	Naju, Korea	2013	MH725922	MH725982	MH726042	–^b
NJBH1325	Japanese pear	Naju, Korea	2013	MH725923	MH725983	MH726043	–
14VNNJ11	Japanese pear	Naju, Korea	2014	MH725924	MH725984	MH726044	–
14VNNJ18	Japanese pear	Naju, Korea	2014	MH725925	MH725985	MH726045	–
14VNNJ19	Japanese pear	Naju, Korea	2014	MH725926	MH725986	MH726046	–
14VNNJ26	Japanese pear	Naju, Korea	2014	MH725927	MH725987	MH726047	–
14VNNJ27	Japanese pear	Naju, Korea	2014	MH725928	MH725988	MH726048	–
NJJS1	Japanese pear	Naju, Korea	2015	MH725929	MH725989	MH726049	–
NJGC1	Japanese pear	Naju, Korea	2015	MH725930	MH725990	MH726050	–
NJAP-1	Japanese pear	Naju, Korea	2015	MH725931	MH725991	MH726051	–
NJSJ-1	Japanese pear	Naju, Korea	2015	MH725932	MH725992	MH726052	–
NJHC-1	Japanese pear	Naju, Korea	2015	MH725933	MH725993	MH726053	–
NJCB-1	Japanese pear	Naju, Korea	2015	MH725934	MH725994	MH726054	–
NJBR-1	Japanese pear	Naju, Korea	2015	MH725935	MH725995	MH726055	–
14VNHD1-11	Japanese pear	Hadong, Korea	2014	MH725936	MH725996	MH726056	–
14VNHD2-3	Japanese pear	Hadong, Korea	2014	MH725937	MH725997	MH726057	–
14VNHD3-08	Japanese pear	Hadong, Korea	2014	MH725938	MH725998	MH726058	–
14VNHD3-31	Japanese pear	Hadong, Korea	2014	MH725939	MH725999	MH726059	–
15VNGNHD1-2	Japanese pear	Hadong, Korea	2015	MH725940	MH726000	MH726060	–
15VNGNHD2-7	Japanese pear	Hadong, Korea	2015	MH725941	MH726001	MH726061	–
15VNGNHD3-7	Japanese pear	Hadong, Korea	2015	MH725942	MH726002	MH726062	–
15VNGNHD3-11	Japanese pear	Hadong, Korea	2015	MH725943	MH726003	MH726063	–
HSPB1	Japanese pear	Hwasung, Korea	2015	MH725944	MH726004	MH726064	–
HSPB2	Japanese pear	Hwasung, Korea	2015	MH725945	MH726005	MH726065	–
HSHJ1	Japanese pear	Hwasung, Korea	2015	MH725946	MH726006	MH726066	–
HSJS1	Japanese pear	Hwasung, Korea	2015	MH725947	MH726007	MH726067	–
HSSK1	Japanese pear	Hwasung, Korea	2015	MH725948	MH726008	MH726068	–
15VNHS1-1	Japanese pear	Hwasung, Korea	2015	MH725949	MH726009	MH726069	–
15VNHS6-9	Japanese pear	Hwasung, Korea	2015	MH725950	MH726010	MH726070	–
14VNMU01	Japanese pear	Cheongju, Korea	2014	MH725951	MH726011	MH726071	–
14VNMU30	Japanese pear	Cheongju, Korea	2014	MH725952	MH726012	MH726072	–
15VNCHJNS-1	Japanese pear	Cheongju, Korea	2015	MH725953	MH726013	MH726073	–
15VNCHJNS-8	Japanese pear	Cheongju, Korea	2015	MH725954	MH726014	MH726074	–
14VNOC07	Japanese pear	Okcheon, Korea	2014	MH725955	MH726015	MH726075	–
14VNOC40	Japanese pear	Okcheon, Korea	2014	MH725956	MH726016	MH726076	–
15VNOCOC-1	Japanese pear	Okcheon, Korea	2014	MH725957	MH726017	MH726077	–
15VNOCAN-8	Japanese pear	Okcheon, Korea	2014	MH725958	MH726018	MH726078	–
14VNSJ11	Japanese pear	Sangju, Korea	2014	MH725959	MH726019	MH726079	–
14VNSJ37	Japanese pear	Sangju, Korea	2014	MH725960	MH726020	MH726080	–
15SAJ-A-6	Japanese pear	Sangju, Korea	2015	MH725961	MH726021	MH726081	–
15SAJ-P-4	Japanese pear	Sangju, Korea	2015	MH725962	MH726022	MH726082	–
15VNJNSC1-2	Japanese pear	Suncheon, Korea	2015	MH725963	MH726023	MH726083	–
15VNJNSC3-19	Japanese pear	Suncheon, Korea	2015	MH725964	MH726024	MH726084	–
14VNULS01	Japanese pear	Ulsan, Korea	2014	MH725965	MH726025	MH726085	–
14VNULS27	Japanese pear	Ulsan, Korea	2014	MH725966	MH726026	MH726086	–
15VNPTAJH-2	Japanese pear	Pyeongtaek, Korea	2015	MH725967	MH726027	MH726087	–
15VNPTAJH-5	Japanese pear	Pyeongtaek, Korea	2015	MH725968	MH726028	MH726088	–
14VNNS05	Japanese pear	Nonsan, Korea	2014	MH725969	MH726029	MH726089	–
14VNNS44	Japanese pear	Nonsan, Korea	2014	MH725970	MH726030	MH726090	–
15VNESSS-4	Japanese pear	Eumseong, Korea	2015	MH725971	MH726031	MH726091	–
15VNESSS-9	Japanese pear	Eumseong, Korea	2015	MH725972	MH726032	MH726092	–
15VNYDYG-1	Japanese pear	Yeongdong, Korea	2015	MH725973	MH726033	MH726093	–
15VNYDYG-5	Japanese pear	Yeongdong, Korea	2015	MH725974	MH726034	MH726094	–
14VNWJ1-02	Japanese pear	Wonju, Korea	2014	MH725975	MH726035	MH726095	–
14VNWJ2-41	Japanese pear	Wonju, Korea	2014	MH725976	MH726036	MH726096	–
KCTC6484	Japanese pear	Korea	-^a	MH725917	MH725977	MH726037	[4]
MAFF615002	Japanese pear	Ibaraki, Japan	1979	MH725918	MH725978	MH726038	[4]
MAFF615003	Japanese pear	Shizuoka, Japan	1980	MH725919	MH725979	MH726039	[4]
MAFF615023	Japanese pear	Kouchi, Japan	1981	MH725920	MH725980	MH726040	[4]
MAFF615029	Japanese pear	Fukuoka, Japan	1993	MH725921	MH725981	MH726041	[4]
JS-115	Japanese pear	Ohita, Japan	1980	HQ434387	HQ434431	HQ434343	[12,33]
Yasato2-1-1	Japanese pear	Ibaraki, Japan	1992	HQ434394	HQ434438	HQ434350	[12,33]
Mamenashi12A No.1-1	Wild pear	Tottori, Japan	1991	HQ434386	HQ434430	HQ434342	[12,33]
Mamenashi12A No.1-3	Wild pear	Tottori, Japan	1991	HQ434388	HQ434432	HQ434344	[12,33]
Mamenashi12A No.1-4	Wild pear	Tottori, Japan	1991	HQ434389	HQ434433	HQ434345	[12,33]
Mamenashi12B No.1-1	Wild pear	Tottori, Japan	1991	HQ434390	HQ434436	HQ434348	[12,33]
Mamenashi12B No.1-2	Wild pear	Tottori, Japan	1991	HQ434392	HQ434434	HQ434346	[12,33]
Mamenashi12B No.53-1	Wild pear	Tottori, Japan	1992	HQ434391	HQ434435	HQ434347	[12,33]
OYO-1	Wild pear	Tochigi, Japan	1999	HQ434393	HQ434437	HQ434349	[12,34]
V. pirina
38995	European pear	Israel	–	HQ434425	HQ434469	HQ434381	[12,35]
38996	European pear	Israel	–	HQ434424	HQ434468	HQ434380	[12,35]
V. inaequalis
HIR-2	Apple	Aomori, Japan	1995	HQ434423	HQ434467	HQ434379	[12]
Ibaraki 1	Apple	Ibaraki, Japan	1998	HQ434422	HQ434378	HQ434378	[12]

^a Collection year unknown.

^b In this study.

Table 2. Nucleotide sequences of 10-mer oligonucleotide primers used for RAPD analysis of Venturia nashicola isolates.

Primers^a	Nucleotide sequence (5′→3′)
OPA-15	TTCCGAACCC
OPB-17	AGGGAACGAG
OPC-04	CCGCATCTAC
OPD-16	AGGGCGTAAG
OPF-01	ACGGATCCTG
OPI-14	TGACGGCGGT
OPJ-10	AAGCCCGAGG
OPJ-12	GTCCCGTGGT
OPJ-20	AAGCGGCCTC
OPO-12	CAGTGCTGTG

^a Primer sequences were provided by Operon Technologies.

Figure 2. Mycological characteristics of Venturia nashicola. (A) 60 d-old colony on PDA at 20 °C in the dark; (B) Conidia; (C) Conidiophore; (D) Pseudothecia, (E) Asci; (F) Ascospores.

Table 3. Comparison of mycological characteristics of the isolates collected in this study and Venturia nashicola isolates described previously.

Characteristics		Isolate from this study	Venturia nashicola^a
Conidia	Shape	Dark brown, long oval or fusiform	Dark brown, long oval or fusiform
	Size (㎛)	8.2–18.8 (12.9)×5.1–7.8 (6.5)	7.5–22.5(14.4)×5.0–7.5(6.0)
Conidiophores	Shape	Brown, clustered, erect	Brown, clustered, erect, simple
	Height (㎛)	10–15	10–20
Pseudothecia	Shape	Wall dark colored, globoid	Wall dark colored, brownish cells, depressed , conic, globoid
	Size (㎛)	55–122 × 59–140	50.0–150 × 53–138
Asci	Shape	Hyaline, club-shaped	Hyaline, clavate or long ovate
	Size (㎛)	38–63 × 5–10	35–60 × 5–10
Ascospore	Shape	Hyaline or light brown, two-celled, shoesole-shaped	Hyaline or light brown, two-celled, shoesole-shaped
	Size (㎛)	12.0–15.0 × 3.0–4.5	10–15 × 3.8–6.3

^a Tanaka and Yamamoto [8].

Figure 3. Comparison of representative sequences of subgroups 1 to 3. (A) ITS2 region. (B) Partial protein sequences of β-tubulin. (C) Translation elongation factor-1α.

Figure 4. Maximum likelihood tree generated by a combined alignment of ITS region including 5.8S rRNA, partial β-tubulin gene and partial translation elongation factor 1-α gene sequences from Venturia nashicola. All V. nashicola sequences were newly generated in this study, except those marked in red, which were retrieved from GenBank. Standard V. nashicola isolates from Korea (KCTC, Korean culture collection) and Japan (MAFF) are indicated in blue. Isolates of V. pirina and V. inaequalis were used as outgroups. The numbers at nodes represent the percentage of their occurrence in 1000 bootstrap replicates.

Figure 5. Collection map of Venturia nashicola isolates from Japanese pear in Korea over 2013–2015 and distribution of subgroups 1 to 3. n=number of isolates.

Figure 6. UPGMA dendrogram of 55 Venturia nashicola isolates collected in this study and five standard V. nashicola isolates based on RAPD polymorphism. Data from 10 different 10-mer primers were combined and used to construct a dendrogram. Origin and year of collection was indicated on the right for individual isolates. Standard V. nashicola isolates of Korea and Japan are indicated in red.

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