S1 Table. Collection sites and the results of genetic

S1 Table. Collection sites and the results of genetic diagnosis of Narcissus plants in this study. Plant Location (town, city, prefecture) Collection date (Isolate)a Hokkaido district NY-HO1 Soen, Chuo-ku, Sapporo, Hokkaido 20 June 2012 NY-HO2 Soen, Chuo-ku, Sapporo, Hokkaido 20 June 2012 NY-HO3 Tonden, Kita-ku, Sapporo, Hokkaido 21 June 2012 NY-HO4 Tonden, Kita-ku, Sapporo, Hokkaido 21 June 2012 NY-HO5 Tonden, Kita-ku, Sapporo, Hokkaido 24 June 2012 NY-HO42 Nango, Shiroishi-ku, Sapporo, Hokkaido 1 June 2013 NY-HO43 Nango, Shiroishi-ku, Sapporo, Hokkaido 1 June 2013 NY-HO44 Kita 48 jo, Kita-ku, Sapporo, Hokkaido 2 June 2013 NY-HO45 Fujino, Minami-ku, Sapporo, Hokkaido 2 June 2013 NY-HO46 Fujino, Minami-ku, Sapporo, Hokkaido 2 June 2013 NY-HO47 Kitanosawa, Minami-ku, Sapporo, Hokkaido 2 June 2013 NY-HO48 Maeda, Teine-ku, Sapporo, Hokkaido 2 June 2013 NY-HO49 Tonden, Kita-ku, Sapporo, Hokkaido 3 June 2013 NY-HO50 Tonden, Kita-ku, Sapporo, Hokkaido 3 June 2013 NY-HO51 Tonden, Kita-ku, Sapporo, Hokkaido 3 June 2013 NY-HO52 Tonden, Kita-ku, Sapporo, Hokkaido 3 June 2013 NY-HO54 Minaminosato, Kitahirosima, Hokkaido 3 June 2013 NY-HO55 Higashikyouei, Kitahirosima, Hokkaido 3 June 2013 NY-HO56 Shinano, Chitose, Hokkaido 3 June 2013 NY-HO186 Shinonome-cho, Chitose, Hokkaido 4 June 2014 NY-HO301 Maruyama, Kuriyama-cho, Yubari-gun, Hokkaido 6 May 2015 NY-HO306 Honcho, Naname-cho, Kameda-gun, Hokkaido 6 May 2015 NY-HO307 Funamicho, Toyoura-cho, Abuta-gun, Hokkaido 7 May 2015 NY-HO308 Fukushima, KImobetsu-cho, Abuta-gun, Hokkaido 7 May 2015 Tohoku district Nambu-machi, Sannohe-gun, Aomori 22 January 2014 NY-A65 Nambu-machi, Sannohe-gun,Aomori 15 May 2014 NY-A178 Sugisawaaratokoro, Yuzawa, Akita 14 June 2014 NY-AK205 Hiroomote, Hiroomote, Akita Akita 25 April 2015 NY-AK285 Nishinagano, Kadonodate-machi, Senboku, Akita 25 April 2015 NY-AK287 Sotsuda, Kitazawako, Senboku, Akita 25 April 2015 NY-AK288 Kyowahunooka, Daisen, Akita 25 April 2015 NY-AK289 Motomiya, Fukushima 23 April 2015 NY-FK266 Akogashima, Atami-machi, Koriyama, Fukushima 23 April 2015 NY-FK270 Yamagata, Inawashiro-machi, Fukushima, Fukushima 23 April 2015 NY-FK275 -, Morioka, Iwate 14 June 2014 NY-IW1 -, Morioka, Iwate 14 June 2014 NY-IW2 Toyama, Shiwa-cho, Shiwa-gun, Iwate 14 June 2014 NY-IW148 Toyama, Shiwa-cho, Shiwa-gun, Iwate 14 June 2014 NY-IW149 Koromogawa-ku, Oshu, Iwate 14 June 2014 NY-IW196 Kawashiri, Nishiwaga-machi, Waga-gun, Iwate 14 June 2014 NY-IW203 Kamiezuriko, Kitakami, Iwate 14 June 2014 NY-IW204 Irimada, Shibata-machi, Shibata-gun, Miyagi 14 June 2014 NY-MY210 Minamihase, Iwanuma, Miyagi 14 June 2014 NY-MY211 Zao-machi, Katta, Miyagi 23 April 2015 NY-MY292 Zao-machi, Katta, Miyagi 23 April 2015 NY-MY293 Zaohotta, Yamagata, Yamagata 15 June 2014 NY-YA193 Hara-machi, Tendo, Yamagata 15 June 2014 NY-YA194 Kubota-machi, Yonezawa, Yamagata 15 June 2014 NY-YA195 -, Tsuruoka, Yamagata 25 April 2015 NY-YA276 Kanto district Tokashiro, Kimitsu, Chiba 26 March 2010 NY-CB1 Sotominowa, Kimitsu, Chiba 26 March 2010 NY-CB2 Sotominowa, Kimitsu, Chiba 26 March 2010 NY-CB3 Ezuki, Kyonan-machi, Awa-gun, Chiba 26 March 2010 NY-CB4 Ezuki, Kyonan-machi, Awa-gun, Chiba 26 March 2010 NY-CB5 Ezuki, Kyonan-machi, Awa-gun, Chiba 26 March 2010 NY-CB9 Ezuki, Kyonan-machi, Awa-gun, Chiba 22 November 2013 NY-CB91 Ezuki, Kyonan-machi, Awa-gun, Chiba 17 March 2015 NY-CB247 17 March 2015 NY-GM252 Fujiki, Tomioka, Gunma 17 March 2015 NY-GM253 Fujiki, Tomioka, Gunma 17 March 2015 NY-GM254 Shiroishi, Fujioka, Gunma 11 November 2013 NY-IB71A Unknown, Ibaraki 17 March 2015 NY-IB248 Kanaya-cho, Mito, Ibaraki Hasse-machi, Miura, Kanagawa 27 March 2010 NY-KN1 a Rows in brown show that

No. clone sequenced by POTYNIB5P 7b

9 8 9

8

10

9 9 10 10 11

9 (5d)

10 (10) 10 (10)

8 10 (5)

8 (1) 10 (8) 10 (1) 10 10 (1) 9 (5) 8 10 (6) 8 10 9 10

Detected virus NLSYV NDc ND ND ND NLSYV NLSYV NLSYV ND ND ND CyEVA ND ND ND NLSYV ND ND ND NLV NLV ND NLSYV ND NLSYV NLSYV ND ND ND ND ND NYSV-like, NLSYV ND ND ND ND NYSV-like NYSV-like ND ND ND ND ND NLSYV NYSV-like, NLSYV, NLV ND ND ND ND NYSV-like, NLSYV NYSV-like, NLSYV NYSV-like, NLSYV NLSYV NYSV-like, NLSYV, NDV NYSV-like, NLSYV NLSYV, NDV NYSV-like, NLSYV NLSYV ND ND NLSYV CyEVA NLSYV

Narcissus plants were infected with narcissus yellow stripe virus (NYSV)-like virus, whereas rows in blue show that those were infected with narcissus late season yellows virus (NLSYV), cyrtanthus elatus virus A (CyEVA), narcissus latent virus (NLV), narcissus degeneration virus (NDV) or ornithogalum mosaic virus (OrMV). b Number of clone sequenced for approximately 600-700 bp by POTYNIB5P primer c Not detected d Number of clone for NYSV-like virus sequence

S1 Table. Continued. Plant Location (town, city, prefecture) (Isolate) Jogashima, Misaki, Miura, Kanagawa NY-KN2 Jogashima, Misaki, Miura, Kanagawa NY-KN3 Jogashima, Misaki, Miura, Kanagawa NY-KN4 Jogashima, Misaki, Miura, Kanagawa NY-KN5 Oba, Fujisawa, Kanagawa NY-KN6 Oba, Fujisawa, Kanagawa NY-KN7 Sekiguchi, Atsugi, Kanagawa NY-KN8 -, Atsugi, Kanagawa NY-KN9 Kamifukuoka, Fujimino, Saitama NY-ST1 -, Toda, Saitama NY-ST2 NY-TC249 Ota, Fujioka-machi, Tochigi, Tochigi NY-TC250 Osawa, Mashiko-machi, Haga-gun, Tochigi NY-TC251 Nogoya-machi, Utsunomiya, Tochigi NY-TK2 -, Koutou-ku, Tokyo -, Akishima, Tokyo NY-TK4 -, Ota-ku, Tokyo NY-TK243 Chubu district Sannomaru, Naka-ku, Nagoya, Aichi NY-AC230 Zoshi, Toyokawa, Aichi NY-AC233 Nagasawa-cho, Toyokawa, Aichi NY-AC234 Hamakitayama, Fukui, Fukui NY-FI3 Hamakitayama, Fukui, Fukui NY-FI9 Hamakitayama, Fukui, Fukui NY-FI11 Gamo, Fukui, Fukui NY-FI15 Hamakitayama, Fukui, Fukui NY-FI23 Nashigadaira, Echizen-cho, Nyuu, Fukui NY-FI29 Nashigadaira, Echizen-cho, Nyuu, Fukui NY-FI30 Chigadaira, Echizen-cho, Nyuu, Fukui NY-FI33 -, -, Niigata NY-NI7 Osato, Agano, Niigata NY-NI260 Kuraoka, Konan-ku, Niigata, Niigata NY-NI263 Hananoyamato, Daiichi Engei, Nagano NY-NN75A Suzaki, Shimoda, Shizuoka NY-SH216 Komakado, Gotemba, Shizuoka NY-SH219 Takasaki, Yaizu, Shizuoka NY-SH236 Hananoyamato, Daiichi Engei, Toyama NY-TY73A Kinki district -, Awaji, Hyogo NY-HG1 Ichinomiya, Awaji, Hyogo NY-HG3 Ichinomiya, Awaji, Hyogo NY-HG5 Ichinomiya, Awaji, Hyogo NY-HG6 Nadakuroiwa, Minamiawaji, Hyogo NY-HG8 Nadakuroiwa, Minamiawaji, Hyogo NY-HG10 ura-cho, Sumoto, Hyogo NY-HG11 Hon-machi, Himeji, Hyogo NY-HG13 Amida-cho, Takasago, Hyogo NY-HG16 Kukuchinishi-cho, Amagasaki, Hyogo NY-HG19 Meishin, Amagasaki, Hyogo NY-HG20 Akurakita, Takarazuka, Hyogo NY-HG25 Sakae, Takarazuka, Hyogo NY-HG24 Kamo, Kawanishi, Hyogo NY-HG27 -, -, Kyoto NY-KY83 -, -, Kyoto NY-KY84 Koazaka-cho, Matsuzaka, Mie NY-ME224 Shihikida, Taki-cho, Taki-gun, Mie NY-ME226 Komei-cho, Tsu, Mie NY-ME229 Minowa, Toyonaka, Osaka NY-OS1 Himemuro, Ikeda, Osaka NY-OS2 Chugoku district Yanohigashi, Akiku, Hiroshima, Hiroshima NY-HR36 Ushirogake, Kawajiri, Kure, Hiroshima NY-HR38 Sunami, Mihara, Hiroshima NY-HR39 Higashiteshiro, Fukuyama, Hiroshima NY-HR40 Kotsu, Higashi-ku, Okayama, Okayama NY-OY1 Kuma, Kita-ku, Okayama, Okayama NY-OY41 Unknown, Shimane NY-SM69A Chinto, Hagi, Yamaguchi NY-YM2 Nabe-cho, Shimonoseki, Yamaguchi NY-YM5 Shikoku district Takanoko-cho, Matsuyama, Ehime NY-EH171 Kurumi, Tambara-cho, Saijo, Ehime NY-EH173 Otesuji, Kochi, Kochi NY-KO163 Aioi-cho, Kochi, Kochi NY-KO164 Ikku, Kochi, Kochi NY-KO165 Ejiri-cho, Sakaide, Kagawa NY-KW1

Collection date 27 March 2010 27 March 2010 27 March 2010 27 March 2010 27 March 2010 27 March 2010 28 March 2010 28 March 2010 28 March 2010 30 March 2010 17 March 2015 17 March 2015 17 March 2015 25 February 2010 28 March 2010 17 March 2015 25 January 2015 25 January 2015 25 January 2015 17 January 2012 17 January 2012 17 January 2012 8 March 2012 8 March 2012 8 March 2012 8 March 2012 8 March 2012 5 April 2010 23 April 2015 24 April 2015 11 November 2013 7 December 2014 7 December 2014 25 January 2015 11 November 2013 12 March 2011 12 March 2011 12 March 2011 12 March 2011 12 March 2011 12 March 2011 12 March 2011 14 March 2011 14 March 2011 10 March 2012 10 March 2012 10 March 2012 10 March 2012 10 March 2012 19 November 2013 19 November 2013 24 January 2015 24 January 2015 24 January 2015 10 March 2012 10 March 2012

No. clones sequenced by POTYNIB5P

9 (1) 9 8 9 10 (10) 7 (2) 10 10 7 10 (5) 10 11 (4) 9 8 10 (3) 10 9 10 9 10 5 (2) 9 10 (10) 10 9 4 8 9 (5) 10 (1) 10 (10) 6 (5) 10 (10) 9 10 7 (7) 9 9 (2) 8 (3) 7

8 March 2013 8 March 2013 8 March 2013 9 March 2013 13 March 2011 9 March 2013 11 November 2013 26 February 2011 27 February 2011

7 (7) 9 (9) 7 6 9 (5)

26 April 2014 26 April 2014 25 April 2014 25 April 2014 25 April 2014 13 March 2011

10 10

10 10 10 (2)

9 (9) 6

Detected virus ND ND ND ND NYSV-like, NLSYV NLSYV NLSYV OrMV NYSV-like NYSV-like, NLSYV ND CyEVA NLSYV, NDV NLSYV NYSV-like, NLSYV NLSYV NYSV-like, NLSYV NLSYV, NDV ND NLSYV, NDV NYSV-like, NLSYV NLSYV, NDV ND NDV NLSYV NLSYV, NDV NLSYV NYSV-like ND NLSYV ND NYSV-like NLSYV NLSYV NLSYV ND NYSV-like, CyEVA ND ND NYSV-like, NLSYV, NDV NYSV-like, NLSYV, NDV NYSV-like ND NYSV-like, NLSYV NYSV-like NLSYV, NDV NLSYV ND NYSV-like ND ND NLSYV ND NYSV-like, NDV NYSV-like, NLSYV NLSYV NYSV-like NYSV-like NLSYV NDV NYSV-like, NLSYV ND NLSYV, OrMV NLSYV, NDV NYSV-like, NLSYV, NDV NYSV-like, NDV NYSV-like ND NYSV-like ND NLSYV

S1 Table. Continued. Plant Location (town, city, prefecture) (Isolate) Oumi, Sakaide, Kagawa NY-KW2 Oumi, Sakaide, Kagawa NY-KW3 Ikushima-cho, Takamatsu, Kagawa NY-KW4 Nakayama-cho, Takamatsu, Kagawa NY-KW5 Danshi-cho, Takamatsu, Kagawa NY-KW6 Kizuno, Otsu-cho, Naruto, Tokushima NY-TS158 Kizuno, Otsu-cho, Naruto, Tokushima NY-TS159 Yoshinaga, Otsu-cho, Naruto, Tokushima NY-TS160 -, Mima, Tokushima NY-TS161 Kyushu district -, Okawa, Fukuoka NY-F1 Yamakawa-machi, Miyama, Fukuoka NY-F2 Kawabaru, Itoshima, Fukuoka NY-F8 Misaka, Itoshima, Fukuoka NY-F9 Tokunoshima-cho, Oshima, Kagoshima NY-KG1 Tokunoshima-cho, Oshima, Kagoshima NY-KG2 Tenokuchi, Kagoshima, Kagoshima NY-KG6 Tenokuchi, Kagoshima, Kagoshima NY-KG7 Yamanokuchi, Kagoshima, Kagoshima NY-KG8 Uenosono, Kagoshima, Kagoshima NY-KG9 Uearata-cho, Kagoshima, Kagoshima NY-KG10 Uearata-cho, Kagoshima, Kagoshima NY-KG11 Arata-cho, Kagoshima, Kagoshima NY-KG12 Uearata-cho, Kagoshima, Kagoshima NY-KG13 Miyabara, Arao, Kumamoto NY-KM1O Miyabara, Arao, Kumamoto NY-KM1P Ozu-machi, Kikuchi, Kumamoto NY-KM9 Higashinagaeura, Ebino, Miyazaki NY-M1 Higashinagaeura, Ebino, Miyazaki NY-M2 Suenaga, Ebino, Miyazaki NY-M3 Takaharu, Nishimorokata-gun, Miyazaki NY-M4 Takazaki-cho, Miyakonojo, Miyazaki NY-M5 -, -, Miyazaki NY-M77 Kunimi-cho, Unzen, Nagasaki NY-N2 Kayaki-cho, Nagasaki, Nagasaki NY-N6 Kurohama-machi, Nagasaki, Nagasaki NY-N9 Nomozaki, Nomo-cho, Nagasaki, Nagasaki NY-N12 Nomozaki, Nomo-cho, Nagasaki, Nagasaki NY-N13 Nomozaki, Nomo-cho, Nagasaki, Nagasaki NY-N14 Uki-machi, Isahaya, Nagasaki NY-N15 Obama-cho, Unzen, Nagasaki NY-N18 Arima-cho, Minamishimabara, Nagasaki NY-N19 Ariake-cho, Shimabara, Nagasaki NY-N20 Takasakiyama, Kozaki, Oita, Oita NY-OI1 Takasakiyama, Kozaki, Oita, Oita NY-OI2 Takasakiyama, Kozaki, Oita, Oita NY-OI3 Tanoyu-machi, Beppu, Oita NY-OI4 Tanoyu-machi, Beppu, Oita NY-OI5 Fujimi-cho, Beppu, Oita NY-OI12 Tenman-cho, Beppu, Oita NY-OI13 Tenman-cho, Beppu, Oita NY-OI14 Hyogo-machi, Saga, Saga NY-SG8 Honjo-machi, Saga, Saga NY-SG10 Honjo-machi, Saga, Saga NY-SG12 Okinawa district Kyoda, Nago, Okinawa NY-OK98 Kyoda, Nago, Okinawa NY-OK100

No. clones sequenced by POTYNIB5P 3 10 (10) 8 7 8 (8)

Detected virus

20 March 2010 24 January 2011 11 December 2011 11 December 2011 22 January 2010 22 January 2010 16 February 2012 16 February 2012 16 February 2012 16 February 2012 16 February 2012 16 February 2012 16 February 2012 16 February 2012 23 January 2011 23 January 2011 28 March 2011 7 May 2012 7 May 2012 7 May 2012 7 May 2012 7 May 2012 15 November 2013 6 March 2009 27 February 2010 27 February 2010 27 February 2010 27 February 2010 27 February 2010 27 February 2010 28 February 2010 28 February 2010 28 February 2010 26 February 2012 26 February 2012 26 February 2012 26 February 2012 26 February 2012 26 February 2012 26 February 2012 26 February 2012 14 March 2010 14 January 2011 8 January 2013

10 (3) 7 9 6 (6) 10 (10) 9 (3) 9

9

NYSV-like, NLSYV, NDV NLSYV NLSYV NYSV-like NYSV-like NYSV-like, NLSYV NLSYV ND ND NYSV-like, NLSYV NYSV-like, NDV NDV NYSV-like NLSYV NYSV-like NYSV-like NLSYV, NDV NLV NYSV-like, CyEVA ND NLSYV ND ND ND ND NLSYV NLSYV ND NYSV-like, NLSYV, NDV NYSV-like, NLSYV ND NYSV-like, NLSYV, CyEVA NYSV-like NYSV-like NYSV-like NYSV-like NLSYV NYSV-like NYSV-like, NLSYV NYSV-like ND NLSYV ND NLSYV, NDV

25 January 2014 25 January 2014

10 (10) 6 (6)

NYSV-like NYSV-like

Collection date 13 March 2011 13 March 2011 13 March 2011 13 March 2011 13 March 2011 24 April 2014 24 April 2014 26 April 2014 26 April 2014

6 (2) 6 (1) 6 9 (9) 10 10 10 6 3 7 (6) 10

8 8 9 (7) 10 (6) 15 (1) 10 (10) 10 (10) 10 (10) 10 (10) 8 8 9 (6) 10 (10) 10

CyEVA NYSV-like NLSYV OrMV NYSV-like NLV ND ND ND