Scientia Agricultura Sinica ›› 2021, Vol. 54 ›› Issue (20): 4326-4336.doi: 10.3864/j.issn.0578-1752.2021.20.007

• PLANT PROTECTION • Previous Articles     Next Articles

Molecular Variation and Phylogenetic Relationship of Apple Scar Skin Viroid in Seven Cultivars of Apple

LI ZiTeng,CAO YuHan,LI Nan,MENG XiangLong,HU TongLe,WANG ShuTong,WANG YaNan(),CAO KeQiang   

  1. College of Plant Protection, Hebei Agricultural University, Baoding 071001, Hebei
  • Received:2021-03-10 Accepted:2021-04-23 Online:2021-10-16 Published:2021-10-25
  • Contact: YaNan WANG E-mail:wyn3215347@163.com

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Abstract:

【Objective】The objective of this study is to explore the molecular variation and phylogenetic relationship of apple scar skin viroid (ASSVd) in different cultivars of apple, and to lay a foundation for further revealing the molecular variation mechanism of ASSVd. 【Method】The different cultivars of apple including Fuji, Tonami, Wang Lin, Mid-Autumn King, Gold Delicious, Xin Nonghong and Xin Nonghuang, infected by ASSVd were used as materials to amplify complete genome sequence by specific primers, and then molecular cloning and sequencing were performed. Biological software DNAMAN was used to analyze the identities of the variant sequences and the MEGA was used to construct a phylogenetic tree. 【Result】A total of 210 sequences of ASSVd were obtained, with a total of 17 variants, with a size of 325-333 nt. Seventeen variants of ASSVd were aligned and analyzed with other published representative isolates. The result showed that all the variants were divided into three groups. Group I includes 10 variants, which are closely related to the reported Baoding Fuji isolate (KR264032.1). Group II includes 6 variants, which are clustered separately. Group III includes one variant, which is closely related to the Xinjiang Fuji isolate (EU031455.1). Based on 8 variation base sites at genome 0-3, 221, 251, 284, and 302, the 17 variants were divided into 6 type including: 1. nt 0-3 (GGTA) + nt 41-46 (TAAAAT) + nt 221 (T) + nt 251 (T) +nt 284 (G) + nt 302 (T); 2. nt 0-3 (XGGT) + nt 41-46 (AGATAX) + nt 221 (T) + nt 251(X) + nt 284 (A) + nt 302 (A); 3. nt 0-3 (XGGT) + nt 41-46 (AGATAX) + nt 221 (X) + nt 251 (T) + nt 284 (A) + nt 302 (A); 4. nt 0-3 (XGGT/GGTA) + nt 41-46 (AGATAX) + nt 221 (T) + nt 251 (T) + nt 284 (A) + nt 302 (A); 5. nt 0-3 (GGTA) + nt 41-46 (TAAAAT) + nt 221 (X) + nt 251 (G) + nt 284 (G) + nt 302 (T); 6. nt 0-3 (GGTA) + nt 41-46 (TAAAAT) + nt 221 (T) + nt 251 (G) + nt 284 (G) + nt 302 (T). X represents missing. There are 6 types of variants in Fuji, type 4 (47.5%) is the main type. There are 3 types of variants in Wang Lin, type 5 (43%) is the main type. There are 3 types of variants in Gold Delicious, type 4 (60%) is the main type. ASSVd obtained from Tonami is type 5 (100%). ASSVd obtained from Mid-Autumn King is type 4 (100%). There are 2 types in Xin Nonghong, type 1 (83.3%) is the main type. There are 3 types in Xin Nonghuang, type 1 (62.5%) is the main type. 【Conclusion】Seventeen variants from 7 cultivars are divided into 6 types according to the 8 variation base sites of ASSVd nt 0-3, 221, 251, 284, and 302. Different apple cultivars carry different ASSVd population structures. The types and proportions of ASSVd variants are different.

Key words: apple scar skin viroid (ASSVd), genome, molecular cloning, molecular evolution, molecular variation

Fig. 1

The fruit symptom of different cultivars of apple infected by ASSVd a-f is the healthy fruit of Fuji, Tonami, Xin Nonghong, Wang Lin, Mid-Autumn King and Xin Nonghuang cultivars; A-F corresponds to the susceptible fruits of Fuji (color dappling), Tonami (color dappling), Xin Nonghong (color dappling), Wang Lin (russeting and distortion), Mid-Autumn King (russeting) and Xin Nonghuang (uneven and rough fruit surface)"

Fig. 2

The identity comparison among 17 variants of ASSVd from 7 cultivars of apple The specific information of each sequence is shown in Fig. 4. The same as Fig. 3"

Fig. 3

The cluster analysis between 17 ASSVd variants from 7 apple cultivars and other representative isolates"

Fig. 4

The phylogenetic relationship between 17 ASSVd variants from 7 apple cultivars and other representative isolates The phylogenetic tree was constructed with MEGA 7.0 by the neighbor-joining method, the Bootstrap was repeated 1 000 times. The description is represented as the isolate/origin and cultivar/accession number. The bootstrap values below 60% are not shown"

Fig. 5

Comparison of the sequences of all the isolates in this study with the ASSVd sequence from Baoding"

Table 1

Base types of ASSVd from different apple cultivars (%)"

苹果品种
Apple cultivar		 碱基类型Base type
Type 1 Type 2 Type 3 Type 4 Type 5 Type 6
富士Fuji 10.0 2.5 2.5 47.5 25.0 12.5
王林Wang Lin 28.4 0 0 0 43.0 28.6
金冠Gold Delicious 0 33.3 6.7 60.0 0 0
斗南Tonami 0 0 0 0 100.0 0
中秋王Mid-Autumn King 0 0 0 100.0 0 0
信侬红Xin Nonghong 83.3 0 0 0 0 16.7
信侬黄Xin Nonghuang 62.5 0 0 0 25.0 12.5

Table 2

Minimum free energy of secondary structure of different ASSVd isolates in this study"

来源
Source		 编号
Number		 长度
Length (nt)		 登录号
Accession number		 碱基类型
Base type		 最小自由能
Minimum free energy (kJ·mol-1)
斗南Tonami DN1 325 MH105019 5 -561.9
斗南Tonami DN1-2 331 MH105020 5 -583.2
富士Fuji FS1-1 329 MG891838 1 -563.1
富士Fuji FS4-1 330 MH105022 4 -565.6
富士Fuji FS4-9 329 MH105023 3 -567.7
富士Fuji FS4-13 329 MH105024 3 -567.7
富士Fuji FS3-4 326 MH105025 2 -558.1
富士Fuji FS3-10 329 MH105026 2 -575.7
王林Wang Lin WL1-5 332 MH105027 6 -568.1
王林Wang Lin WL1-6 331 MH105028 5 -583.2
王林Wang Lin WL2-2 333 MH105029 6 -577.8
王林Wang Lin WL3 328 MH105030 1 -558.1
信侬红Xin Nonghong Xnho1 332 MH105031 6 -576.1
信侬红Xin Nonghong Xnho1-3 332 MH105032 1 -579.5
信侬黄Xin Nonghuang Xnhu1-3 332 MH105033 6 -572.3
中秋王Mid-Autumn King ZQW7 331 MH105034 4 -563.5
金冠Gold Delicious GD3-23 329 MH105035 2 -575.7
[1] 赵玲玲, 刘娟, 宋来庆, 张学勇, 张硕, 姜中武. 烟台市富士苹果上苹果锈果类病毒分子变异分析. 植物保护学报, 2018, 45(4):856-863.
ZHAO L L, LIU J, SONG L Q, ZHANG X Y, ZHANG S, JIANG Z W. Genetic analysis of apple scar skin viroid from Fuji apple in Yantai, China. Journal of Plant Protection, 2018, 45(4):856-863. (in Chinese)
[2] 王国平, 洪霓, HADIDI A. 中国果树类病毒的发生及其研究进展. 果树学报, 2005, 22(1):51-54.
WANG G P, HONG N, HADIDI A. Occurrence and research progress of fruit tree viroid diseases in China. Journal of Fruit Science, 2005, 22(1):51-54. (in Chinese)
[3] 郝璐, 叶婷, 陈善义, 王少杰, 周颖, 范在丰, 国立耘, 周涛. 我国北方部分苹果主产区病毒病的发生与检测. 植物保护, 2015, 41(2):158-161.
HAO L, YE T, CHEN S Y, WANG S J, ZHOU Y, FAN Z F, GUO L Y, ZHOU T. Occurrence and detection of virus diseases in some major apple-producing regions in northern China. Plant Protection, 2015, 41(2):158-161. (in Chinese)
[4] DARÒS J A, ELENA S F, FLORES R. Viroids: An Ariadne’s thread into the RNA labyrinth. EMBO Reports, 2006, 7(6):593-598.
doi: 10.1038/sj.embor.7400706
[5] FLORES R, RANDLES J W, BAR-JOSEPH M, DIENER T O. A proposed scheme for viroid classification and nomenclature. Archives of Virology, 1998, 143(3):623-629.
doi: 10.1007/s007050050318
[6] 陈建刚, 王海波. 苹果锈果类病毒RNA序列的生物信息学分析. 安徽农业科学, 2010, 38(8):4112-4114, 4125.
CHEN J G, WANG H B. Analysis of the biological information of the RNA sequence of apple rust fruit-like virus. Journal of Anhui Agricultural Sciences, 2010, 38(8):4112-4114, 4125. (in Chinese)
[7] 郗娜娜, 李紫腾, 张静怡, 孟祥龙, 王亚南, 曹克强. 苹果锈果类病毒实时荧光定量反转录PCR检测及其在苹果树体内的扩散转移规律. 植物保护学报, 2020, 47(6):1304-1312.
XI N N, LI Z T, ZHANG J Y, MENG X L, WANG Y N, CAO K Q. Detection of apple scar skin viroid by real-time fluorescence quantitative reverse transcription PCR and its movement in an apple tree. Journal of Plant Protection, 2020, 47(6):1304-1312. (in Chinese)
[8] 廖明安, 冷怀群, 任雅君, 罗明静, 李焕秀. 苹果无病毒与带病毒幼树某些内含物及生育的差别. 中国果树, 1993(2):6-8.
LIAO M A, LENG H Q, REN Y J, LUO M J, LI H X. Differences between some inclusions and fertility in apple virus-free and viral saplings. China Fruits, 1993(2):6-8. (in Chinese)
[9] 王际轩, 刘志, 谢秀华, 吴斌, 佟兆国. 苹果无病毒树的生长和结果表现. 园艺学报, 2000, 27(3):157-160.
WANG J X, LIU Z, XIE X H, WU B, TONG Z G. The reaction of virus-free apple tree growth and fruit production. Acta Horticulturae Sinica, 2000, 27(3):157-160. (in Chinese)
[10] 胡国君, 张尊平, 范旭东, 任芳, 李正男, 董雅凤. 我国主要苹果病毒及其研究进展. 中国果树, 2017(3):71-74, 82.
HU G J, ZHANG Z P, FAN X D, REN F, LI Z N, DONG Y F. Advances in research of mainly apple viruses in China. China Fruits, 2017(3):71-74, 82. (in Chinese)
[11] SHARMA U, WATPADE S, GUPTA B, RAIGOND B, KUMARI N, BHARDWAJ P, HANDA A, GUPTA P. Economic losses due to infection by apple scar skin viroid in Himachal Pradesh, India. VirusDisease, 2020, 31(4):490-496.
doi: 10.1007/s13337-020-00625-8
[12] STEGER G, PERREAULT J P. Structure and associated biological functions of viroids. Advances in Virus Research, 2016, 94:141-172.
[13] DI SERIO F, FLORES R, VERHOEVEN J T J, LI S F, PALLÁS V, RANDLES J W, SANO T, VIDALAKIS G, OWENS R A. Current status of viroid taxonomy. Archives of Virology, 2014, 159(12):3467-3478.
doi: 10.1007/s00705-014-2200-6
[14] 张志想. 啤酒花矮化类病毒寄主适应性和致病性研究[D]. 北京: 中国农业科学院, 2012.
ZAHNG Z X. Host adaptation and pathogenicity of hop stunt viroid[D]. Beijing: Chinese Academy of Agricultural Sciences, 2012. (in Chinese)
[15] FLORES R, GAGO-ZACHERT S, SERRA P, SANJUAN R, ELENA S F. Viroids: Survivors from the RNA world?. Annual Review of Microbiology, 2014, 68:395-414.
doi: 10.1146/micro.2014.68.issue-1
[16] FLORES R, GAS M E, MOLINA-SERRANO D, NOHALES M Á, CARBONELL A, GAGO S, DE LA PENA M, DARÒS J A. Viroid replication: Rolling-circles, enzymes and ribozymes. Viruses, 2009, 1(2):317-334.
doi: 10.3390/v1020317
[17] DING B. Viroids: Self-replicating, mobile, and fast-evolving noncoding regulatory RNAs. Wiley Interdisciplinary Reviews-RNA, 2010, 1(3):362-375.
doi: 10.1002/wrna.22
[18] KOVALSKAVA N, HAMMOND R W. Molecular biology of viroid-host interactions and disease control strategies. Plant Science, 2014, 228:48-60.
doi: 10.1016/j.plantsci.2014.05.006
[19] FLORES R, MINOIA S, CARBONELL A, GISEL A, DELGADO S, LÓPEZ-CARRASCO A, NAVARRO B, DI SERIO F. Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Research, 2015, 209:136-145.
doi: 10.1016/j.virusres.2015.02.027
[20] HADIDI A, HANSEN A J, PARISH C L, YANG X. Scar skin and dapple apple viroids are seed-borne and persistent in infected apple trees. Research in Virology, 1991, 142(4):289-296.
doi: 10.1016/0923-2516(91)90015-U
[21] 郭瑞. 几种园艺植物上发生的类病毒的种类鉴定及序列多样性分析[D]. 北京: 中国农业科学院, 2006.
GUO R. Detection and sequence diversity analysis of viroids isolated from several perennial plants in China[D]. Beijing: Chinese Academy of Agricultural Sciences, 2006. (in Chinese)
[22] 陈炜, 田波. 苹果锈果病组织中发现的环状类病毒RNA. 科学通报, 1985(17):1360.
CHEN W, TIAN B. Study on the rust disease viroid RNA found in the tissues of apple. Chinese Science Bulletin, 1985(17):1360. (in Chinese)
[23] 刘娟. 山东东部地区苹果锈果类病毒分子变异研究[D]. 烟台: 烟台大学, 2014.
LIU J. Molecular variability of apple scar skin viriod in east of Shandong Province[D]. Yantai: Yantai University, 2014. (in Chinese)
[24] 朱慧. 来源梨的苹果褪绿叶斑病毒和两种类病毒的分子特性研究[D]. 武汉: 华中农业大学, 2014.
ZHU H. Study on the molecular characteristics of apple chlorotic leaf spot virus and two viriods from pear. Wuhan: Huazhong Agricultural University, 2014. (in Chinese)
[25] 查富蓉. 侵染苹果的类病毒与果实症状间的相关性及分子特性分析[D]. 武汉: 华中农业大学, 2015.
ZHA F R. Molecular characterization and correlation with fruit symptoms of the viroids infecting apple[D]. Wuhan: Huazhong Agricultural University, 2015. (in Chinese)
[26] 刘洪玉, 孙子豪, 李保华, 王彩霞. 侵染‘舞美’苹果的苹果锈果类病毒检测与全序列分析. 植物保护, 2019, 45(4):176-179.
LIU H Y, SUN Z H, LI B H, WANG C X. Detection and full sequence analysis of apple scar skin viroid in ‘Maypole’ apple. Plant Protection, 2019, 45(4):176-179. (in Chinese)
[27] FLORES R, HERNÁNDEZ C, DE ALBA A E M, DARÒS J A, DI SERIO F. Viroids and viroid-host interactions. Annual Review of Phytopathology, 2005, 43:117-139.
doi: 10.1146/phyto.2005.43.issue-1
[28] 黄家风, 许文博. 植物类病毒研究进展. 石河子大学学报(自然科学版), 2007, 25(3):276-281.
HUANG J F, XU W B. Advances in studying plant viroids. Journal of Shihezi University (Natural Science), 2007, 25(3):276-281. (in Chinese)
[29] KEESE P, SYMONS R H. Domains in viroids: Evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proceedings of the National Academy of Sciences of the United States of America, 1985, 82(14):4582-4586.
[30] 陈冉冉, 谢吉鹏, 叶婷, 董云浩, 国立耘, 周涛. 我国部分苹果产区苹果锈果类病毒的检测和全序列分析. 植物保护, 2017, 43(6):97-102.
CHEN R R, XIE J P, YE T, DONG Y H, GUO L Y, ZHOU T. Detection and full nucleotide sequences analysis of apple scar skin viroid isolates in some apple producing areas of China. Plant Protection, 2017, 43(6):97-102. (in Chinese)
[31] WALIA Y, DHIR S, ZAIDI A A, HALLAN V. Apple scar skin viroid naked RNA is actively transmitted by the whitefly Trialeurodes vaporariorum. RNA Biology, 2015, 12(10):1131-1138.
doi: 10.1080/15476286.2015.1086863
[32] FLORES R, NAVARRO B, DELGADO S, SERRA P, DI SERIO F. Viroid pathogenesis: A critical appraisal of the role of RNA silencing in triggering the initial molecular lesion. FEMS Microbiology Reviews, 2020, 44(3):368-398.
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