中国农业科学 ›› 2020, Vol. 53 ›› Issue (23): 4791-4801.doi: 10.3864/j.issn.0578-1752.2020.23.006
邹林峰1(),涂丽琴2,沈建国3,杜振国1,蔡伟4,季英华2(
),高芳銮1(
)
收稿日期:
2020-07-02
接受日期:
2020-07-24
出版日期:
2020-12-01
发布日期:
2020-12-09
通讯作者:
季英华,高芳銮
作者简介:
邹林峰,E-mail: 基金资助:
ZOU LinFeng1(),TU LiQin2,SHEN JianGuo3,DU ZhenGuo1,CAI Wei4,JI YingHua2(
),GAO FangLuan1(
)
Received:
2020-07-02
Accepted:
2020-07-24
Online:
2020-12-01
Published:
2020-12-09
Contact:
YingHua JI,FangLuan GAO
摘要:
【目的】番茄褪绿病毒(tomato chlorosis virus,ToCV)是长线形病毒科(Closteroviridae)毛形病毒属(Crinivirus)成员,现已成为我国番茄和其他蔬菜作物上最为常见的病毒之一。研究旨在查明ToCV的进化历史,尤其是该病毒何时何地传入我国,并阐明其适应性进化机制。【方法】根据ToCV外壳蛋白(coat protein,CP)基因两侧保守区设计1对特异性引物,对随机抽取的13个ToCV分离物进行扩增克隆,将测序获得的新序列与GenBank下载的含有采样时间和地理信息的序列合并得到103条ToCV CP基因序列,采用日期随机化检验(date-randomization test,DRT)检测数据集中的时间信号,并应用贝叶斯谱系动力学框架重建该病毒的进化动态。同时,应用系统发育与性状关联分析(phylogeny-trait association analysis)评估地理因素对ToCV适应性进化的影响。【结果】13 个ToCV分离物均成功扩增出预期大小(约800 bp)的特异性片段,核苷酸序列与已报道的ToCV不同分离物CP 基因序列一致性均在98%以上;基于聚类排列的日期随机化检验结果显示,通过实际采样时间和日期随机化的数据集分别推断获得的替代速率在95%置信区间之间没有存在重叠,表明本研究的数据集具有足够的时间信号,可以用于后续的贝叶斯分子定年(Bayesian molecular dating)分析。贝叶斯系统发育分析显示ToCV的最近共祖时间(the most recent common ancestor)为1920年(95%置信区间:1849—1976),该病毒约于2005年左右从美国引入中国。该病毒的CP基因替代速率约为1.12×10 -3替代/位点/年(95%置信区间:6.08×10 -4—1.73×10 -3),与动物RNA病毒的相当,表明ToCV正处于快速进化之中。此外,系统发育分析与性状关联分析结果显示ToCV分离物与其来源地区的关联系数(association index)、简约分值(parsimony score)和最大单系分支(maximum monophyletic clade)统计检验均呈极显著水平(P<0.01),表明地理因素与ToCV适应性进化之间存在很强的关联性。【结论】ToCV正处于快速进化动态,该病毒的适应性进化主要受地理因素所驱动。研究结果将有助于增加对ToCV流行病学的认识,可为制定有效的防控策略提供依据。
邹林峰,涂丽琴,沈建国,杜振国,蔡伟,季英华,高芳銮. 番茄褪绿病毒的进化动态与适应性进化特征[J]. 中国农业科学, 2020, 53(23): 4791-4801.
ZOU LinFeng,TU LiQin,SHEN JianGuo,DU ZhenGuo,CAI Wei,JI YingHua,GAO FangLuan. The Evolutionary Dynamics and Adaptive Evolution of Tomato Chlorosis Virus[J]. Scientia Agricultura Sinica, 2020, 53(23): 4791-4801.
表1
本研究用到的ToCV分离物信息"
分离物 Isolate | 国家 Country | 采样日期 Sampling date | 序列登录号 Accession number | 分离物 Isolate | 国家 Country | 采样日期 Sampling date | 序列登录号 Accession number | |
---|---|---|---|---|---|---|---|---|
BR: Taquara:15 | 巴西Brazil | 2015 | KY569401 | Gr-535 | 希腊Greece | 2008 | EU284744 | |
ToC-Br2 | 巴西Brazil | 2006 | JQ952601 | To-Il1970 | 希腊Greece | 2011 | HG380085 | |
BJ | 中国China | 2012-10-26 | KC311375 | To-Il1857 | 希腊Greece | 2011 | HG380088 | |
SDSG | 中国China | 2012-10 | KC709510 | To-Il2002 | 希腊Greece | 2011 | HG380089 | |
Nanjing | 中国China | 2014-05-12 | KJ815045 | To-Il2010 | 希腊Greece | 2011 | HG380090 | |
14HD-12 | 中国China | 2014-09-25 | KP335046 | To-Rh1933 | 希腊Greece | 2011 | HG380084 | |
15HD-8 | 中国China | 2014-09-25 | KR184675 | To-Rh1835 | 希腊Greece | 2011 | HG380087 | |
15-PG-9 | 中国China | 2015-03-25 | KT751008 | To-Se2042 | 希腊Greece | 2011 | HG380086 | |
NGXJZ | 中国China | 2014-08-03 | KX272755 | 1 | 毛里求斯Mauritius | 2007-02 | FM206381 | |
HBCZ | 中国China | 2014-08-03 | KP217195 | 2 | 毛里求斯Mauritius | 2007-02 | FM206382 | |
HBHS | 中国China | 2014-08-03 | KP217196 | BK2-2 | 韩国South Korea | 2017-06-27 | MG001345 | |
HBLF | 中国China | 2014-08-03 | KP217199 | BS-4 | 韩国South Korea | 2017-06-27 | MG001346 | |
HBSJZ | 中国China | 2014-08-03 | KP217200 | N-2 | 韩国South Korea | 2017-06-17 | MG001347 | |
HNAYHX | 中国China | 2014-08-04 | KP264983 | JN2 | 韩国South Korea | 2013 | MG813910 | |
HNZZZM1 | 中国China | 2014-08-04 | KP264984 | NS | 韩国South Korea | 2013 | MG813911 | |
HNZZZM2 | 中国China | 2014-08-04 | KP264985 | IS17 | 韩国South Korea | 2013 | KP114525 | |
JLCC | 中国China | 2015-08-15 | KU306111 | YG | 韩国South Korea | 2013 | KP114528 | |
LNDL | 中国China | 2015-08-15 | KU204707 | IS29 | 韩国South Korea | 2013 | KP114529 | |
LNLZ | 中国China | 2016-10-18 | MF278016 | JJ3 | 韩国South Korea | 2013 | KP114533 | |
NMHHHT | 中国China | 2015-07-15 | KU204709 | JJ5 | 韩国South Korea | 2013 | KP114534 | |
ToCV-YL1 | 中国China | 2016-11-20 | MF346383 | JN1 | 韩国South Korea | 2013 | KP114536 | |
SDTAFC-Bemisia tabaci | 中国China | 2012-10-20 | KC812621 | HP | 韩国South Korea | 2013 | KP114537 | |
Shandong 12-1 | 中国China | 2015-11-01 | KY679886 | HS | 韩国South Korea | 2013 | KP137099 | |
Shandong 28-2 | 中国China | 2015-11-01 | KY679887 | JJ | 韩国South Korea | 2013 | KP137101 | |
Shandong 18-3 | 中国China | 2015-11-01 | KY679888 | 2.5 | 西班牙Spain | 2010 | KJ200305 | |
SDTADP | 中国China | 2012-10-20 | KC812619 | MM8 | 西班牙Spain | 2005 | KJ200307 | |
SDTAFC | 中国China | 2012-10-20 | KC812620 | Pl-1-2 | 西班牙Spain | 1997 | KJ200309 | |
SDLC | 中国China | 2012-10-20 | KC812622 | AT80/99-IC | 西班牙Spain | 2014 | KJ740257 | |
JD | 中国China | 2016-03-30 | KX900412 | AT80/99 | 西班牙Spain | 2006 | DQ136146 | |
JD-H | 中国China | 2014-03-30 | KX987242 | XS | 中国China | 2011-11-19 | KY618797 | |
FQ-J | 中国China | 2014-03-30 | KY471019 | TN11 | 中国China | 1998 | MF795557 | |
SDTAMZ | 中国China | 2012-10-20 | KC812623 | Merkez | 土耳其Turkey | 2015-02-03 | KY419527 | |
PD-KJ1 | 中国China | 2015-12-15 | KY206012 | Kas | 土耳其Turkey | 2015-02-03 | KY419528 | |
PD-KJ2 | 中国China | 2015-12-15 | KY206014 | AKSU8 | 土耳其Turkey | 2012 | MF576337 | |
SDQD | 中国China | 2015-08-16 | KT809400 | ALANYA42 | 土耳其Turkey | 2012 | MF576338 | |
SDZB | 中国China | 2014-08-22 | KR072213 | ANTALYA6 | 土耳其Turkey | 2012 | MF576339 | |
SXJZ | 中国China | 2016-08-20 | KX853540 | ANTALYA22 | 土耳其Turkey | 2012 | MF576340 | |
ToCV-TJ6 | 中国China | 2014-08-07 | KP219722 | FETHIYE72 | 土耳其Turkey | 2012 | MF576341 | |
ToCV-YN | 中国China | 2016-10-20 | KY471138 | FINIKE1 | 土耳其Turkey | 2012 | MF576342 | |
BB6* | 中国China | 2019-03-21 | MN939023 | GAZIPASA4 | 土耳其Turkey | 2012 | MF576343 | |
EB1* | 中国China | 2017-04-06 | MN939024 | KEMER20 | 土耳其Turkey | 2012 | MF576344 | |
EB2* | 中国China | 2019-03-14 | MN939025 | KUMLUCA32 | 土耳其Turkey | 2012 | MF576345 | |
EB6* | 中国China | 2019-03-14 | MN939026 | KUMLUCA39 | 土耳其Turkey | 2012 | MF576346 | |
XMF3* | 中国China | 2017-04-12 | MN939027 | MANAVGAT6 | 土耳其Turkey | 2012 | MF576347 | |
XMF4* | 中国China | 2017-03-30 | MN939028 | SERIK48 | 土耳其Turkey | 2012 | MF576348 | |
XMF5* | 中国China | 2017-03-30 | MN939029 | TRAntToCV | 土耳其Turkey | 2018-03 | MK248741 | |
XMF7* | 中国China | 2017-04-17 | MN939030 | Florida | 美国United States | 2005 | AY903448 | |
XMF8* | 中国China | 2017-04-17 | MN939031 | Amelia | 美国United States | 2010-11-03 | HQ879840 | |
XS3* | 中国China | 2019-03-14 | MN939032 | FL47 | 美国United States | 2010-11-03 | HQ879841 | |
XS5* | 中国China | 2019-03-14 | MN939033 | Tygress | 美国United States | 2010-11-03 | HQ879842 | |
YRDR03* | 中国China | 2017-04-27 | MN939034 | Shanty | 美国United States | 2010-11-03 | HQ879843 | |
YRDR12* | 中国China | 2017-04-27 | MN939035 |
表2
分子钟模型和树先验不同组合的对数边际似然值"
分子钟模型Molecular clock model | 树先验模型Tree prior | 对数边际似然值Log marginal likelihood |
---|---|---|
不相关对数正态分布的宽松分子钟 Uncorrelated lognormal relaxed clock | 贝叶斯天际线 Bayesian skyline | -3347.81/-3347.15 |
不相关对数正态分布的宽松分子钟 Uncorrelated lognormal relaxed clock | 恒定大小 Constant size | -3348.44/-3349.36 |
不相关对数正态分布的宽松分子钟 Uncorrelated lognormal relaxed clock | 指数增长 Exponential growth | -3353.59/-3355.58 |
严格分子钟 Strict clock | 贝叶斯天际线Bayesian skyline | -3369.38/-3366.75 |
严格分子钟 Strict clock | 恒定大小Constant size | -3368.88/-3365.99 |
严格分子钟 Strict clock | 指数增长Exponential growth | -3372.35/-3371.24 |
表4
ToCV地理结构的系统发育-性状关联检验"
统计 Statistic | 观察平均值(95%置信区间) Observed mean (95% CI) | 零假设平均值(95%置信区间) Null mean (95% CI) | P值 P-value |
---|---|---|---|
AI | 0.20 (0.02-0.44) | 8.03 (7.36-8.71) | <0.001 |
PS | 12.24 (11.00-14.00) | 50.11 (48.24-51.68) | <0.001 |
MC (巴西Brail) | 1.93 (1.00-2.00) | 1.00 (1.00-1.00) | <0.01 |
MC (中国大陆Mainland China) | 32.77 (20.00-50.00) | 3.64 (2.80-5.60) | <0.01 |
MC (希腊Greece) | 2.87 (2.00-4.00) | 1.18 (1.00-1.83) | <0.01 |
MC (毛里求斯Mauritius) | 2.00 (2.00-2.00) | 1.00 (1.00-1.00) | <0.01 |
MC (韩国South Korea) | 7.00 (7.00-7.00) | 1.47 (1.10-2.01) | <0.01 |
MC (西班牙Spain) | 4.17 (4.00-5.00) | 1.06 (1.00-1.25) | <0.01 |
MC (中国台湾Taiwan, China) | 2.00 (2.00-2.00) | 1.00 (1.00-1.00) | <0.01 |
MC (土耳其Turkey) | 10.39 (6.00-14.00) | 1.49 (1.03-2.05) | <0.01 |
MC (美国United States) | 3.25 (2.00-5.00) | 1.05 (1.00-1.17) | <0.01 |
[1] |
FIALLO-OLIVÉ E, NAVAS-CASTILLO J . Tomato chlorosis virus, an emergent plant virus still expanding its geographical and host ranges. Molecular Plant Pathology, 2019,20(9):1307-1320.
doi: 10.1111/mpp.12847 pmid: 31267719 |
[2] |
WINTERMANTEL W M, WISLER G C . Vector specificity, host range, and genetic diversity of tomato chlorosis virus. Plant Disease, 2006,90(6):814-819.
doi: 10.1094/PD-90-0814 pmid: 30781245 |
[3] |
PEREIRA L, LOURENÇÃO A, SALAS F J, BENTO J M, REZENDE J A, PEÑAFLOR M F . Infection by the semi-persistently transmitted tomato chlorosis virus alters the biology and behaviour of Bemisia tabaci on two potato clones. Bulletin of Entomological Research, 2019,109(5):604-611.
doi: 10.1017/S0007485318000974 pmid: 30616696 |
[4] |
WISLER G C, LI R H, LIU H Y, LOWRY D S, DUFFUS J E . Tomato chlorosis virus: A new whitefly-transmitted, phloem-limited, bipartite closterovirus of tomato. Phytopathology, 1998,88(5):402-409.
doi: 10.1094/PHYTO.1998.88.5.402 pmid: 18944918 |
[5] |
MARTINEZ-ZUBIAUR Y, FIALLO-OLIVE E, CARRILLO-TRIPP J, RIVERA-BUSTAMANTE R . First report of tomato chlorosis virus infecting tomato in single and mixed infections with tomato yellow leaf curl virus in Cuba. Plant Disease, 2008,92(5):836.
doi: 10.1094/PDIS-92-5-0836B pmid: 30769606 |
[6] | MACEDO M A, BARRETO S S, HALLWASS M, INOUE-NAGATA A K . High incidence of tomato chlorosis virus alone and in mixed infection with begomoviruses in two tomato fields in the Federal District and Goiás state, Brazil. Tropical Plant Pathology, 2014,39(6):449-452. |
[7] | DAVINO S, DAVINO M, BELLARDI M G, AGOSTEO G E . Pepino mosaic virus and tomato chlorosis virus causing mixed infection in protected tomato crops in Sicily. Phytopathologia Mediterranea, 2008,47(1):35-41. |
[8] |
LEFKOWITZ E J, DEMPSEY D M, HENDRICKSON R C, ORTON R J, SIDDELL S G, SMITH D B . Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Research, 2018,46(Database issue):D708-D717.
doi: 10.1093/nar/gkx932 |
[9] |
ALZHANOVA D V, NAPULI A J, CREAMER R, DOLJA V V . Cell-to-cell movement and assembly of a plant closterovirus: Roles for the capsid proteins and Hsp70 homolog. The EMBO Journal, 2001,20(24):6997-7007.
doi: 10.1093/emboj/20.24.6997 pmid: 11742977 |
[10] |
DOLJA V V, KREUZE J F, VALKONEN J P T . Comparative and functional genomics of closteroviruses. Virus Research, 2006,117(1):38-51.
doi: 10.1016/j.virusres.2006.02.002 pmid: 16529837 |
[11] |
SATYANARAYANA T, GOWDA S, MAWASSI M, ALBIACH- MARTÍ M R, AYLLÓN M A, ROBERTSON C, GARNSEY S M, DAWSON W O . Closterovirus encoded HSP70 homolog and p61 in addition to both coat proteins function in efficient virion assembly. Virology, 2000,278(1):253-265.
doi: 10.1006/viro.2000.0638 pmid: 11112500 |
[12] |
AGRANOVSKY A A, LESEMANN D E, MAISS E, HULL R, ATABEKOV J G . “Rattlesnake” structure of a filamentous plant RNA virus built of two capsid proteins. Proceedings of the National Academy of Sciences of the United States of America, 1995,92(7):2470-2473.
doi: 10.1073/pnas.92.7.2470 pmid: 7708667 |
[13] |
ZHAO L M, LI G, GAO Y, LIU Y J, SUN G Z, ZHU X P . Molecular detection and complete genome sequences of tomato chlorosis virus isolates from infectious outbreaks in China. Journal of Phytopathology, 2014,162(10):627-634.
doi: 10.1111/jph.12236 |
[14] |
ZHAO R N, WANG R, WANG N, FAN Z F, ZHOU T, SHI Y C, CHAI M . First report of tomato chlorosis virus in China. Plant Disease, 2013,97(8):1123.
doi: 10.1094/PDIS-12-12-1163-PDN pmid: 30722472 |
[15] | 汤亚飞, 何自福, 佘小漫, 蓝国兵 . 侵染广东番茄的番茄褪绿病毒分子鉴定. 植物保护, 2017,43(2):133-137. |
TANG Y F, HE Z F, SHE X M, LAN G B . Molecular identification of tomato chlorosis virus infecting tomato in Guangdong Province. Plant Protection, 2017,43(2):133-137. (in Chinese) | |
[16] | 王翠琳, 冯佳, 孙晓辉, 王少立, 赵静, 刘金亮, 竺晓平 . 北方四省区番茄褪绿病毒的分子鉴定. 植物保护, 2017,43(2):141-145. |
WANG C L, FENG J, SUN X H, WANG S L, ZHAO J, LIU J L, ZHU X P . Molecular identification of tomato chlorosis virus from four provinces or autonomous region in northern China. Plant Protection, 2017,43(2):141-145. (in Chinese) | |
[17] | 刘微, 史晓斌, 唐鑫, 张宇, 张德咏, 周序国, 刘勇 . 云南番茄褪绿病毒和番茄黄化曲叶病毒复合侵染的分子鉴定. 园艺学报, 2018,45(3):552-560. |
LIU W, SHI X B, TANG X, ZHANG Y, ZHANG D Y, ZHOU X G, LIU Y . Molecular Identification of tomato chlorosis virus and tomato yellow leaf curl virus in Yunnan Province. Acta Horticulturae Sinica, 2018,45(3):552-560. (in Chinese) | |
[18] | 王雪忠, 张战泓, 郑立敏, 唐鑫, 史晓斌, 刘勇 . 番茄褪绿病毒在湖南省首次发生. 中国蔬菜, 2018(8):27-31. |
WANG X Z, ZHANG Z H, ZHENG L M, TANG X, SHI X B, LIU Y . First report of the cccurance of tomato chlorosis virus in Hunan Province. China Vegetables, 2018(8):27-31. (in Chinese) | |
[19] |
WEI K, LI Y . Global evolutionary history and spatio-temporal dynamics of dengue virus type 2. Scientific Reports, 2017,7:45505.
doi: 10.1038/srep45505 pmid: 28378782 |
[20] |
LIU D, SHI W, SHI Y, WANG D, XIAO H, LI W, BI Y, WU Y, LI X, YAN J , et al. Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: Phylogenetic, structural, and coalescent analyses. The Lancet, 2013,381(9881):1926-1932.
doi: 10.1016/S0140-6736(13)60938-1 |
[21] |
FAYE O, FREIRE C C, IAMARINO A, FAYE O, DE OLIVEIRA J V, DIALLO M, ZANOTTO P M, SALL A A . Molecular evolution of Zika virus during its emergence in the 20 th century . PLoS Neglected Tropical Diseases, 2014,8(1):e2636.
doi: 10.1371/journal.pntd.0002636 pmid: 24421913 |
[22] |
YASAKA R, OHBA K, SCHWINGHAMER M W, FLETCHER J, OCHOA-CORONA F M, THOMAS J E, HO S Y, GIBBS A J, OHSHIMA K . Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand. Journal of General Virology, 2015,96(3):701-713.
doi: 10.1099/jgv.0.000007 |
[23] |
YASAKA R, FUKAGAWA H, IKEMATSU M, SODA H, KORKMAZ S, GOLNARAGHI A, KATIS N, HO S Y W, GIBBS A J, OHSHIMA K . The timescale of emergence and spread of turnip mosaic potyvirus. Scientific Reports, 2017,7:4240.
doi: 10.1038/s41598-017-01934-7 pmid: 28652582 |
[24] |
DUAN G, ZHAN F, DU Z, HO S Y W, GAO F . Europe was a hub for the global spread of potato virus S in the 19th century. Virology, 2018,525:200-204.
doi: 10.1016/j.virol.2018.09.022 pmid: 30296680 |
[25] |
GAO F, LIU X, DU Z, HOU H, WANG X, WANG F, YANG J . Bayesian phylodynamic analysis reveals the dispersal patterns of tobacco mosaic virus in China. Virology, 2019,528:110-117.
doi: 10.1016/j.virol.2018.12.001 pmid: 30594790 |
[26] |
ZHANG D, GAO F, JAKOVLIĆ I, ZOU H, ZHANG J, LI W X, WANG G T . PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 2020,20(1):348-355.
doi: 10.1111/1755-0998.13096 pmid: 31599058 |
[27] |
KATOH K, STANDLEY D M . MAFFT Multiple Sequence Alignment Software Version 7: Improvements in performance and usability. Molecular Biology and Evolution, 2013,30(4):772-780.
doi: 10.1093/molbev/mst010 |
[28] |
SIRONI M, CAGLIANI R, FORNI D, CLERICI M . Evolutionary insights into host-pathogen interactions from mammalian sequence data. Nature Reviews Genetics, 2015,16(4):224-236.
doi: 10.1038/nrg3905 pmid: 25783448 |
[29] |
HUSON D H . SplitsTree: Analyzing and visualizing evolutionary data. Bioinformatics, 1998,14(1):68-73.
doi: 10.1093/bioinformatics/14.1.68 pmid: 9520503 |
[30] |
MARTIN D P, MURRELL B, GOLDEN M, KHOOSAL A, MUHIRE B . RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution, 2015, 1(1): vev003.
doi: 10.1093/ve/vev003 pmid: 27774277 |
[31] |
MURRAY G G R, WANG F, HARRISON E M, PATERSON G K, MATHER A E, HARRIS S R, HOLMES M A, RAMBAUT A, WELCH J J . The effect of genetic structure on molecular dating and tests for temporal signal. Methods in Ecology and Evolution, 2016,7(1):80-89.
doi: 10.1111/2041-210X.12466 pmid: 27110344 |
[32] |
DRUMMOND A J, SUCHARD M A, XIE D, RAMBAUT A . Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 2012,29(8):1969-1973.
doi: 10.1093/molbev/mss075 |
[33] |
DUCHÊNE S, DUCHÊNE D, HOLMES E C, HO S Y W . The performance of the date-randomization test in phylogenetic analyses of time-structured virus data. Molecular Biology and Evolution, 2015,32(7):1895-1906.
doi: 10.1093/molbev/msv056 pmid: 25771196 |
[34] |
KALYAANAMOORTHY S, MINH B Q, WONG T K F, VON HAESELER A, JERMIIN L S . ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 2017,14(6):587-589.
doi: 10.1038/nmeth.4285 pmid: 28481363 |
[35] |
BAELE G, LEMEY P, BEDFORD T, RAMBAUT A, SUCHARD M A, ALEKSEYENKO A V . Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Molecular Biology and Evolution, 2012,29(9):2157-2167.
doi: 10.1093/molbev/mss084 |
[36] |
PARKER J, RAMBAUT A, PYBUS O G . Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 2008,8(3):239-246.
doi: 10.1016/j.meegid.2007.08.001 pmid: 17921073 |
[37] |
刘勇, 李凡, 李月月, 张松柏, 高希武, 谢艳, 燕飞, 张安盛, 戴良英, 程兆榜 , 等. 侵染我国主要蔬菜作物的病毒种类、分布与发生趋势. 中国农业科学, 2019,52(2):239-261.
doi: 10.3864/j.issn.0578-1752.2019.02.005 |
LIU Y, LI F, LI Y Y, ZHANG S B, GAO X W, XIE Y, YAN F, ZHANG A S, DAI L Y, CHENG Z B ,et al. Identification, distribution and occurrence of viruses in the main vegetables of China. Scientia Agricultura Sinica, 2019,52(2):239-261. (in Chinese)
doi: 10.3864/j.issn.0578-1752.2019.02.005 |
|
[38] |
DUFFY S, SHACKELTON L A, HOLMES E C . Rates of evolutionary change in viruses: Patterns and determinants. Nature Reviews Genetics, 2008,9(4):267-276.
doi: 10.1038/nrg2323 pmid: 18319742 |
[39] |
RIEUX A, BALLOUX F . Inferences from tip-calibrated phylogenies: A review and a practical guide. Molecular Ecology, 2016,25(9):1911-1924.
doi: 10.1111/mec.13586 pmid: 26880113 |
[40] |
GAO F, JIN J, ZOU W, LIAO F, SHEN J . Geographically driven adaptation of chilli veinal mottle virus revealed by genetic diversity analysis of the coat protein gene. Archives of Virology, 2016,161(5):1329-1333.
doi: 10.1007/s00705-016-2761-7 pmid: 26831930 |
[41] |
GAO F, ZOU W, XIE L, ZHAN J . Adaptive evolution and demographic history contribute to the divergent population genetic structure of potato virus Y between China and Japan. Evolutionary Applications, 2017,10(4):379-390.
doi: 10.1111/eva.12459 pmid: 28352297 |
[42] |
谢丽雪, 张小艳, 郑姗, 张立杰, 李韬 . 侵染西番莲的夜来香花叶病毒的分子鉴定及特异性检测. 中国农业科学, 2017,50(24):4725-4734.
doi: 10.3864/j.issn.0578-1752.2017.24.006 |
XIE L X, ZHANG X Y, ZHENG S, ZHANG L J, LI T . Molecular identification and specific detection of telosma mosaic virus infecting passion fruit. Scientia Agricultura Sinica, 2017,50(24):4725-4734. (in Chinese)
doi: 10.3864/j.issn.0578-1752.2017.24.006 |
[1] | 丁天波, 刘晓蓓, 李洁, 魏可可, 褚栋. 番茄褪绿病毒实时荧光定量PCR检测技术的建立[J]. 中国农业科学, 2018, 51(10): 2013-2022. |
|