Presence of Diverse Sugarcane Bacilliform Viruses Infecting Sugarcane in China Revealed by Pairwise Sequence Comparisons and Phylogenetic Analysis
Presence of Diverse Sugarcane Bacilliform Viruses Infecting Sugarcane in China Revealed by Pairwise Sequence Comparisons and Phylogenetic Analysis
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DOI：
10.5423/ppj.oa.08.2018.0156
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发表时间：
2019-02-01
影响因子：
2.3
通讯作者：
Gao, San-Ji
中科院分区：
文献类型：
--
作者：
Ahmad, Kashif;Sun, Sheng-Ren;Gao, San-Ji
甘蔗杆状病毒属杆状病毒科，是侵染甘蔗的一种重要的DNA病毒复合体。为了探索侵染甘蔗的甘蔗巴纳病毒复合体的遗传多样性，利用已发表的针对甘蔗病毒基因组逆转录酶/核糖核酸酶H(RT/RNaseH)区的引物SCBV-F和SCBV-R，对采自福建、云南和海南的392份甘蔗叶片样本进行了SCBV-F和SCBV-R的聚合酶链式反应检测。从63份SCBV阳性样本中克隆了111个扩增片段(726个碱基)，并对其进行了序列测定。根据本研究的SCBV序列和34个已发表的代表18个不同系统群或基因型(SCBV-A至-R)的序列，构建了相邻连接的系统发育树。从SCBV-A到SCBV-T，所有经SCBV检测的分离物均可分为20个SCBV系统发育群。在本研究中报道的9个SCBV系统群中，提出了两个新的系统群：SCBV-S和SCBV-T，它们在RT/RNaseH区序列同源性为90.0-93.2%，遗传距离为0.07-0.11。与已发表的SCBV系统群间序列同源性为57.6~92.2%，遗传距离为0.09~0.66；SCBV-T与已发表的SCBV系统群序列同源性为58.4~90.0%，遗传距离为0.11~0.63。此外，甘蔗杆状MO病毒和甘蔗杆状IM病毒是中国首次报道，它们最初分别聚在甘蔗杆状病毒-E和甘蔗杆状病毒-F的系统发育群中。我们的发现将有助于理解感染甘蔗的Badna病毒物种复合体中存在的遗传异质性水平。
Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H. region, are proposed. SCBV-S had 57.6- 92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.