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Ligustrum Virus A Isolates from Syringa lindl: Identification and Whole Genome Sequence Analysis
WANGYunxuan, LIULi, SUNChunhui, LUShuhao, LIANGYuqing, CUIWenli, GAOJiayi, LIYongqiang
Ligustrum Virus A Isolates from Syringa lindl: Identification and Whole Genome Sequence Analysis
To identify and characterize the candidate viruses infecting Beijing lilac (Syringa lindl) associated with the symptoms of leaf chlorosis, mosaic and leaf curling, small RNA deep sequencing and RT-PCR were conducted with the diseased leaf samples. Ligustrum virus A (LVA) was detected and the complete genome sequences of two isolates were obtained. The Beijing lilac isolate LVA-NXY is 8488 nt in length, while the isolate LVA-HLG is 8478 nt. Sequence similarity analysis showed that LVA-NXY and LVA-HLG were most similar to the LVA-DBLQ isolate from Forsythia suspensa in Shenyang, China. No recombination events were detected among the seven reported LVA isolates. The phylogenetic tree based on the genome sequences indicated that LVA-NXY and LVA-HLG clustered together with LVA-DBLQ and the Syringa vulgaris isolate LVA-DX in the same branch, showing a close phylogenetic relationship. This study reports the complete genome sequence of ligustrum virus A infecting Beijing lilac and explores the molecular characteristics and evolutionary relationships of the virus which provides a theoretical basis for the study of genetic variation and the control of lilac virus disease.
Syringa lindl / Ligustrum virus A / small RNA / genome / sequence analysis / molecular characteristics / phylogenetic relationship {{custom_keyword}} /
表1 本研究中所用引物 |
引物名称 | 序列(5′-3′) | 引物位置 | 产物大小/bp |
---|---|---|---|
LVA-NXY-F | ATGTCGAATCCACCGGAAGG | 7232~7252 | 290 |
LVA-NXY-R | GATGCCCCAAAGGATGTCAG | 7502~7522 | |
LVA-HLG-F | GAGTAACCAGCCTCCGCCTC | 7281~7300 | 310 |
LVA-HLG-R | GACCCTCCAACTTGACCGC | 7573~7591 | |
LVA-NXY-F1 | CCATTCACATCCGGCATG | 282~300 | 3169 |
LVA-NXY-R1 | GCTGCCGTCCAACAAACAC | 3431~3451 | |
LVA-NXY-F2 | TTTGTTGGACGGCAGCAC | 3434~3452 | 3081 |
LVA-NXY-R2 | CACAGCAATTCCCCAACCTC | 6495~6515 | |
LVA-NXY-F3 | TGGGGAACTGCTGTGCGCTC | 6500~6520 | 1748 |
LVA-NXY-R3 | CATACGAGGAAGTCCCGCCCC | 8227~8248 | |
LVA-HLG-F1 | GCAATGCCGCACTCTCATCC | 281~301 | 3498 |
LVA-HLG-R1 | GCTGACCTCTGACCCCTCGAAG | 3195~3217 | |
LVA-HLG-F2 | GAGGGGTCAGAGGTCAGCGTG | 3199~3220 | 3067 |
LVA-HLG-R2 | GCGCACAATGTGTACTCGTCGAC | 6243~6266 | |
LVA-HLG-F3 | CATTGTGCGCTCGGGATTTAC | 6251~6276 | 1979 |
LVA-HLG-R3 | GATACACTCTATAGCAGCGATGGC | 8278~8230 | |
NXY-5RACE-out | GGTGGATAGACAAGTGTAGCAAG | 679~701 | 701 |
NXY-5RACE-in | CAAGGTCTCTCAAAGTAGAATCTGC | 541~565 | 565 |
NXY-3RACE-out | GTCAAAGAACTTGCAGGTGTGAG | 7741~7763 | 748 |
NXY-3RACE-in | CCGCTATGGGTTTCAACTACAAC | 7838~7860 | 651 |
HLG-5RACE-out | GGATCTCATCATGCAAGAACACG | 594~616 | 616 |
HLG-5RACE-in | CCTGGATTTATCTGCACTCGTGAC | 445~468 | 468 |
HLG-3RACE-out | GTTCGTCTGTTATTGCGCTAGTGC | 7632~7655 | 847 |
HLG-3RACE-in | CAACTACAATACTCGGTTCGCAG | 7848~7870 | 631 |
表2 LVA-NXY与其他LVA分离物序列一致性对比(核苷酸/氨基酸) |
分离物 | LVA-DBLQ | LVA-DX | LVA-Sob | LVA-SK | LVA-SNU |
---|---|---|---|---|---|
开放阅读框1 ORF1 | 95.41/98.07 | 81.33/93.24 | 72.94/81.91 | 72.74/81.81 | 72.24/82.33 |
开放阅读框2 ORF2 | 93.95/95.22 | 82.28/89.57 | 70.19/70.74 | 69.03/69.87 | 64.51/60.61 |
开放阅读框3 ORF3 | 94.77/95.33 | 83.08/92.52 | 74.15/85.98 | 73.23/85.98 | 72.92/84.11 |
开放阅读框4 ORF4 | 95.11/96.67 | 90.76/93.33 | 75.54/73.33 | 74.46/73.33 | 75.00/76.67 |
开放阅读框5 ORF5 | 96.84/98.98 | 86.12/96.26 | 73.70/85.37 | 73.93/85.03 | 74.94/86.39 |
开放阅读框6 ORF6 | 97.51/98.32 | 91.41/95.80 | 79.50/83.19 | 78.67/83.19 | 76.19/77.97 |
表3 LVA-HLG与其他LVA分离物序列一致性对比(核苷酸/氨基酸) |
分离物 | LVA- DBLQ | LVA-DX | LVA-Sob | LVA-SK | LVA-SNU |
---|---|---|---|---|---|
开放阅读框1 ORF1 | 75.68/86.74 | 74.73/86.33 | 71.85/81.05 | 71.60/81.00 | 71.53/80.95 |
开放阅读框2 ORF2 | 70.89/73.91 | 72.19/77.39 | 69.61/71.18 | 69.75/72.05 | 65.95/63.20 |
开放阅读框3 ORF3 | 76.62/89.72 | 76.62/89.72 | 71.38/85.05 | 70.77/85.05 | 71.08/84.11 |
开放阅读框4 ORF4 | 76.09/81.67 | 77.17/86.67 | 70.65/75.00 | 70.65/75.00 | 69.57/73.33 |
开放阅读框5 ORF5 | 77.65/91.50 | 77.54/91.84 | 71.11/85.71 | 72.23/85.37 | 73.48/86.39 |
开放阅读框6 ORF6 | 85.60/90.76 | 84.49/90.76 | 81.16/83.19 | 80.06/83.19 | 77.03/79.66 |
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