| Literature DB >> 24131521 |
Zhaobang Cheng, Shuo Li, Ruizhen Gao, Feng Sun, Wancai Liu, Guohui Zhou, Jianxiang Wu, Xueping Zhou, Yijun Zhou1.
Abstract
BACKGROUND: Rice and maize dwarf diseases caused by the newly introduced Southern rice black-streaked dwarf virus (SRBSDV) have led to severe economic losses in South China in recent years. The distribution and diversity of SRBSDV have not been investigated in the main rice and maize growing areas in China. In this study, the distribution of SRBSDV in China was determined by using reverse transcription-polymerase chain reaction (RT-PCR).Entities:
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Year: 2013 PMID: 24131521 PMCID: PMC4015479 DOI: 10.1186/1743-422X-10-307
Source DB: PubMed Journal: Virol J ISSN: 1743-422X Impact factor: 4.099
Figure 1RT-PCR identification of SRBSDV and RBSDV isolates from rice and maize samples in China. A: Simultaneous detection of SRBSDV and RBSDV from infected plant samples. Line M, DNA Markers; line 1, RBSDV positive control; line 2, SRBSDV positive control; line 3–24, rice or maize samples from fields; line 25, negative control. B: RT-PCR analysis of SRBSDV outer CP genes. Line M, DNA Markers; Line 1–14, partial SRBSDV isolates.
RT-PCR detection of SRBSDV and RBSDV in samples collected from different geographic regions in China
| Shandong | 7 | 87 | 18 | 0 | 69 | 0 | 0.00 | 18 | 17 | 69 | 46 | 72.41 | 0 |
| Anhui | 23 | 273 | 256 | 119 | 17 | 0 | 43.59 | 256 | 85 | 17 | 0 | 31.14 | 0 |
| Hunan | 15 | 141 | 141 | 126 | 0 | 0 | 89.36 | 141 | 0 | 0 | 0 | 0.00 | 0 |
| Jiangxi | 17 | 192 | 192 | 134 | 0 | 0 | 69.79 | 192 | 23 | 0 | 0 | 11.98 | 0 |
| Jiangsu | 22 | 235 | 231 | 5 | 4 | 0 | 2.13 | 231 | 130 | 4 | 4 | 57.02 | 0 |
| Guangxi | 29 | 493 | 490 | 412 | 3 | 0 | 83.57 | 490 | 0 | 3 | 0 | 0.00 | 0 |
| Guangdong | 22 | 439 | 439 | 372 | 0 | 0 | 84.74 | 439 | 0 | 0 | 0 | 0.00 | 0 |
| Zhejiang | 7 | 38 | 32 | 26 | 6 | 2 | 73.68 | 32 | 5 | 6 | 0 | 13.16 | 0 |
| Fujian | 9 | 140 | 134 | 119 | 6 | 6 | 89.29 | 134 | 0 | 6 | 0 | 0.00 | 0 |
| Hubei | 13 | 65 | 65 | 56 | 0 | 0 | 86.15 | 65 | 0 | 0 | 0 | 0.00 | 0 |
| Sichuan | 1 | 11 | 11 | 1 | 0 | 0 | 9.09 | 11 | 0 | 0 | 0 | 0.00 | 0 |
| Yunnan | 10 | 48 | 48 | 31 | 0 | 0 | 64.58 | 48 | 0 | 0 | 0 | 0.00 | 0 |
| Shanghai | 5 | 12 | 12 | 0 | 0 | 0 | 0.00 | 12 | 10 | 0 | 0 | 83.33 | 0 |
| Chongqing | 3 | 18 | 18 | 13 | 0 | 0 | 72.22 | 18 | 0 | 0 | 0 | 0.00 | 0 |
| Guizhou | 6 | 74 | 74 | 69 | 0 | 0 | 93.24 | 74 | 0 | 0 | 0 | 0.00 | 0 |
| Hainan | 3 | 133 | 133 | 54 | 0 | 0 | 40.60 | 133 | 0 | 0 | 0 | 0.00 | 0 |
| Hebei | 2 | 5 | 0 | 0 | 5 | 0 | 0.00 | 0 | 0 | 5 | 5 | 100.00 | 0 |
| Total | 194 | 2404 | 2294 | 1537 | 110 | 8 | 64.27 | 2294 | 270 | 110 | 55 | 13.52 | 0 |
aTotal 2404 samples were collected from different geographic areas in China between 2009 and 2010.
Figure 2Distribution of SRBSDV in China between 2009 and 2010. Locations (counties) where SRBSDV was found are marked as gray shadows.
Nucleotide (top right) and amino acid (bottom left) sequence identities (%) of outer CP genes among SRBSDV isolates from China
| FJYA4 | | 98.6 | 99.1 | 98.2 | 98.6 | 98.7 | 98.6 | 98 | 99.1 | 99.3 | 98.4 | 99.1 | 98.9 | 98.9 | 99.3 |
| CQFD1 | 98.6 | | 98.9 | 98 | 98.4 | 98.6 | 98.4 | 97.8 | 98.9 | 99.1 | 98.2 | 98.9 | 98.7 | 98.7 | 99.1 |
| AHDZ2 | 99.1 | 98.9 | | 98.6 | 98.9 | 99.1 | 98.9 | 98.4 | 99.5 | 99.6 | 98.7 | 99.5 | 99.3 | 99.3 | 99.6 |
| ZJWY1 | 98.2 | 98 | 98.6 | | 99.1 | 99.3 | 99.1 | 98.6 | 98.6 | 98.7 | 98.9 | 98.6 | 98.4 | 98.7 | 98.7 |
| ZJDY4 | 98.6 | 98.4 | 98.9 | 99.1 | | 99.6 | 99.5 | 98.9 | 98.9 | 99.1 | 99.3 | 98.9 | 98.7 | 99.1 | 99.1 |
| ZJDY2 | 98.7 | 98.6 | 99.1 | 99.3 | 99.6 | | 99.6 | 99.1 | 99.1 | 99.3 | 99.5 | 99.1 | 98.9 | 99.3 | 99.3 |
| YNFN1 | 98.6 | 98.4 | 98.9 | 99.1 | 99.5 | 99.6 | | 98.9 | 98.9 | 99.1 | 99.3 | 98.9 | 98.7 | 99.1 | 99.1 |
| JXNC135 | 98.0 | 97.8 | 98.4 | 98.6 | 98.9 | 99.1 | 98.9 | | 98.4 | 98.6 | 98.7 | 98.4 | 98.2 | 98.6 | 98.6 |
| JSXY1 | 99.1 | 98.9 | 99.5 | 98.6 | 98.9 | 99.1 | 98.9 | 98.4 | | 99.6 | 98.7 | 99.5 | 99.3 | 99.3 | 99.6 |
| HNCX1 | 99.3 | 99.1 | 99.6 | 98.7 | 99.1 | 99.3 | 99.1 | 98.6 | 99.6 | | 98.9 | 99.6 | 99.5 | 99.5 | 99.8 |
| HNCJ1 | 98.4 | 98.2 | 98.7 | 98.9 | 99.3 | 99.5 | 99.3 | 98.7 | 98.7 | 98.9 | | 98.7 | 98.6 | 98.9 | 98.9 |
| HBCY6 | 99.1 | 98.9 | 99.5 | 98.6 | 98.9 | 99.1 | 98.9 | 98.4 | 99.5 | 99.6 | 98.7 | | 99.3 | 99.3 | 99.6 |
| GZSD1 | 98.9 | 98.7 | 99.3 | 98.4 | 98.7 | 98.9 | 98.7 | 98.2 | 99.3 | 99.5 | 98.6 | 99.3 | | 99.1 | 99.5 |
| GXLC4 | 98.9 | 98.7 | 99.3 | 98.7 | 99.1 | 99.3 | 99.1 | 98.6 | 99.3 | 99.5 | 98.9 | 99.3 | 99.1 | | 99.5 |
| GDSX1 | 99.3 | 99.1 | 99.6 | 98.7 | 99.1 | 99.3 | 99.1 | 98.6 | 99.6 | 99.8 | 98.9 | 99.6 | 99.5 | 99.5 |
FJYA4: Yongan, Fujian province; CQFD1: Fengdu, Chongqing province; AHDZ2: Dongzhi, Anhui province; ZJWY1: Wuyi, Zhejiang province. ZJDY4 and ZJDY2: Dongyang, Zhejiang province; YNFN1: Funing, Yunnan province; JXNC135: Nanchang, Jiangxi province; JSXY1: Xinyi, Jiangsu province; HNCX1: Chenxi, Hunan province; HNCJ1: Changjiang, Hainan province; HBCY6: Chongyang, Hubei province; GZSD1: Sandu, Guizhou province; GXLC4: Luocheng, Guangxi province; GDSX1: Suixi, Guangdong province. The number after abbreviation was the numbering of isolate samples. ZJDY4 and ZJDY2 isolates were from maize, and others were from rice.
Figure 3Phylogenetic analysis of SRBSDV based on outer CP gene nucleotide sequence showing the relationships of SRBSDV isolates from different geographic regions in China. Trees were constructed by MEGA 4.0 using the neighbor-joining method with 1000 bootstrap replications (bootstrap values were showed where >50%). Trees were rooted with RBSDV segment 10 (AY050489) as outgroup, and two reported SRBSDV isolates (EU784840, EU523360) were also included as references. Bars indicated numbers of nucleotide substitutions per site.