Sequence recombination and conservation of Varroa destructor virus-1 and deformed wing virus in field collected honey bees (Apis mellifera).
Sequence recombination and conservation of Varroa destructor virus-1 and deformed wing virus in field collected honey bees (Apis mellifera).
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DOI：
10.1371/journal.pone.0074508
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Possee RD
中科院分区：
文献类型：
--
作者：
Wang H;Xie J;Shreeve TG;Ma J;Pallett DW;King LA;Possee RD
我们使用Illumina技术对来自野外收集的蜜蜂（Apis mellifera）和熊蜂（Bombus pascuorum）的小RNA进行测序。组装sRNA读段，并将所得重叠群用于在GenBank中搜索病毒同源物。匹配 瓦螨 获得了A.意大利但不是 B。pascuorum。进一步分析表明，流行病毒群由VDV-1和5'-DWV-VDV 1-DWV-3 '嵌合体组成。通过RT-PCR、cDNA克隆和桑格测序证实了嵌合体基因组中的重组连接。然后，我们通过使用GenBank序列和本研究中获得的深度测序数据，专注于病毒基因组中保守的短片段（CSF，大小> 25 nt）。大多数CSF位点证实了物种间（GenBank序列）和种群内（本研究数据集）水平的保守性。然而，在GenBank序列中保守的核苷酸位置可能是可变的，在种群内的水平。使用深度测序数据在许多位点观察到高突变率（Pi> 10%），表明序列保守性可能并不总是保持在群体水平。病毒-宿主相互作用和开发针对VDV1/DWV感染的RNAi治疗的策略进行了讨论。
We sequenced small (s) RNAs from field collected honeybees (Apis mellifera) and bumblebees ( Bombus pascuorum ) using the Illumina technology. The sRNA reads were assembled and resulting contigs were used to search for virus homologues in GenBank. Matches with Varroa destructor virus-1 (VDV1) and Deformed wing virus (DWV) genomic sequences were obtained for A. mellifera but not B . pascuorum . Further analyses suggested that the prevalent virus population was composed of VDV-1 and a chimera of 5’-DWV-VDV1-DWV-3’. The recombination junctions in the chimera genomes were confirmed by using RT-PCR, cDNA cloning and Sanger sequencing. We then focused on conserved short fragments (CSF, size > 25 nt) in the virus genomes by using GenBank sequences and the deep sequencing data obtained in this study. The majority of CSF sites confirmed conservation at both between-species (GenBank sequences) and within-population (dataset of this study) levels. However, conserved nucleotide positions in the GenBank sequences might be variable at the within-population level. High mutation rates (Pi>10%) were observed at a number of sites using the deep sequencing data, suggesting that sequence conservation might not always be maintained at the population level. Virus-host interactions and strategies for developing RNAi treatments against VDV1/DWV infections are discussed.
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