全面分析长尾叩头虫核型多角体病毒的单分子测序衍生的完整基因组和全转录组。
Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus.
机构信息
Department of Molecular Biology, Genentech Inc., 1 DNA WAY, South San Francisco, CA, 94080, USA.
AgriGenome Labs Private Limited, 501, SCK01 Building, SmartCity Kochi, Infopark Road, Kakkanad, Kochi, Kerala, 682 042, India.
出版信息
Sci Rep. 2018 Jun 12;8(1):8924. doi: 10.1038/s41598-018-27084-y.
We sequenced the Hyposidra talaca NPV (HytaNPV) double stranded circular DNA genome using PacBio single molecule sequencing technology. We found that the HytaNPV genome is 139,089 bp long with a GC content of 39.6%. It encodes 141 open reading frames (ORFs) including the 37 baculovirus core genes, 25 genes conserved among lepidopteran baculoviruses, 72 genes known in baculovirus, and 7 genes unique to the HytaNPV genome. It is a group II alphabaculovirus that codes for the F protein and lacks the gp64 gene found in group I alphabaculovirus viruses. Using RNA-seq, we confirmed the expression of the ORFs identified in the HytaNPV genome. Phylogenetic analysis showed HytaNPV to be closest to BusuNPV, SujuNPV and EcobNPV that infect other tea pests, Buzura suppressaria, Sucra jujuba, and Ectropis oblique, respectively. We identified repeat elements and a conserved non-coding baculovirus element in the genome. Analysis of the putative promoter sequences identified motif consistent with the temporal expression of the genes observed in the RNA-seq data.
我们使用 PacBio 单分子测序技术对 Hyposidra talaca NPV（HytaNPV）双链环状 DNA 基因组进行了测序。我们发现，HytaNPV 基因组长 139089bp，GC 含量为 39.6%。它编码 141 个开放阅读框（ORF），包括 37 个杆状病毒核心基因、25 个鳞翅目杆状病毒保守基因、72 个已知杆状病毒基因和 7 个 HytaNPV 基因组特有的基因。它是一个 II 组α杆状病毒，编码 F 蛋白，缺乏 I 组α杆状病毒病毒中发现的 gp64 基因。通过 RNA-seq，我们证实了在 HytaNPV 基因组中鉴定的 ORF 的表达。系统发育分析表明，HytaNPV 与感染其他茶虫的 BusuNPV、SujuNPV 和 EcobNPV 最为接近，分别感染茶尺蠖、酸枣、枣镰翅野螟。我们在基因组中鉴定了重复元件和保守的非编码杆状病毒元件。对假定启动子序列的分析确定了与 RNA-seq 数据中观察到的基因的时间表达一致的基序。
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