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A New Method to Obtain the Complete Genome Sequence of Multiple-Component Circular ssDNA Viruses by Transcriptome Analysis

文献类型： 外文期刊

作者： Yu, Nai-tong 1 ; Zhang, Yu-liang 1 ; Wang, Jian-hua 1 ; Liu, Zhi-xin 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Key Lab Biol & Genet Resources Trop Crops, Minist Agr & Rural Affairs, Haikou, Hainan, Peoples R China

2.Hainan Key Lab Trop Microbe Resources, Haikou, Hainan, Peoples R China

关键词： multi-component; DNA virus; nanovirids; transcriptomic sequencing; genome assembly

期刊名称：FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY （ 影响因子：5.89； 五年影响因子：5.973 ）

ISSN： 2296-4185

年卷期： 2020 年 8 卷

页码：

收录情况： SCI

摘要： Circular single-stranded DNA (ssDNA) viruses are widely distributed globally, infecting diverse hosts ranging from bacteria, archaea, and eukaryotes. Among these, the genome ofBanana bunchy top virus(BBTV) comprises at least six circular, ssDNA components that are similar to 1 kb in length. Its genome is usually amplified and obtained at the DNA level. However, RNA-based techniques to obtain the genome sequence of such multi-component viruses have not been reported. In this study, transcriptome sequencing analysis showed that the full-length of BBTV each genomic component was transcribed into viral mRNA (vmRNA). Accordingly, the near-complete genome of BBTV B2 isolate was assembled using transcriptome sequencing data from virus-infected banana leaves. Assembly analysis of BBTV-derived reads indicated that the full-length sequences were obtained for DNA-R, DNA-U3, DNA-S, DNA-M, DNA-N, NewS2, and Sat4 components, while two gaps (73 and 25 nt) missing in the DNA-C component which was further filled by reverse transcription-PCR (RT-PCR). The RT-qPCR analysis indicated that the vmRNA levels of coding regions were 3.19-103.53 folds higher than those of non-coding regions, implying that the integrity of genome assembly depended on the transcription level of non-coding region. In conclusion, this study proposes a new approach to obtain the genome of nanovirids, and provides insights for studying the transcriptional mechanism of the familyNanoviridae,Genomoviridae, andGeminiviridae.

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