An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids

作者：Roberto A. Barrero, Kathryn Napier, J. H. Cunnington, Lia W. Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás Szabó, Simon Bulman, Adam Hunter, L. I. Ward, Mark Whattam, M. Bellgard · 发表于：BMC Bioinformatics · 年份：2017 · DOI：10.1186/s12859-016-1428-4 · 被引用次数：56 · 研究领域：Plant Virus Research Studies、Plant and Fungal Interactions Research、Bacteriophages and microbial interactions

BACKGROUND: Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways. Here we optimise the assembly of viral sequences by using specific small RNA subsets. RESULTS: We sequenced the small RNA fractions of 21 plants held at quarantine glasshouse facilities in Australia and New Zealand. Benchmarking of several de novo assembler tools yielded SPAdes using a kmer of 19 to produce the best assembly outcomes. We also found that de novo assembly using 21-25 nt small RNAs can result in chimeric assemblies of viral sequences and plant host sequences. Such non-specific assemblies can be resolved by using 21-22 nt or 24 nt small RNAs subsets. Among the 21 selected samples, we identified contigs with sequence similarity to 18 viruses and 3 viroids in 13 samples. Most of the viruses were assembled using only 21-22 nt long virus-derived siRNAs (viRNAs), except for one Citrus endogenous pararetrovirus that was more efficien...