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

BMC Bioinformatics

Methodology Article

Matthew I. Bellgard¹  Tamas Szabo¹  Roberto A. Barrero¹  Adam Hunter¹  Kathryn R. Napier²  Mark Whattam³  James Cunnington³  Lisa Ward⁴  Lia Liefting⁴  Sandi Keenan⁵  Rebekah A. Frampton⁵  Simon Bulman⁵ 

[1] Centre for Comparative Genomics, Murdoch University, 6150, Murdoch, WA, Australia;Centre for Comparative Genomics, Murdoch University, 6150, Murdoch, WA, Australia;Plant Biosecurity Cooperative Research Centre, 2617, Canberra, ACT, Australia;Department of Agriculture and Water Resources, 3064, Mickleham, VIC, Australia;Ministry for Primary Industries, Wellington, New Zealand;The New Zealand Institute for Plant Food and Research Limited, Better Border Biosecurity, 7608, Lincoln, New Zealand;

关键词: Bioinformatics;    Plant biosecurity;    Next generation sequencing;    Plant viruses and viroids;    Quarantine;    viRNAs;    Virus diagnosis;    Yabi;    Small RNA-Seq;    Workflows;   

DOI  :  10.1186/s12859-016-1428-4

 received in 2016-07-12, accepted in 2016-12-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundDetection 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.ResultsWe 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 efficiently assembled using 24 nt long viRNAs. All three viroids found in this study were fully assembled using either 21–22 nt or 24 nt viRNAs. Optimised analysis workflows were customised within the Yabi web-based analytical environment. We present a fully automated viral surveillance and diagnosis web-based bioinformatics toolkit that provides a flexible, user-friendly, robust and scalable interface for the discovery and diagnosis of viral pathogens.ConclusionsWe have implemented an automated viral surveillance and diagnosis (VSD) bioinformatics toolkit that produces improved viruses and viroid sequence assemblies. The VSD toolkit provides several optimised and reusable workflows applicable to distinct viral pathogens. We envisage that this resource will facilitate the surveillance and diagnosis viral pathogens in plants, insects and invertebrates.

【 授权许可】

CC BY   
© The Author(s). 2017