Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLASTC wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browserbased form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting.Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu)

Phytophthora in horticultural nursery green waste : a risk to plant health

Phytophthora is a genus of destructive plant pathogens. Certain species are damaging to native ecosystems, forestry, and the horticultural sector, and there is evidence of their dissemination in plant imports. Horticultural nurseries are central nodes of the plant trade and previous studies have found a high diversity of Phytophthora associated with plant nursery stock. It was subsequently hypothesized that green waste disposal sites in nurseries could harbour diverse Phytophthora communities and act as a pathogen reservoir and conduit, facilitating further Phytophthora infection of nursery stock and its spread into the wider environment. This project identified Phytophthora species associated with green waste at three Scottish nurseries by sampling material from waste piles, water run-off from piles, and roots from discarded plants. Species were identified using a baiting method and sequencing of environmental DNA. Plant nursery green waste was shown to harbour diverse and varied Phytophthora species assemblages, with differences among nurseries reflecting biosecurity management practices. Eighteen Phytophthora species were detected in the samples, including the highly destructive pathogens P. ramorum and P. austrocedri. Results suggest that the improved management of waste, for example through effective on-site composting, is essential to reduce the risk of Phytophthora pathogens spreading from nurseries into the wider environment

PHYTO-THREATS: addressing threats to UK forests and woodlands from Phytophthora; identifying risks of spread in trade and methods for mitigation

The multidisciplinary ‘Phyto-threats’ project was initiated in 2016 to address the increasing risks to UK forest and woodland ecosystems from trade-disseminated Phytophthora. A major component of this project was to examine the risk of Phytophthora spread through nursery and trade practices. Close to 4000 water and root samples were collected from plant nurseries located across the UK over a three-year period. Approximately half of the samples tested positive for Phytophthora DNA using a metabarcoding approach with 63 Phytophthora species identified across nurseries, including quarantine-regulated pathogens and species not previously reported in the UK. Phytophthora diversity within nurseries was linked to high-risk management practices such as use of open rather than closed water sources. Analyses of global Phytophthora risks identified biological traits and trade pathways that explained global spread and host range, and which may be of value for horizon-scanning. Phytophthoras having a higher oospore wall index and faster growth rates had wider host ranges, whereas cold-tolerant species had broader geographic and latitudinal ranges. Annual workshops revealed how stakeholder and sector ‘appetite’ for nursery accreditation increased over three years, although an exploratory cost-benefit analysis indicated that the predicted benefits of introducing best practice expected by nurseries outweigh their costs only when a wider range of pests and diseases (for example, Xylella) is considered. However, scenario analyses demonstrated the significant potential carbon costs to society from the introduction and spread of a new tree-infecting Phytophthora: Thus, the overall net benefit to society from nurseries adopting best practice could be substantial

The 21st annual Bioinformatics Open Source Conference (BOSC 2020, part of BCC2020) [version 1; peer review: not peer reviewed]

Launched in 2000 and held every year since, the Bioinformatics Open Source Conference (BOSC) is a volunteer-run meeting coordinated by the Open Bioinformatics Foundation (OBF) that covers open source software development and open science in bioinformatics. Most years, BOSC has been part of the Intelligent Systems for Molecular Biology (ISMB) conference, but in 2018, and again in 2020, BOSC partnered with the Galaxy Community Conference (GCC). This year's combined BOSC + GCC conference was called the Bioinformatics Community Conference (BCC2020, bcc2020.github.io). Originally slated to take place in Toronto, Canada, BCC2020 was moved online due to COVID-19. The meeting started with a wide array of training sessions; continued with a main program of keynote presentations, talks, posters, Birds of a Feather, and more; and ended with four days of collaboration (CoFest). Efforts to make the meeting accessible and inclusive included very low registration fees, talks presented twice a day, and closed captioning for all videos. More than 800 people from 61 countries registered for at least one part of the meeting, which was held mostly in the Remo.co video-conferencing platform

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. To streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo’s implementation and describe its broad range of functionality for designing, testing, and executing Galaxy tools, workflows, and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers

Characterisation of the transcriptome of <em>Aphelenchoides besseyi</em> and identification of a GHF 45 cellulase

While the majority of Aphelenchoides species are fungivorous, some species are plant parasites that have retained the ability to feed on fungi. Aphelenchoides besseyi is an important and widespread pathogen that causes ‘white tip’ disease on rice. This migratory endoparasitic nematode makes a significant contribution to the estimated $US 16 billion worth of damage caused by nematodes to rice crops. Here we describe a small-scale analysis of the transcriptome of A. besseyi. After sequencing, QC and assembly, approximately 5000 contigs were analysed. Bioinformatic analysis allowed 375 secreted proteins to be identified, including orthologues of proteins known to be secreted by other nematodes. One contig could encode an A. besseyi orthologue of a GHF45 cellulase, similar to those present in Bursaphelenchus xylophilus. No transcripts similar to GHF5 cellulases were present in this dataset