Genome-Enhanced Detection and Identification (GEDI) of plant pathogens

View article
PeerJ

Main article text

 

Introduction

Materials and Methods

Pipeline development

Module 1: genomic resources

Module 2: discovering homologous gene clusters

Module 3: filtering false positives

Module 4: assay design

Computational testing and experimental screening

Testing the cutoff filters

Pipeline runs

In silico screening for intra-taxon variation

Experimental screening

Results

Computational testing

Filtering simulations

Pipeline run on Phytophthora

Pipeline run on Dothideomycetes

Pipeline run on Pucciniales

In silico screening for intra-taxa variation

Experimental screening

Discussion

Conclusions

Supplemental Information

Nucleotidic identity between pairwise genomes with a (A) Phytophthora dataset of 11 species and a (B) Dothideomycete dataset of 16 species

Neighbor-joining trees on the left were reconstructed from the matrix of nucleotidic identity between pairs of genomes presented on the right. For the Phytophthora dataset, the phylogenetic clades as defined in Blair et al., 2008 are indicated on the phylogenetic tree.

DOI: 10.7717/peerj.4392/supp-1

Relationships between the proportion of “unique” candidates and the average nucleotidic identity between genomes in the Phytophthora and Dothideomycetes datasets

(A) Unique candidates as predicted in Module 2 of the pipeline (OrthoMCL search); (B) unique candidates retained after Module 3 (filtering with BLASTp and BLASTn with e-value cutoff of 1e–05).

DOI: 10.7717/peerj.4392/supp-2

Proportions of “unique” candidates retained after BLASTp and BLASTn filtering according to different e-value cutoffs

(A) Filtering results for Phytophthora ramorum and P. kernoviae used as target species with the Phytophthora dataset; (B) filtering results for Sphaerulina musiva and Didymella zeae-maydis used as target species with the Dothideomycetes dataset.

DOI: 10.7717/peerj.4392/supp-3

Supplementary tables

Table S1. Assembly statistics and gene content for the Dothideomycete genome sequences generated or downloaded in this study. Table S2. Assembly statistics and gene content for the rust genome sequences generated or downloaded in this study. Table S3. Assembly statistics and gene content for the Phytophthora genome sequences generated or downloaded in this study.

DOI: 10.7717/peerj.4392/supp-4

Supplementary text

DOI: 10.7717/peerj.4392/supp-5

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Nicolas Feau conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, approved the final draft and also wrote the paper.

Stéphanie Beauseigle, Sandra Cervantes-Arango, Padmini Herath and Hesther Yueh performed the experiments, approved the final draft.

Marie-Josée Bergeron, Monique L. Sakalidis and Clement K.M. Tsui performed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Guillaume J. Bilodeau performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Inanc Birol and Philippe Tanguay analyzed the data, contributed reagents/materials/analysis tools, approved the final draft.

Braham Dhillon and Angela L. Dale analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Steven J.M. Jones analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Josyanne Lamarche and Dario I. Ojeda performed the experiments, analyzed the data, approved the final draft.

Greg Taylor performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, approved the final draft.

Adnan Uzunovic contributed reagents/materials/analysis tools, approved the final draft.

Richard C. Hamelin conceived and designed the experiments, approved the final draft and also wrote the paper.

Data Availability

The following information was supplied regarding data availability:

The raw data used is already public and the pipeline only uses a series of already published software or scripts; these are described in the text and the figures.

Funding

This work was funded by Genome Canada, Genome British Columbia, the Canadian Forest Service (Genomics Research and Development Initiative, GRDI), Canadian Food Inspection Agency, FP Innovations and Boreal Genomics through a Large Scale Applied Research Project (LSARP 2112; Genome Canada) grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

26 Citations 6,093 Views 1,046 Downloads

Your institution may have Open Access funds available for qualifying authors. See if you qualify

Publish for free

Comment on Articles or Preprints and we'll waive your author fee
Learn more

Five new journals in Chemistry

Free to publish • Peer-reviewed • From PeerJ
Find out more