Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

Robert A Syme; Kar-Chun Tan; James K Hane; Kejal Dodhia; Thomas Stoll; Marcus Hastie; Eiko Furuki; Simon R Ellwood; Angela H Williams; Yew-Foon Tan; Alison C Testa; Jeffrey J Gorman; Richard P Oliver

doi:10.1371/journal.pone.0147221

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

PLoS One. 2016 Feb 3;11(2):e0147221. doi: 10.1371/journal.pone.0147221. eCollection 2016.

Authors

Affiliations

¹ Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
² Curtin Institute for Computation, Curtin University, Bentley, WA, Australia.
³ Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia.
⁴ Telethon Kids Institute, Subiaco, WA, Australia.

Abstract

Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ascomycota / genetics*
Ascomycota / metabolism*
Computational Biology / methods
Gene Expression Profiling* / methods
Genome, Fungal*
Genomics* / methods
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation
Proteome
Proteomics* / methods
Transcriptome

Substances

Proteome

Grants and funding

This work was supported through access to facilities managed by BioPlatforms Australia (http://www.bioplatforms.com) and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative and Grains Research and Development Corporation (http://www.grdc.com.au) research grant CUR00012. This research was undertaken with the assistance of resources provided at the NCI Specialised Facility in Bioinformatics at The University of Queensland through the National Computational Merit Allocation Scheme supported by the Australian Government and by iVEC through the use of advanced computing resources located at the Pawsey Supercomputing Centre. RAS received funding through scholarships from GRDC (GRS10061) and Curtin University (http://www.curtin.edu.au). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.