title: Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics.
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.
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Robert A
authors: RA
authors: Syme
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Kar-Chun
authors: KC
authors: Tan
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.|Curtin Institute for Computation, Curtin University, Bentley, WA, Australia.
authors: James K
authors: JK
authors: Hane
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Kejal
authors: K
authors: Dodhia
authors: Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia.
authors: Thomas
authors: T
authors: Stoll
authors: Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia.
authors: Marcus
authors: M
authors: Hastie
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Eiko
authors: E
authors: Furuki
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Simon R
authors: SR
authors: Ellwood
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Angela H
authors: AH
authors: Williams
authors: Telethon Kids Institute, Subiaco, WA, Australia.
authors: Yew-Foon
authors: YF
authors: Tan
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Alison C
authors: AC
authors: Testa
authors: Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia.
authors: Jeffrey J
authors: JJ
authors: Gorman
authors: Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia.
authors: Richard P
authors: RP
authors: Oliver
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D020543:Proteome; D040901:Proteomics / Q000379:methods; D059467:Transcriptome
chemical_list: D020543:Proteome