title: Next-generation re-sequencing as a tool for rapid bioinformatic screening of presence and absence of genes and accessory chromosomes across isolates of Zymoseptoria tritici.
abstract: The wheat pathogen Zymoseptoria tritici possesses a large number of accessory chromosomes that may be present or absent in its genome. The genome of the reference isolate IPO323 has been assembled to a very high standard and contains 21 full length chromosome sequences, 8 of which represent accessory chromosomes. The IPO323 reference, when combined with low-cost next-generation sequencing and bioinformatics, can be used as a powerful tool to assess the presence or absence of accessory chromosomes. We present an outline of a range of bioinformatics techniques that can be applied to the analysis of presence-absence variation among accessory chromosomes across 13 novel isolates of Z. tritici.
authors.affiliation: Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australia.
authors.forename: Megan C
authors.initials: MC
authors.lastname: McDonald
authors.affiliation: CCDM Bioinformatics, Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia.
authors.forename: Angela H
authors.initials: AH
authors.lastname: Williams
authors.affiliation: NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Milgate
authors.affiliation: Charles Sturt University, Wagga Wagga, Australia.
authors.forename: Julie A
authors.initials: JA
authors.lastname: Pattemore
authors.affiliation: Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australia.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Solomon
authors.affiliation: CCDM Bioinformatics, Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia; Curtin Institute for Computation, Curtin University, Perth, Australia. Electronic address: James.Hane@curtin.edu.au.
authors.forename: James K
authors.initials: JK
authors.lastname: Hane
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D015825:Chromosomes, Fungal; D019295:Computational Biology; D005800:Genes, Fungal; D005820:Genetic Testing; D059014:High-Throughput Nucleotide Sequencing
keywords: Accessory chromosome; Comparative genomics; Next-generation sequencing; Presence–absence variation; Zymoseptoria tritici