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

Megan C McDonald; Angela H Williams; Andrew Milgate; Julie A Pattemore; Peter S Solomon; James K Hane

doi:10.1016/j.fgb.2015.04.012

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

Fungal Genet Biol. 2015 Jun:79:71-5. doi: 10.1016/j.fgb.2015.04.012.

Authors

Megan C McDonald¹, Angela H Williams², Andrew Milgate³, Julie A Pattemore⁴, Peter S Solomon¹, James K Hane⁵

Affiliations

¹ Plant Science Division, Research School of Biology, The Australian National University, Canberra, Australia.
² CCDM Bioinformatics, Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia.
³ NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, Australia.
⁴ Charles Sturt University, Wagga Wagga, Australia.
⁵ 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.

PMID: 26092791
DOI: 10.1016/j.fgb.2015.04.012

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.

Keywords: Accessory chromosome; Comparative genomics; Next-generation sequencing; Presence–absence variation; Zymoseptoria tritici.

MeSH terms

Ascomycota / genetics*
Chromosomes, Fungal
Computational Biology*
Genes, Fungal*
Genetic Testing*
High-Throughput Nucleotide Sequencing*