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

• Published in: Fungal genetics and biology Vol. 79; pp. 71 - 75
• Main Authors: McDonald, Megan C., Williams, Angela H., Milgate, Andrew, Pattemore, Julie A., Solomon, Peter S., Hane, James K.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2015
• Subjects: Accessory chromosome; Ascomycota - genetics; Chromosomes, Fungal; Comparative genomics; Computational Biology; Genes, Fungal; Genetic Testing; High-Throughput Nucleotide Sequencing; Next-generation sequencing; Presence–absence variation; Triticum aestivum; Zymoseptoria tritici; Comparative genomics; Zymoseptoria tritici; Next-generation sequencing; Accessory chromosome; Presence–absence variation
• ISSN: 1087-1845; 1096-0937
• DOI: 10.1016/j.fgb.2015.04.012

•Next-generation 100bp paired-end sequencing of 13 novel Z. tritici isolate genomes.•Prediction of accessory chromosome presence–absence profiles by NGS read alignment.•Prediction of accessory chromosome presence–absence profiles by de novo assembly.•Summary of presence–absence profiles and chromosomal mutation rates. 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.