Wheat blast: A review from a genetic and genomic perspective
Md. Motaher Hossain
Abstract
Genomic information contributes to understanding the molecular mechanisms that lead to fungal pathogenicity and developing novel disease control techniques. Identifying genetic differences in fungal infections like M. oryzae may indicate whether the fungus can circumvent disease-resistant cultivars. Researchers around the globe are digging into wheat blast pathogen with a new de novo fungal genome assembly, population sequence data, and other approaches. To date, the genome of more than 50 M. oryzae isolates has been sequenced and is publicly available.2,3 Different isolates possess similar genomic sizes and overall genomic structures. The ∼40 megabase pair (Mb) genome of M. oryzae is transposon-rich and has around 13,000 genes spread across seven chromosomes (Zhang H. F. et al., 2016). Many genes involved in the growth and infection phase of M. oryzae were discovered in distinct isolates. Some strains include hundreds of isolate-specific genes and several isolate-specific duplication events; moreover, each genome contains a substantial number of poorly conserved transposon-like elements (Xue et al., 2012). Gladieux et al. (2018) used whole-genome sequence data from 76 M. oryzae isolates collected from 12 grass and cereal genera, including wheat and rice, to predict the genetic characteristics of M. oryzae lineages and to review the species status of the wheat-infecting populations. Species recognition utilizing a genealogical concordance, published data, or the extraction of previously used loci from genomic assemblies did not support the categorization of wheat blast isolates as a new species (Pyricularia graminis-tritici). Multiple divergent lineages within M. oryzae were identified, each preferentially linked with a single host genus, implying incipient speciation in response to host shift or range expansion. Gene flow analyses demonstrated that genetic exchanges contributed to the formation of numerous lineages within M. oryzae, even when incomplete lineage sorting was considered. The findings of this study gave a better understanding of the eco-evolutionary mechanisms underlying M. oryzae diversification and demonstrated the utility of genomic data for epidemiological surveillance. Peng et al. (2019) presented a nearly complete reference genome sequence of MoT B71, an aggressive Bolivian field isolate. The genome was assembled using Pacific Biosciences long reads and Illumina short reads. Along with seven core chromosomes found in the fungal genome, the fungal sequences fell into a dispensable mini-chromosome that contained repetitive sequences and effector gene sequences nabbed from the ends of the fungal chromosome. Together with re-sequencing data for eight more fungal isolates, their results hint that the mini-chromosome contributes to the evolution of the wheat blast pathogen’s effector repertoire. No mini-chromosome was found in an early field strain, but at least two from another isolate contain distinct effector genes and core chromosome end sequences. The mini-chromosome is densely packed with transposons, most typically seen at the ends of core chromosomes. Additionally, transposons in mini-chromosomes lack the distinctive signature of genome defenses against repeat-induced point (RIP) mutations. These findings collectively show that dispensable mini-chromosomes and core chromosomes follow distinct evolutionary paths and that mini-chromosomes and core chromosome ends are connected in the wheat pathogen genome as a mobile, rapidly changing effector compartment.