Mycobiology.  2018 Dec;46(4):361-369. 10.1080/12298093.2018.1542970.

Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context

Affiliations
  • 1Convergence Research Center for Smart Farm Solution, Korea Institute of Science and Technology, Gangneung25451, Korea.
  • 2Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk38541, Korea. jjeon@yu.ac.kr

Abstract

The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.

Keyword

rice blast fungus; gene emergence time; phylostratigraphy; evolution; orphan genes

MeSH Terms

Base Composition
Bias (Epidemiology)
Child
Child, Orphaned
Codon
Fungi*
Genome
Humans
Magnaporthe
Methods
Oryza
Reproduction, Asexual
Virulence
Virulence Factors
Codon
Virulence Factors
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