Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context
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 evoluti...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2018-10-01
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| Series: | Mycobiology |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/12298093.2018.1542970 |
| _version_ | 1811305607554138112 |
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| author | Jaeyoung Choi Jong-Joon Lee Junhyun Jeon |
| author_facet | Jaeyoung Choi Jong-Joon Lee Junhyun Jeon |
| author_sort | Jaeyoung Choi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T08:29:27Z |
| format | Article |
| id | doaj.art-e06cd9c909f64eb0885d6d9e24c91d3f |
| institution | Directory Open Access Journal |
| issn | 1229-8093 2092-9323 |
| language | English |
| last_indexed | 2024-04-13T08:29:27Z |
| publishDate | 2018-10-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Mycobiology |
| spelling | doaj.art-e06cd9c909f64eb0885d6d9e24c91d3f2022-12-22T02:54:19ZengTaylor & Francis GroupMycobiology1229-80932092-93232018-10-0146436136910.1080/12298093.2018.15429701542970Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic ContextJaeyoung Choi0Jong-Joon Lee1Junhyun Jeon2Convergence Research Center for Smart Farm Solution, Korea Institute of Science and TechnologyYeungnam UniversityYeungnam UniversityThe 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.http://dx.doi.org/10.1080/12298093.2018.1542970rice blast fungusgene emergence timephylostratigraphyevolutionorphan genes |
| spellingShingle | Jaeyoung Choi Jong-Joon Lee Junhyun Jeon Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context Mycobiology rice blast fungus gene emergence time phylostratigraphy evolution orphan genes |
| title | Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context |
| title_full | Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context |
| title_fullStr | Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context |
| title_full_unstemmed | Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context |
| title_short | Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context |
| title_sort | genomic insights into the rice blast fungus through estimation of gene emergence time in phylogenetic context |
| topic | rice blast fungus gene emergence time phylostratigraphy evolution orphan genes |
| url | http://dx.doi.org/10.1080/12298093.2018.1542970 |
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