Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes
As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-06-01
|
| Series: | Pathogens |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-0817/10/7/807 |
| _version_ | 1827688788813414400 |
|---|---|
| author | Daniel Gómez-Pérez Eric Kemen |
| author_facet | Daniel Gómez-Pérez Eric Kemen |
| author_sort | Daniel Gómez-Pérez |
| collection | DOAJ |
| description | As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome. |
| first_indexed | 2024-03-10T10:03:35Z |
| format | Article |
| id | doaj.art-6cc78c50392049eb96c7584924cd35a7 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-10T10:03:35Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-6cc78c50392049eb96c7584924cd35a72023-11-22T01:43:14ZengMDPI AGPathogens2076-08172021-06-0110780710.3390/pathogens10070807Predicting Lifestyle from Positive Selection Data and Genome Properties in OomycetesDaniel Gómez-Pérez0Eric Kemen1Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, GermanyCenter for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, GermanyAs evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.https://www.mdpi.com/2076-0817/10/7/807oomyceteslifestyleevolution |
| spellingShingle | Daniel Gómez-Pérez Eric Kemen Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes Pathogens oomycetes lifestyle evolution |
| title | Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes |
| title_full | Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes |
| title_fullStr | Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes |
| title_full_unstemmed | Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes |
| title_short | Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes |
| title_sort | predicting lifestyle from positive selection data and genome properties in oomycetes |
| topic | oomycetes lifestyle evolution |
| url | https://www.mdpi.com/2076-0817/10/7/807 |
| work_keys_str_mv | AT danielgomezperez predictinglifestylefrompositiveselectiondataandgenomepropertiesinoomycetes AT erickemen predictinglifestylefrompositiveselectiondataandgenomepropertiesinoomycetes |