Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.
Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5578625?pdf=render |
| _version_ | 1818911221853716480 |
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| author | Carmen Hermida-Carrera Mario A Fares Ángel Fernández Eustaquio Gil-Pelegrín Maxim V Kapralov Arnau Mir Arántzazu Molins José Javier Peguero-Pina Jairo Rocha Domingo Sancho-Knapik Jeroni Galmés |
| author_facet | Carmen Hermida-Carrera Mario A Fares Ángel Fernández Eustaquio Gil-Pelegrín Maxim V Kapralov Arnau Mir Arántzazu Molins José Javier Peguero-Pina Jairo Rocha Domingo Sancho-Knapik Jeroni Galmés |
| author_sort | Carmen Hermida-Carrera |
| collection | DOAJ |
| description | Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML. |
| first_indexed | 2024-12-19T22:55:16Z |
| format | Article |
| id | doaj.art-f812e20e7fc6436e9675b6f8a54377a9 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T22:55:16Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-f812e20e7fc6436e9675b6f8a54377a92022-12-21T20:02:40ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01128e018397010.1371/journal.pone.0183970Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.Carmen Hermida-CarreraMario A FaresÁngel FernándezEustaquio Gil-PelegrínMaxim V KapralovArnau MirArántzazu MolinsJosé Javier Peguero-PinaJairo RochaDomingo Sancho-KnapikJeroni GalmésPhylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML.http://europepmc.org/articles/PMC5578625?pdf=render |
| spellingShingle | Carmen Hermida-Carrera Mario A Fares Ángel Fernández Eustaquio Gil-Pelegrín Maxim V Kapralov Arnau Mir Arántzazu Molins José Javier Peguero-Pina Jairo Rocha Domingo Sancho-Knapik Jeroni Galmés Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. PLoS ONE |
| title | Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. |
| title_full | Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. |
| title_fullStr | Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. |
| title_full_unstemmed | Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. |
| title_short | Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. |
| title_sort | positively selected amino acid replacements within the rubisco enzyme of oak trees are associated with ecological adaptations |
| url | http://europepmc.org/articles/PMC5578625?pdf=render |
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