ArticlePloS one2017
Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 papers.
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13 citing papers in PubMed, 17 citations in OpenAlex.
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- Chloroplast genome structure analysis ofFrontiers in plant science · 2024Article
- Molecular evolution and phylogenomic analysis of complete chloroplast genomes ofEcology and evolution · 2023Article
- Evolutionary and phylogenetic analyses of 11Frontiers in plant science · 2023Article
- Complete Chloroplast Genome of Topotype Material of the Coast Live OakMicrobiology resource announcements · 2022Article
- Targeted metabolite profiling as a top-down approach to uncover interspecies diversity and identify key conserved operational features in the Calvin-Benson cycle.Journal of experimental botany · 2021Article
- Molecular Evolution of rbcL in Orthotrichales (Bryophyta): Site Variation, Adaptive Evolution, and Coevolutionary Patterns of Amino Acid Replacements.Journal of molecular evolution · 2021Article
- Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromPeerJ · 2021Article
- Evolution of Rosaceae Plastomes Highlights UniqueFrontiers in plant science · 2021Article
- Genomics of Clinal Local Adaptation inG3 (Bethesda, Md.) · 2020Article
- Exceptionally high rates of positive selection on the rbcL gene in the genus Ilex (Aquifoliaceae).BMC evolutionary biology · 2019Article
- Metabolite profiles reveal interspecific variation in operation of the Calvin-Benson cycle in both C4 and C3 plants.Journal of experimental botany · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
11 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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