One-third of the plastid genes evolved under positive selection in PACMAD grasses
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We demonstrate that rbcL underwent strong positive selection during the C 3 –C 4 photosynthetic transitions in PACMAD grasses, in particular the 3′ end of the gene. In contrast, selective pressures on other plastid genes vary widely and environmental drivers remain to be identified.
Plastid genomes have been widely used to infer phylogenetic relationships among plants, but the selective pressures driving their evolution have not been systematically investigated. In our study, we analyse all protein-coding plastid genes from 113 species of PACMAD grasses (Poaceae) to evaluate the selective pressures driving their evolution. Our analyses confirm that the gene encoding the large subunit of RubisCO (rbcL) evolved under strong positive selection after C3–C4 photosynthetic transitions. We highlight new codons in rbcL that underwent parallel changes, in particular those encoding the C-terminal part of the protein. C3–C4 photosynthetic shifts did not significantly affect the evolutionary dynamics of other plastid genes. Instead, while two-third of the plastid genes evolved under purifying selection or neutrality, 25 evolved under positive selection across the PACMAD clade. This set of genes encode for proteins involved in diverse functions, including self-replication of plastids and photosynthesis. Our results suggest that plastid genes widely adapt to changing ecological conditions, but factors driving this evolution largely remain to be identified.
KeywordsC4 photosynthesis Chloroplast Plastome rbcL Poaceae Positive selection
JH and GB are members of the Laboratoire Evolution and Diversité Biologique (EDB) part of the LABEX “TULIP” managed by Agence Nationale de la Recherche (ANR-10-LABX-0041). We also acknowledge an Investissement d’Avenir grant of the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01). PAC is funded by a Royal Society University Research Fellowship (Grant number URF120119). This study received support from the PhyloAlps project, and we thank M. Boleda, H. Holota and A. Iribar. We also thank Maria S. Vorontsova for providing plant material. We thank JD Washburn for kindly sharing data before their accessibility on GenBank, and RC Hall for sharing shotgun data for two grass species.
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