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Planta

, Volume 247, Issue 1, pp 255–266 | Cite as

One-third of the plastid genes evolved under positive selection in PACMAD grasses

Original Article

Abstract

Main conclusion

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.

Keywords

C4 photosynthesis Chloroplast Plastome rbcL Poaceae Positive selection 

Notes

Acknowledgements

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.

Supplementary material

425_2017_2781_MOESM1_ESM.docx (767 kb)
Supplementary material 1 (DOCX 766 kb)

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Laboratoire Evolution and Diversité Biologique (EDB, UMR 5174)CNRS/ENSFEA/IRD/Université Toulouse IIIToulouseFrance
  2. 2.Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK

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