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Dates and rates in grape’s plastomes: evolution in slow motion

  • Giovanni ZeccaEmail author
  • Fabrizio Grassi
  • Vazha Tabidze
  • Ia Pipia
  • Adam Kotorashvili
  • Nato Kotaria
  • Tengiz Beridze
Original Article
  • 4 Downloads

Abstract

The family Vitaceae includes the domesticated grapevine (Vitis vinifera), one of the most economically important crops in the world. Despite the importance of Vitaceae, there is still considerable controversy surrounding their phylogenetic relationships and evolutionary timescales. Moreover, variation in rates of molecular evolution among Vitaceae remains mostly unexplored. The present research aims to fill these knowledge gaps through the analysis of plastome sequences. Thirteen newly sequenced grape plastomes are presented and their phylogenetic relationships examined. Divergence times and absolute substitution rates are inferred under different molecular clocks by the analysis of 95 non-coding plastid regions and 43 representative accessions of the major lineages of Vitaceae. Furthermore, the phylogenetic informativeness of non-coding plastid regions is investigated. We find strong evidence in favor of the random local clock model and rate heterogeneity within Vitaceae. Substitution rates decelerate in Ampelocissus, Ampelopsis, Nekemias, Parthenocissus, Rhoicissus, and Vitis, with genus Vitis showing the lowest values up to a minimum of ~ 4.65 × 10−11 s/s/y. We suggest that liana-like species of Vitaceae evolve slower than erect growth habit plants and we invoke the “rate of mitosis hypothesis” to explain the observed pattern of the substitution rates. We identify a reduced set of 20 non-coding regions able to accurately reconstruct the phylogeny of Vitaceae and we provide a detailed description of all 152 non-coding regions identified in the plastomes of subg. Vitis. These polymorphic regions will find their applications in phylogenetics, phylogeography, and population genetics as well in grapes identification through DNA barcoding techniques.

Keywords

Divergence time estimation Grapevine Rate of mitosis hypothesis Substitution rate Vitaceae Vitis 

Notes

Acknowledgements

Georgian part of research was funded by Mr. Kakha Bendukidze (1956–2014) via his Knowledge Fund, a funding organization of the Free University of Tbilisi and Agricultural University of Georgia. We thank Penelope Barrington for insightful discussion and English revision. We acknowledge the anonymous reviewers for providing useful suggestions to improve this manuscript.

Author contributions

GZ and FG participated in study design, did phylogenetic and statistical analyses, did figures and supplementary material, interpreted the results, and wrote the manuscript. VT did most of the lab experiments, obtaining plant materials, DNA isolation and assembly of plastid DNA reads. IP participated in plastid DNA isolation and construction of DNA libraries. AK and NK provided construction of shotgun genomic DNA libraries and Illumina sequencing. TB participated in design and coordination of the study, interpretation of results, and critical revision of manuscript. All authors read and approved the final manuscript.

Supplementary material

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Supplementary material 1 (PDF 3798 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of BiosciencesUniversity of MilanMilanItaly
  2. 2.Department of BiologyUniversity of BariBariItaly
  3. 3.Institute of Molecular GeneticsAgricultural University of GeorgiaTbilisiGeorgia
  4. 4.National Center for Disease Control and Public Health (NCDC&PH)TbilisiGeorgia

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