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

Area of Science:

• Plant evolutionary biology
• Molecular phylogenetics
• Genomics

Background:

• The Vitaceae family, including the economically vital grapevine (Vitis vinifera), has poorly understood phylogenetic relationships and evolutionary timelines.
• Variation in molecular evolution rates within Vitaceae remains largely unexplored, hindering a comprehensive understanding of their diversification.

Purpose of the Study:

• To resolve phylogenetic uncertainties and evolutionary timescales within Vitaceae using plastome sequence analysis.
• To investigate the variation in molecular evolution rates and identify key genomic regions for phylogenetic reconstruction in Vitaceae.

Main Methods:

• Sequencing and analysis of 13 new grape plastomes alongside existing data for 43 accessions representing major Vitaceae lineages.
• Inference of divergence times and absolute substitution rates using various molecular clock models on 95 non-coding plastid regions.
• Evaluation of the phylogenetic informativeness of non-coding plastid regions.

Main Results:

• Strong support for the random local clock model and significant rate heterogeneity across Vitaceae plastomes.
• Observed deceleration of substitution rates in liana-like genera (Ampelocissus, Ampelopsis, Nekemias, Parthenocissus, Rhoicissus, Vitis), with Vitis exhibiting the slowest rates.
• Identification of 20 optimal non-coding regions for accurate Vitaceae phylogeny reconstruction and a detailed catalog of 152 non-coding regions in subg. Vitis.

Conclusions:

• The study supports the
• rate of mitosis hypothesis
• to explain slower evolution in liana-like species compared to erect-growing ones.
• The identified non-coding regions are valuable for phylogenetics, phylogeography, population genetics, and DNA barcoding for grape identification.