A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant.

Adam J Orr,William Foley,Reed A Cartwright,David Kainer,Robert Lanfear,Alejandro Morales-Suarez,Ji-Fan Hsieh,Amanda Padovan,Tonya Haff,Carsten Külheim,Lindell Bromham,Carlos Bustos-Segura

doi:10.1098/rspb.2019.2364

Abstract

Somatic mutations can have important effects on the life history, ecology, and evolution of plants, but the rate at which they accumulate is poorly understood and difficult to measure directly. Here, we develop a method to measure somatic mutations in individual plants and use it to estimate the somatic mutation rate in a large, long-lived, phenotypically mosaic Eucalyptus melliodora tree. Despite being 100 times larger than Arabidopsis, this tree has a per-generation mutation rate only ten times greater, which suggests that this species may have evolved mechanisms to reduce the mutation rate per unit of growth. This adds to a growing body of evidence that illuminates the correlated evolutionary shifts in mutation rate and life history in plants.

Highlights

Trees grow from multiple meristems which contain stem cells that divide to produce the somatic and reproductive tissues
We present a solution to the challenges of measuring the somatic mutation rate that leverages the phylogeny-like structure of the plant itself to estimate the genome-wide somatic mutation rate of the individual
Our strategy includes an inbuilt positive control, because we can ask whether the phylogenetic tree we reconstruct from the set of putative somatic mutations across the eight branch tips reflects the known physical structure of the tree

Summary

Introduction

Trees grow from multiple meristems which contain stem cells that divide to produce the somatic and reproductive tissues. Our strategy includes an inbuilt positive control, because we can ask whether the phylogenetic tree we reconstruct from the set of putative somatic mutations across the eight branch tips reflects the known physical structure of the tree (i.e. whether phylogeny correctly reconstructs ontogeny, as is expected for plant development in most cases, but see below).

Results

Conclusion