Rates and patterns of molecular evolution in bryophyte genomes, with focus on complex thalloid liverworts, Marchantiopsida

Anna-Malin Linde,D Magnus Eklund,Nils Cronberg,John L Bowman,Ulf Lagercrantz

doi:10.1016/j.ympev.2021.107295

Anna-Malin Linde, D Magnus Eklund + Show 3 more

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https://doi.org/10.1016/j.ympev.2021.107295

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Abstract

Plants commonly referred to as “bryophytes” belong to three major lineages of non-vascular plants: the liverworts, the hornworts and the mosses. They are unique among land plants in having a dominant haploid generation and a short-lived diploid sporophytic generation. The dynamics of selection acting on a haploid genome differs from those acting on a diploid genome: new mutations are directly exposed to selection. The general aim of this paper is to investigate the diversification rateof bryophytes - measured as silent site substitution rate representing neutral evolution (mutation rate) and the nonsynonymous to synonymous substitution rate ratio (dN/dS) representing selective evolution - and compare it with earlier studies on vascular plants. Results show that the silent site substitution rate is lower for liverworts as compared to angiosperms, but not as low as for gymnosperms. The selection pressure, measured as dN/dS, isnot remarkably lower for bryophytes as compared to other diploid dominant plants as would be expected by the masking hypothesis, indicating that other factors are more important than ploidy.

Highlights

The rate of molecular evolution as measured by the number of nucleotide sequence changes per unit time, varies between species, and between and within genes in a genome
De La Torre et al (2017) used 42 highly conserved single-copy genes shared between angiosperms and gymnosperms to calculate synony mous site substitution rates and dN/dS
Since synonymous substitution rate is primarily influenced by mutation rate, assuming that synonymous sites are neutral, our data suggests lower rates of mutations per year in bryophytes compared to angio sperms, but not as low as for gymnosperms

Summary

Introduction

The rate of molecular evolution as measured by the number of nucleotide sequence changes per unit time, varies between species, and between and within genes in a genome. Substitutions that affect the protein sequence (non-synonymous ones) are clearly less common than substitutions that do not affect the amino acid sequence (synonymous ones), due to widespread selection for conserved protein function. When dN/dS is larger than one it indicates that substitutions in the protein-coding gene were enriched for those that altered the amino acids states, suggesting diversifying (posi tive) selection. When an amino acid change is neutral, the rate of fixation will be the same as that of a syn onymous mutation and dN/dS equals one. The value of dN/dS is independent of variations in mutation rate from gene to gene because it compares synonymous and nonsynonymous changes within the same gene

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