Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes.

Gitte Petersen,Jerrold I Davis,Gregory T Ross,Craig F Barrett,Athanasios Zervas,Sean W Graham,Argelia Cuenca,Ole Seberg,Dan Mishmar

doi:10.1371/journal.pone.0177606

Abstract

The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.

Highlights

Compared to the mitochondrial genome of most other eukaryotes, the structure of the mitogenome of land plants is astonishingly dynamic
In this study we focus on a clade of monocots, Alismatales, which several studies have shown to be a hotspot of mitochondrial anomalies, including pronounced intron loss, substitution rate variation, extremely different levels of RNA editing and potential abundant incorporation of retrotranscribed gene sequences [18,19,20,21,22]
The Stratiotes aloides mitogenome could be assembled into a 349,058 bp circular structure whereas the mitogenome of Zostera marina was assembled into a shorter linear structure of just 191,481 bp (Fig 1, Table 1)

Summary

Introduction

Compared to the mitochondrial genome (mitogenome) of most other eukaryotes, the structure of the mitogenome of land plants is astonishingly dynamic. More than a hundred mitogenomes covering most major clades of land plants have been completely sequenced, and the more than 75 mitogenomes from angiosperms reveal an intriguing evolutionary history: changes in size, structure, gene and intron content, horizontal gene transfer (HGT) and transfer of DNA between genomic compartments, extensive RNA editing, extreme differences in substitution rates and frequent incorporation of retrotranscribed sequences (reviewed in [1, 2]). Plant mitogenomes are usually shown as single, circular structures, but increasing evidence suggests that they can be multichromosomal with the individual structures taking diverse shapes, i.e. being circular, linear or branched [3]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Methods

Results

Conclusion