Abstract
Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.
Highlights
They share many unifying features, the green algae (Chlorophyta) are a diverse group with genomes that vary considerably in structure and gene content (Yurina & Odintsova, 2016)
The goal of this study is to evaluate the characteristics of mitochondrial genomes in the Bryopsidales, as well as to determine the evolutionary forces that have shaped organelle genome dynamics in the Bryopsidales
The O. quekettii mitochondrial genome encodes all genes commonly found in Chlorophyta mitochondrial genomes, including most ribosomal protein genes, which have been unevenly retained in plant mitochondria (Palmer et al, 2000; Mower, Sloan & Alverson, 2012), and are missing in some Chlorophyta lineages such as the Chlorophyceae and Pedinomonas (e.g. Fig. S3)
Summary
They share many unifying features, the green algae (Chlorophyta) are a diverse group with genomes that vary considerably in structure and gene content (Yurina & Odintsova, 2016). Most work on Chlorophyta genomes to date has focused on organellar genomes, with in excess of 150 chloroplast and 70 mitochondrial genomes published on GenBank. These organelle genome data have been used for phylogenetic analyses to resolve lineage relationships within the Chlorophyta (Fučíková et al, 2014; Cremen et al, 2018) and. As with many plastid-bearing taxa, more effort has been made to sequence and characterise chloroplast genomes rather than mitochondrial, as plastid genomes tend to be favoured for their use in phylogenetic studies due to high coding content, relatively conserved genome and simple inheritance patterns (Smith & Keeling, 2015; Fang et al, 2017). Mitochondrial genomes tend to show greater abnormalities in structure than plastid genomes (Burger, Gray & Lang, 2003), and some of the most unusual genomic features have been observed in eukaryotic mitochondrial genomes (Smith & Keeling, 2015)
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