720 likes | 1.03k Views
Genomic gigantism in plant mitochondria. Andy Alverson. Outline. Mitochondrial genome size evolution Cucurbitaceae Silene. Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella. The three plant genomes. The disparate trajectories of organelle genomes.
E N D
Genomic gigantism in plant mitochondria Andy Alverson
Outline • Mitochondrial genome size evolution • Cucurbitaceae • Silene Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella
The disparate trajectories of organelle genomes 1kb = 1000 base pairs
The disparate trajectories of organelle genomes 1kb = 1000 base pairs
The disparate trajectories of organelle genomes Mutation pressure hypothesis (Lynch et al. 2006. Science) 1kb = 1000 base pairs
Estimatedmitochondrial genome sizes in Cucurbitaceae Ward et al. 1981
Estimatedmitochondrial genome sizes in Cucurbitaceae Prediction: Larger genomes have lower mutation rates Ward et al. 1981
Actualmitochondrial genome sizes in Cucurbitaceae Alverson et al. 2010. Mol. Biol. Evol.
CUA CUC CUG CUU CCA CCC CCG CCU GGA GGC GGG GGU Leu Pro Gly Estimating the mutation rate of a genome • Multiple codons for the same amino acid • Synonymous mutations • do not change the amino acid • invisible to natural selection ≈ neutral • rate of neutral change ≈ mutation rate
Coding sequences in cucurbit mitochondrial genomes 17% 7% 19% 5% 4% Total coding:
Nuclear–mitochondrial sequence exchange Huang et al. 2009
The cucumber mitochondrial and nuclear genomes share a lot of DNA 33% of the mitochondrial genome Alverson et al. 2011. Plant Cell.
The cucumber mitochondrial and nuclear genomes share a lot of DNA 33% of the mitochondrial genome Alverson et al. 2011. Plant Cell.
Outline • Mitochondrial genome size evolution • Cucurbitaceae • Silene Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella
Dan Sloan Doug Taylor University of Virginia Mitochondrial genome evolution in Silene
Mutation rate and mitochondrial genome size ? ? ? ? 16 kb
Mutation rate and mitochondrial genome size ? ? 253 kb 426 kb 16 kb
Mutation rate and mitochondrial genome size 253 kb 426 kb 16 kb 6,728 kb 11,318 kb
Large multi-chromosomal mitochondrial genomes Silene noctiflora (6.7 Mb) • 59 chromosomes • 66–192 kb in length
Genome size summary and conclusions • Unprecedented size and structural variation in plant mitochondrial genomes
Genome size summary and conclusions • Unprecedented size and structural variation in plant mitochondrial genomes • Theory: Low mutation rate Larger genome size
Genome size summary and conclusions • Unprecedented size and structural variation in plant mitochondrial genomes • Theory: Low mutation rate Larger genome size • Cucurbitaceae and Silene show the opposite pattern
Genome size summary and conclusions • Unprecedented size and structural variation in plant mitochondrial genomes • Theory: Low mutation rate Larger genome size • Cucurbitaceae and Silene show the opposite pattern • What drives genome size evolution in plant mitochondria? • mutation rate? Not likely. • intramolecular recombination? Maybe.
Genome size summary and conclusions • Unprecedented size and structural variation in plant mitochondrial genomes • Theory: Low mutation rate Larger genome size • Cucurbitaceae and Silene show the opposite pattern • What drives genome size evolution in plant mitochondria? • mutation rate? Not likely. • intramolecular recombination? Maybe. • Much of the "extra" intergenic DNA may derive from the chloroplast and the nuclear genomes
Outline • Mitochondrial genome size evolution • Cucurbitaceae • Silene Horizontal gene transfer (HGT) in the mitochondrial genome of Amborella
The Amborella mitochondrial genome: another monster! Arabidopsis Amborella total size = 3.9 Mb
Features in the Amborella mitochondrial genome Native mito
Features in the Amborella mitochondrial genome Native mito chloroplast-derived
Features in the Amborella mitochondrial genome Native mito chloroplast-derived Foreign angiosperm mito
Features in the Amborella mitochondrial genome Native mito chloroplast-derived Foreign angiosperm mito Foreign moss mito
Features in the Amborella mitochondrial genome Native mito chloroplast-derived Foreign angiosperm mito Foreign moss mito Foreign green algal mito
Features in the Amborella mitochondrial genome Native mito
Features in the Amborella mitochondrial genome Native mito Native chloroplast Foreign angiosperm mito Foreign moss mito Foreign green algal mito
cob Amborella other angiosperms mosses green algae N
Other genes show the same pattern as cob Amborella other angiosperms mosses N green algae N N N = native
Insights into the mechanism of horizontal transfer What the Amborella mitochondrial genome has: What the Amborella mitochondrial genome lacks: