Plant of the Day! Rafflesia arnoldii (Euphorbiaceae) Parasitic (host Tetrastigma) No stems, leaves or true roots Largest single flower (>1 m, 10kg) Corpse flower, diclinous 1/100 flowering plants are parasitic HGT can occur between parasites and hosts Plant of the Day! Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 1

Organelle Genome Evolution Describe the origin of the organelle genomes Describe the evidence for gene transfer between the organelle and nuclear genomes and discuss hypotheses concerning the mechanism of gene transfer Discuss hypotheses concerning the maintenance of organelle genomes Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 2

endosymbiotic theory >1.5 billion years ? The mitochondria: evolved from aerobic bacteria (α- proteobacteria- rickettsias) and a host The chloroplasts: evolved from a heterotrophic eukaryote and a cyanobacteria Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 3

Evidence for Endosymbiotic Theory -Circular molecule - No histones - Protein synthesizing machinery (ribosomes, tRNA, rRNA) - Some antibiotics block protein synthesis within the mitochondria and chloroplasts - Structurally similarity - Reproduce through fission -Strong phylogenetic evidence Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 4

Primary endosymbiosis Plant ancestor Primary endosymbiosis Primary endosymbiosis amoeba Secondary endosymbiosis Secondary endosymbiosis Secondary endosymbiosis Tertiary endosymbioses Tertiary endosymbiosis Keeling 2004

Plant chloroplasts

Structure of Plant cp Genomes LSC – 84 kb SSC – 18 kb IR – 25 kb (each)) Dempewolf et al., 2010

Gene transfer and comparative analysis Comparisons of nuclear, organelle and candidate prokaryotic ancestor genomes? -Ancient transfer events Comparison of organelle genes and nuclear genes of the same species? -Recent transfer events

Chloroplast Gene Transfer NUPTS (nuclear plastid DNA) : Arabidopsis has 11kb from 17 insertions rice chromosome 10 has a 33kb and a 131kb insertion and 26 more over 80bp each

Chloroplast Gene Transfer InfA (translation initiation factor) transferred to nuclear genome (~24x) Mutational decay/loss of cp sequence ~18% of protein coding genes in Arabidopsis are from the plastid (transit peptide coding region) Endosymbiotic gene replacement Millen et al 2001

Chloroplast Gene Transfer Rate estimates from tobacco chloroplasts 1 transfer in 5 million leaf cells 1 transfer in 16 000 pollen grains Higher rates of transfer in the pollen? Degradation of the organelle genomes in pollen could make DNA fragments available for uptake

Plant mitochondria kbp # protein coding genes

Wheat mtDNA 452,528 bp

Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . Plant mitochondrial genomes undergo intra- or intermolecular recombination via repeated sequences subgenomic molecules (loop out) or isomeric forms (flip flop) 15

Mitochondrial Gene Transfer NUMTS: complete mt genome sequences in cat nuclei >296 in humans, from 106 to 14.5 kbp each (older NUMTs more abundant-tandem repeats) rice chromosome 10 has 57 NUMTS ranging from 80-2552bp Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . Do larger nuclear genomes have more NUMTS? 16

Mitochondrial Gene Transfer rate estimates: 1 plasmid transfer to nucleus in 20,000 yeast cells (integration rare) Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 17

Mitochondrial Gene Transfer Evidence for parallel transfer and loss e.g. rps10 gene independently transferred to nucleus numerous times Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . Adams et al 2000 18

Mechanisms Bulk DNA – recombination between escaped organelle DNA and nuclear DNA Expt. transfer in yeast Non-coding sequence frequently transferred Whole organelle sequences transferred MUST HAPPEN cDNA intermediates Nuclear copies of organelle genes often lack organelle-specific introns and edited sites MAY HAPPEN Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 19

Why are the organelle genomes maintained? Hydrophobicity -hydrophobic proteins are poorly imported (excess of membrane embedded proteins) Fitness advantage if coding sequence and regulation are in same location Other constraints (e.g. RNA editing, genetic code) Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 20

Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 21

Observation: Plants larger in invasive range with increased RO and may be the reason my they spread rapidly in the invaded range . 22