Julius B. Lucks/Meetings and Notes/SMBE2007/extreme genomes 1

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Patrick Keeling: Nuclear Genome Diversity


  • Botany: U British Columbia


  • Keeling and Slamovits, 2005, Curr. Opin, Genet. Div.
  • dynoflaggelites and ameoba have large genomes
  • 2 small genome groups
    • microsporidia - related to fungi - obligate intracell parasites
      • huge tube that can peirce cell that they can travel into
    • nucleomorphs - organells found in algae: cryptomonads, chloracniophytes
      • have engulfed another algae and kept it as a symbiont
  • Keeling 2005, Trends Ecol. Evol.

How genomes get small

  • reduction - massive gene loss
    • host-dependance - loss of whole pathways
  • compaction - 2x compaction of yeost
    • very short intergenic regions
    • reduced number and size of introns
    • genes shorter
  • how does this affect how genomes work?
    • most eukaryotic - promoter upstream and terminator downstream
    • reduced genomes - transcripts overlap - opposite strands (transcriptional collision), or same strand (promoter occlusion)
      • like some viruses
    • Williams, PNAS, 2005
  • keep all tRNAs and ribosomal RNAs - ribosomal RNAs at the telomeres

Comparison of Antonospora and Encephalitozoon

  • promoter regions of a gene can be inside coding region upstream of it

Pygmy Introns (Nucleomorphs)

  • cryptomonid - 17 introns of about 50 bases (Douglas, Nature, 2001)
    • lost many
  • chloracachniophyte - 841 introns 18,19,29,21 bp (Gilson, 2006, PNAS)
    • retained all, but shrunk
    • GTnnnnAG - GT/AG boundaries - spliceosomal introns

Shrinking Proteins

  • genes shorter - Katinka, 2003
    • 9% reduction compared to yeast
  • want to reduce DNA that bad?
  • reduction of complexity of the proteome?
  • ostreococcus tauri - picoplankton - one of smallest organisms known
  • 12.5 mbp, 8,166 proteins, gene density 1.54 genes/kbp (in between yeast and the extremes)


  • intron loss by reverse transcriptase mediated gene replacement
  • Koonin: any lifestyle differences between the cryptomonids and chloracachniophytes?

Jeffrey Palmer: Horizontal gene transfer gone wild in plant mitochondrial genes


  • Amborella trichopoda mtDNA: 4 Mb - outside:native::5:1
  • bacteria - maybe 1/2 of genome can be from outside sources
  • Parkinson, Adams, Palmer, Curr. Biol, 9, 1481, 1999 - Amborella one of 1st angiosperms (flowing plants)
  • Amborella contains foreign mitochondrial genes of moss and angiosperm origin
  • grows only on new caledania (next to Australia) (80% of plants are endemic there (only live there))
  • mtDNA:
    • Human 16 kb
    • Arabidobsis 367 kb
    • Zea 570 kb
    • Amborella 4,000 kb!
  • does not have
    • foreign chloroplast DNA
    • foreign nuclear DNA
    • bacterial DNA
    • mtDNA from fungi and other 'not-green' plants
  • Frequent fusion and fission fof plant mitochondria - PNAS
    • phylogenetic gulf in fusion mechanisms between (animals/fungi) & plants- Hoppins et al Ann Rev Biochem 76,751,2007
    • chloroplasts don't fuse like mitochondria
  • mtDNA retains synteny of its foreign acquisitions

How does foreign mtDNA get into Amborella's mitochondria

  • how do mitochondria get from one plant into cells of another
    • direct plant-to-plant contact
      • grows in wet env - lots of epiphytes, epaphylls - mosses, lichens
      • how get into germ line?
        • large tree that gets wounded and dies back - suckers grow off at sites of wounding
        • suckering - cellular dediffertiation - recreate meristems - promotes mitochondrial fusion
          • mascerate foreign substances in a wound to get foreign sources
        • other plants that grow like this have same mitochondrial size?
    • biological vectoring agents - viruses, bacteria, insects
    • illegitimate pollination
  • of 250 forign mt genes - probably very few functional

Atsushi Nakabachi: Smallest cellular genome


  • RIKEN (Intitute of Physical and Chemical Research)

Words to Look Up

  • Chromosome FISH


  • Carsonella ruddii 160 kb genome
    • endocellular symbiotic bacterium of psyllids
  • E. coli - 4000 genes (Human 23,000, Yeast 6,000)
  • prokaryotes - simpler body plans and lifestyles
    • gene density high, no introns so gene #'s proportional to genome sizes
  • endocellular prasites (prokaryotes) have smaller genomes
  • insects - bacteriocytes (in body cavity) - host cells specialized to harbor symbionts
    • host live in nutrient poor environments
    • obligate mutualisw
  • Host: Bacteriocyte : Symbiont
    • Carpenter Ant: midgut epithelium : Blochmannia floidanus
    • Tsetse flies: specialized epithelial cells : Wiggleswortha glossinidia
    • Aphids: body cavity: Buchnera aphidicula

General featurs of bacterial symbiont genomes

  • massive reduction in genome sizes (420-800kb)
  • AT-richness (20-30% GC-content)
  • gene inactivation and deletion - relaxed selection, small pop size, mutational pressure due to loss of DNA repair genes
  • general correlation between GC-content and Genome size


  • hakcberry petiole gall psyllid - related to aphids - body cavity bacteriacyte
    • Pachypsylla venusta
    • Carsonella primary symbiont
  • 16.5% GC-content, 0.16 Mb
    • 15.9% protein coding regieons
  • single chromosome no plasmids
  • 159,662 bp
    • < 1/2 of 2nd smallest genome
    • approx same as chloroplast genomes
  • no insertion sequences, phages or transposons
  • 182 predicted ORFs - 136 putative functions
    • avg length 826 bp (not shorter than in other bacteriocyte symbionts (981-1006 bp))
    • in bacteria approx 1 kb
  • 97.3% protein and RNA coding regions (other bacteriocyte symbionts 77-80%)
    • due to numerous overlaping ORFs
    • majority are tandem out of frame overlaps on same strand
  • COG classification of ORFs
    • mostly in translation (35%), and amino acid metabolism (18%)
  • phyllids and aphids feed only on plant ploem sap - poor in essential AAs - need symbionts to synthesize some AAs
  • apparently no genes for cell division
  • no genes for cell envelope biogenesis (biosynthesis of fatty acid, phospholipid, lipopolysacharide)
  • no genes for lipid or nucleotide metabolism
  • many known genes necc for glycolysis and TCA cylle missing
  • only 2 transporter genes retained
  • few genes for DNA rep, recomb and repair - helicase (dnaB), primase (dnaG), alpha (dnaE) and epsilon (dnaQ) subunits of DNA pol III, and recA retained

How can Survive?

  • biological processes shared by prokaryotes and metazoa
    • compensation for metazoa-like processes of host psyllids (synthesis of non-essential AAs)
  • proteins gained multiple functions?
  • genes transferred to host nuclear genome?
    • have happened to mitochondria and chloroplasts (endosymbiont to organelle)
    • transfer of genes, acquisition of promoters, evolution of protein translocation


  • have you seen Carsonella divide?
    • tubular structure - have to be short before transfer to next generation of insect - cell div should happen before this
  • biased nucleotide usage in leading and lagging strands - see this as well?
  • does cell wall of Carsonella have peptidoglycan? - not known