Genomewide analyses of the evolutionary impact of transposable elements

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Genome-wide analyses of the evolutionary impact
of transposable elements

• D.R. Hoen, N. Juretic, R.K. Cowan, K. Park, T.E.
  Bureau
• McGill University, Montreal, Canada
• www.biology.mcgill.ca/faculty/bureau/

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transposable elements (TE)

• mobile, replicate
• repetitive, abundant, diverse
• contribute to host genome evolution
• genome plasticity
• heterochromatin
• centromere telomere
• mammalian adaptive immune system
• de novo gene formation
• transcriptional regulation

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diversity

• classes
• retrotransposons
• mRNA is reverse-transcribed
• LTR
• DNA transposons
• DNA excises then re-inserts
• TIR
• other
• e.g. helitron - rolling circle replication
• superfamilies, families
• within each family
• autonomous non-autonomous
• active families evolve rapidly
• existing elements degenerate
• mainly not under selection
• insertions, deletions, truncations are common

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TE of rice (IRGSP japonica)
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recent ongoing studies

• transduplication
• duplicated host genomic fragments incorporated
  into DNA TE
• rogue gene creation
• transduplicate adopts selfish function
• domestication
• transposase gene adopts host function

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Mutator-like elements (MULEs)

• first identified in maize
• studies focus on rice Arabidopsis genomes

• long terminal inverted repeats (TIRs)
• 9 - 11 bp target site duplications (TSDs)
• mudrA encodes MURA transposase
• hyper-variable internal regions

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MULE identification

• standard approaches confounded by hyper-variable
  internal regions
• locate TIRs by homology
• pair TIRs
• orientation
• similarity
• distance
• TSDs
• permit nesting
• too numerous to do manually
• e.g. gt 8,000 in rice

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1. transduplication

• duplicated genomic fragments in DNA TE
• genes
• mechanism unknown
• maize, Arabidopsis, rice
• rice genome-wide study
• methods
• MULE internal sequences similar to genes
• cDNA or CD
• expressed transduplicate
• Can they encode functional proteins?

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examples
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results

• 8,274 MULEs
• 1,337 contain transduplicates
• sometimes multiple genes
• 77 transcribed
• all are pseudogenes
• cannot encode proteins
• contain disablements
• truncated CDs, premature stop codons, frameshifts
• dN/dS
• evolutionary significance?
• rare gene formation
• RNA-mediated gene silencing
• N. Juretic, D.R. Hoen, P.M. Harrison, T.E.
  Bureau. The evolutionary fate of MULE-mediated
  duplications of host gene fragments in rice.
  Genome Research, in press.

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2. rogue gene creation

• large fraction of Arabidopsis MULEs share a
  common 2nd ORF
• unrelated to mudrB
• widely conserved domain
• KAONASHI (KI)
• role?

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MULEs with KI are mobile
met1/cmt3

• transposon display
• modified AFLP
• TE-specific primer
• met1 / cmt3
• elevated transposition
• KI-containing MULE

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KI is differentially expressed

• same MULE
• same mutant
• and others
• elevated expression

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KI is diverse
KAONASHI
host clade 1
host clade 2
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KI is conserved
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summary

• KI appears to be a novel selfish gene
• 95 members
• divergent
• conserved
• expressed
• mobile
• originated by transduplication mechanism?
• function?
• some plant pathogens encode proteins containing
  same conserved domain
• thought to interfere with host defenses
• increases transposition rate?

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3. domestication

• transposase adopts host function
• only known cases in plants
• FAR1, FHY3, FRS
• derived from MULE transposase gene mudrA
• DAYSLEEPER
• newly discovered
• P. Bundock P. Hooykaas. Nature, 14 July 2005,
  282-284.
• derived from hAT transposase gene
• key evolutionary question
• How frequently does domestication lead to the
  formation of new genes?
• multi-genome study
• rice Arabidopsis ( others)

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methods

• find all mudrA-like genes in rice Arabidopsis
• eliminate those inside MULEs
• group candidate genes by phylogenetic analysis
• focus on group most taxonomically widespread
• expression
• synteny
• synonymous substitution rate
• R.K. Cowan, D.R. Hoen, D.J. Schoen, T.E. Bureau.
  MUSTANG is a novel family of transposase genes
  found in diverse angiosperms. Mol. Biol. Evol. In
  Press.

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MUG is taxonomically diverse
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(No Transcript)
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summary

• MUG is a novel family of genes
• domesticated mudrA
• domestication is rare
• only 2 extant gene families were derived from
  mudrA prior to monocot / dicot split
• FAR related
• MUG

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presentation summary

• transduplication
• selfish gene creation
• domestication
• publications, presentation, posters at
• www.biology.mcgill.ca/faculty/bureau/

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acknowledgements

• research supervisors
• Thomas Bureau
• Daniel Schoen
• Bureau Lab members
• Nikoleta Juretic
• Rebecca Cowan
• Kyong-Cheul Park
• also
• Paul Harrison
• Nabil Elrouby
• Richard Bruskiewich (IRRI)
• Takuji Sasaki (IRGSP)