Identification of Transposable Elements Using Multiple Alignments of Related Genomes

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Identification of Transposable Elements Using
Multiple Alignments of Related Genomes

• I690 Paper Presentation
• Yin Wu

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Transposable Elements

• Transposable Elements (TEs) are the chief cause
  of gapped regions in up to 10 of currently
  sequenced genomes.
• Alignment gaps which have little or no alignment
  to other genomes lead to signatures within
  multiple alignments that can be used to identify
  TEs.

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Multiple Alignments BTW Related Genomes
By aligning genomes of related species, it is
possible to identify TEs. Consider a speciation
event causing the recent divergence of genomes S1
and S2. We expect to see some gaps in the
alignment due to small insertions and deletions.
Those long and repeated gaps are likely to be
TEs. When additional related genomes are added
to the alignments, the chance of mis-alignment
decreases.
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Method

• Multiple alignment of homologous regions of
  related genomes to find Insertion Regions (IR)
• Local alignment of each set of IRs to find
  Repeated Insertion Regions (RIR)
• Filter and assemble RIRs.

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Types of Insertions
Micr-satellite (NOT TE)
Tandem Repeats
Nested Repeats
Concatenated Repeats
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Filter and assemble RIRs

• Micro-satellite regions Short (lt20 bp) repeats
  with close and sequential hits to self.
• Tandem repeats Long (gt30 bp) repeats which
  sequentially align to both self and to
  subcomponents in other IRs.

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Filter and assemble RIRs (contd)

• Nested repeats Long non-overlapping (gt30 bp)
  that sequentially align to other IRs, where there
  is no intersection between the set of IRs to
  which each subcomponent aligned.
• Concatenated repeats IRs within a certain
  genomic distance (lt700 bp) that align
  sequentially to other insertion regions.

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Case Study

• Case study on four drosophila genomes
• Melanogaster, Yakuba, Pseudoobscura, and Virilis
• The result is compared against the BDBP natural
  TE annotation set. (http//www.fruitfly.org/p_disr
  upt/TE.html)

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Case Study (contd)
Conserved Region
Insertion Region (gap)
Annotated TEs
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Case Study (contd)
Chr arm BDGP Trans Not in Alignment Not in RIR (false neg) In RIR (true pos)
X 276 8 52 216
2L 305 16 62 227
2R 312 3 52 257
3L 288 13 65 210
3R 288 5 64 219
4 102 21 33 48
1571 66 349 1156
100 4.2 22 74
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Case Study (contd)

• Identification of new instances of known TE
  families
• 355 instances of recent elements
• 232 instances of ancient elements
• Proposed new families in euchromatin
• Define a cluster of RIRs to be a new family if
  the intracluster variability is within certain
  threshold
• Six new families of TEs are proposed, each
  containing more than five instances.

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Limitation

• The proposed method is dependent on the
  annotation of homologous regions (to avoid gene
  rearrangements).
• Inversion and translocation are not detected by
  this method.