Ongoing Synteny Analysis of the Monodelphis Genome

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Ongoing Synteny Analysis of the Monodelphis
Genome

• Synteny Subgroup

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Methodology

• Full pairwise genomic alignments (masked)
• Clustering of well-behaved runs of alignments

• Pairwise syntenic maps--key parameters
• minimum allowed segment size,
• maximum alignment-free gap allowed within segment
• minimum number of anchors
• Does not rely on feature annotations (genes)

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Alignment Clusters

• Heuristics to handle duplications
• Example alignments surrounding OCTN gene family

M11
D2
D2
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Monodelphis Synteny
Chicken
Dog
Human
Monodelphis
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Number of rearrangements vs. syntenic resolution
Inter- and intrachromosomal events
Human vs Dog Human vs Rat Human vs
Mouse Human vs Monodelphis
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Monodelphis as an Outgroup
Use monodelphis to assign rearrangements to
phylogenetic tree
Reconstruct ancestral karyotype? Is this
biologically interesting?
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Human X vs Dog, Chicken
Xp
Xq
Human
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Human X vs Dog, Chicken,Mono
Xp
Xq
Human
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300Kb Region in Human
Syntenic anchors on HSA20
Human (300Kb)
Dog (247Kb)
Human (300Kb)
Mouse (256Kb)
Human (300Kb)
Monodelphis (320Kb)
truncated
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Anchors in Global Synteny Maps
Number of anchors in 500Kb maps
human vs dog 1623K human vs mouse
648K human vs mono 321K human vs chicken
127K