Landscape of a tree genome

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Landscape of a tree genome A case study with
Populus
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How is our tree of interest, phylogenetically
placed ?
Eucalyptus
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
Populus
Arabidopsis
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Tailoring the genome
Greedy assemblers
The genome assembly process
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
Align-layout-consensus
BAC-by-BAC (hierarchical) sequencing
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Tailoring the genome
Large insert clones (BACs)
Genewise Genscan GeneMark
Gene Prediction
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
ESTwise Blast Genome Threading
Creating supportive biological evidences
Gene Annotation
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Populus genes statistics
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
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Populus genome duplication events
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
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Populus gene content
Populus has substantially more protein- coding
genes than Arabidopsis
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
Most common domains occur in Populus compared
with Arabidopsis in a ratio ranging from 1.41
to 1.81.
The common eurosid gene set 11,666
protein-coding genes
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SNP Polymorphisms
Populus is a highly polymorphic taxon and
substantial numbers of SNPs are present even
within a single individual
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
..suggesting that the majority of coding regions
in the Populus genome are subject to purifying
selection
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Gene Family evolution
The expansion of several gene families has
contributed to the evolution of Populus biology.
Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome
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Eucalyptus Genome

• The Euca genome typically,
• Relatively smaller genome (600MB)
• No evidence for recent polyploidization
• Extensive genome synteny across species
• Transformation models are already developed in
  Euca
• Extensive opportunity for comparative genomics
  with Populus

Phylogeny Assembly Annotation Populus
Genome Organization Gene content SNPs Gene family
Evol. Euca Genome

• 3 MB of shared DNA of E. grandis revealed,
• GC content of 40.15
• Genic regions composed of 38.95 introns and
  45.51 exons
• Only 5.8 was represented by repetitive elements

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