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Conservation of Divergent Transcript in FungiPhilip R. Kensche, Martin Oti, Bas E. Dutilh, Martijn A. Huynen
Center for Molecular and Biomolecular Informatics / Nijmegen Center for Molecular Life Sciences,Radboud University Medical Center. PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
PMID 18375009, email: [email protected]
C Bm i
IntroductionWe quantified the conservation of divergent (←→), co-oriented (→→) and convergent (→←) genes in the genomes of 19 asco- and basidio-myceteous fungi. Divergent gene orientation is most conserved, which suggests an abundance of bidirectional promoters.
Acknowledgements This work was funded by the Netherlands Bioinformatics Centre (NBIC), which is supported by the Netherlands Ge-nomics Initiative (NGI) and by the European Union’s Sixth Framework Programme EPISTEM (CT-2005-019067).
Divergent gene pairs are more conserved in orientation ...
Hemiasco-mycota
Euasco-mycota
Basidio-mycota
divergence time (My)
log 1
0(fra
ctio
n of
con
serv
ed g
ene
pairs
)
−3
−2
−1
0
0 100 200 300 400 500
divergentco-orientedconvergent
... although they have longer in-tergenic spacers.
distance between transcript
kern
ele
dens
ity
−400 0400
8001200
16002000
2400
divergentco-orientedconvergent
If separation of genes was only dependent on intergenic distance (neutral model), than the more conserved divergent gene pairs should have shorter intergenic spacers.
Quantify the conservation of individual gene pairsGene pairs were scored by how long their orien-tation was maintained during fungal evolution.We assumed that a gene pair gained its orienta-tion exactly once during this time (Dollo parsi-mony).
conservation score (My)
convergent
co-oriented
divergent
101.5 102.0 102.5 103.0 103.5
Conservation of orientation correlates with co-expression ...
conservation score (My)
co−e
xpre
ssio
n (S
pear
man
)
−0.5
0.0
0.5
1.0
0 2000
divergent
0 2000
co-oriented
0 2000
convergent
... independent of spacer length.
divergentcooriented
convergentnot adjacent
co-expression (Spearman)
kern
el d
ensi
ty
−0.5 0.0 0.5 1.0
coexpression ~ conservationspacer ~ conservationspacer ~ coexpression
−0.2 −0.1 0.0 0.1
divergent
−0.1 0.0 0.1
co-oriented
−0.1 0.0 0.1
convergent
Kendall’s τpartial Kendall’s τ
Conserved divergent gene pairs are functionally related!
area under ROC curve (AUC)
phylogenetic profilingconvergentco-oriented
divergent
0.45 0.50 0.55 0.60
Interactions from KEGG, MIPS, and Yeast GRID.Higher conservation of functionally related gene pairs only for divergent gene pairs (one-sided U-test, p=1.65×10-2).
