- beg-evodevo@psb.ugent.be - maillist.psb.ugent.be

[Beg-evodevo] Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli -- Hanada et al. 148 (2): 993 -- PLANT PHYSIOLOGY
by Klaas Vandepoele 09 Oct '08

09 Oct '08

http://www.plantphysiol.org/cgi/content/abstract/148/2/993 -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-evodevo] Phylogenetic and chromosomal analyses of multiple ...[BMC Evol Biol. 2008] - PubMed Result
by Yves Van de Peer 28 Sep '08

28 Sep '08

http://www.ncbi.nlm.nih.gov/pubmed/18803835?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] Whole-Genome Duplications in the Ancestral Vertebr...[J Mol Evol. 2008] - PubMed Result
by Yves Van de Peer 28 Sep '08

28 Sep '08

http://www.ncbi.nlm.nih.gov/pubmed/18815825?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] Metabolic innovations towards the human lineage
by Klaas Vandepoele 16 Sep '08

16 Sep '08

Metabolic innovations towards the human lineage Shiri Freilich email, Leon Goldovsky email, Christos A Ouzounis email and Janet M Thornton Background We describe a function-driven approach to the analysis of metabolism which takes into account the phylogenetic origin of biochemical reactions to reveal subtle lineage-specific metabolic innovations, undetectable by more traditional methods based on sequence comparison. The origins of reactions and thus entire pathways are inferred using a simple taxonomic classification scheme that describes the evolutionary course of events towards the lineage of interest. We investigate the evolutionary history of the human metabolic network extracted from a metabolic database, construct a network of interconnected pathways and classify this network according to the taxonomic categories representing eukaryotes, metazoa and vertebrates. Results It is demonstrated that lineage-specific innovations correspond to reactions and pathways associated with key phenotypic changes during evolution, such as the emergence of cellular organelles in eukaryotes, cell adhesion cascades in metazoa and the biosynthesis of complex cell-specific biomolecules in vertebrates. Conclusions This phylogenetic view of metabolic networks puts gene innovations within an evolutionary context, demonstrating how the emergence of a phenotype in a lineage provides a platform for the development of specialized traits. BMC Evolutionary Biology 2008, 8:247doi:10.1186/1471-2148-8-247 http://www.biomedcentral.com/1471-2148/8/247/abstract

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[Beg-evodevo] Widespread conservation of genetic redundancy duri...[Trends Genet. 2008] - PubMed Result
by Yves Van de Peer 14 Sep '08

14 Sep '08

http://www.ncbi.nlm.nih.gov/pubmed/18786741?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] PLoS Genetics: Evolutionary Convergence on Highly-Conserved 3′ Intron Structures in Intron-Poor Eukaryotes and Insights into the Ancestral Eukaryotic Genome
by Klaas Vandepoele 10 Sep '08

10 Sep '08

Abstract The presence of spliceosomal introns in eukaryotes raises a range of questions about genomic evolution. Along with the fundamental mysteries of introns' initial proliferation and persistence, the evolutionary forces acting on intron sequences remain largely mysterious. Intron number varies across species from a few introns per genome to several introns per gene, and the elements of intron sequences directly implicated in splicing vary from degenerate to strict consensus motifs. We report a 50-species comparative genomic study of intron sequences across most eukaryotic groups. We find two broad and striking patterns. First, we find that some highly intron-poor lineages have undergone evolutionary convergence to strong 3′ consensus intron structures. This finding holds for both branch point sequence and distance between the branch point and the 3′ splice site. Interestingly, this difference appears to exist within the genomes of green alga of the genus /Ostreococcus/, which exhibit highly constrained intron sequences through most of the intron-poor genome, but not in one much more intron-dense genomic region. Second, we find evidence that ancestral genomes contained highly variable branch point sequences, similar to more complex modern intron-rich eukaryotic lineages. In addition, ancestral structures are likely to have included polyT tails similar to those in metazoans and plants, which we found in a variety of protist lineages. Intriguingly, intron structure evolution appears to be quite different across lineages experiencing different types of genome reduction: whereas lineages with very few introns tend towards highly regular intronic sequences, lineages with very short introns tend towards highly degenerate sequences. Together, these results attest to the complex nature of ancestral eukaryotic splicing, the qualitatively different evolutionary forces acting on intron structures across modern lineages, and the impressive evolutionary malleability of eukaryotic gene structures. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.100… -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-evodevo] Abstract | Preferential regulation of duplicated genes by microRNAs in mammals
by Klaas Vandepoele 28 Aug '08

28 Aug '08

http://genomebiology.com/2008/9/8/R132/abstract -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-evodevo] Coexpression of Linked Genes in Mammalian Genomes Is Generally Disadvantageous
by Tine Blomme 01 Aug '08

01 Aug '08

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[Beg-evodevo] NRG :: Horizontal gene transfer in eukaryotic evolution
by Klaas Vandepoele 29 Jul '08

29 Jul '08

Horizontal gene transfer in eukaryotic evolution Patrick J. Keeling^1 <http://www.nature.com/nrg/journal/v9/n8/full/nrg2386.html#a1> & Jeffrey D. Palmer^2 <http://www.nature.com/nrg/journal/v9/n8/full/nrg2386.html#a2> <http://www.nature.com/nrg/journal/v9/n8/authors/nrg2386.html> -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-evodevo] Comparative genomics: Lining up is hard to do
by Klaas Vandepoele 20 Jul '08

20 Jul '08

http://www.nature.com/nrg/journal/v9/n8/full/nrg2420.html Fulltext: Nature Reviews Genetics 9, 573 (August 2008) | doi:10.1038/nrg2420 Comparative genomics: Lining up is hard to do Tanita Casci Comparisons between proteins or between DNA stretches tell a story about the evolutionary past. Unfortunately, however, which story they tell often depends on which method is used to line up the sequences. A new method claims to improve the accuracy of current alignments by making use not only of the similarity between sequences but also their phylogenetic history. Commonly used methods for aligning multiple sequences rely on sequential pairwise alignments between sequences --- the most closely related sequences are aligned first, followed by progressively more distant ones, all the way down the evolutionary tree. The problem with these so-called 'progressive algorithms' is that it is impossible to distinguish insertions from deletions when using only two sequences, causing biases that distort subsequent alignments. Traditional implementations of this algorithm set a higher penalty for insertions than for deletions and deem the former less likely to have occurred. These biases are particularly problematic when there are multiple neighbouring insertions or deletions --- for example, such insertions end up being aligned one under the other even though, by definition, they are not evolutionarily related. Misleading alignments caused by these false homologies are propagated, and lead to incorrect inferences about sequence evolution. Two sequences do not contain information about whether a length difference between them is caused by an insertion or a deletion --- however, in a multiple (as opposed to pairwise) alignment there are more than two sequences. The new phylogeny-aware algorithm uses outgroup information from related sequences to infer which of the two possible changes has happened. It does so by 'flagging' the gaps (length changes) made in earlier alignments so that they can be accounted for in future alignments without incurring a penalty. The re-use of a flagged gap also indicates that a particular length change was created by an insertion; the gap can then be labelled as a 'permanent' insertion and correctly kept distinct from any neighbouring ones. The new algorithm, called PRANK <http://www.ebi.ac.uk/goldman-srv/prank/>, was tested on simulated sequence data. Traditional methods were shown to introduce biases, and therefore misalignments, even when sequences are closely related. PRANK performs better than traditional methods in this situation and shows no bias as the sequences get more diverged and become harder to align. It is striking that traditional methods are error prone even when sequences get increasingly similar --- indicating that denser species sampling and more DNA sequencing cannot correct the algorithmic flaw in the alignment. Correct alignment remains a challenge, but less so than in the past. Why have programs traditionally performed so badly? The authors suggest that alignments were historically developed to compare protein sequences, in which any biases would be likely to cluster harmlessly in unconstrained regions. Given the increasingly widespread analysis of genomic DNA for understanding evolution there is a pressing need to get these methods up to scratch. Links WEB SITE * PRANK <http://www.ebi.ac.uk/goldman-srv/prank> Top of page <http://www.nature.com/nrg/journal/v9/n8/full/nrg2420.html#top> References and links ORIGINAL RESEARCH PAPER 1. Löytynoja, A & Goldman, N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320, 1632--1635 (2008) * Article <http://dx.doi.org/10.1126/science.1158395> * PubMed <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=P…> * ChemPort <http://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg…> FURTHER READING

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