June 2008 - beg-evodevo@psb.ugent.be

[Beg-evodevo] Escape from adaptive conflict after duplication in an anthocyanin pathway gene : Abstract : Nature
by Klaas Vandepoele 26 Jun '08

26 Jun '08

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature07092.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/ --------------------------------------------------------- Not shy of a spark, a knife twists at the thought that I should fall short of the mark

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[Beg-evodevo] The amphioxus genomes...
by Klaas Vandepoele 23 Jun '08

23 Jun '08

One in Nature http://www.nature.com/nature/journal/v453/n7198/abs/nature06967.html and one in GR http://www.genome.org/cgi/content/abstract/gr.073676.107v1 -- 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/ --------------------------------------------------------- Not shy of a spark, a knife twists at the thought that I should fall short of the mark

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[Beg-evodevo] On the origin of new genes in Drosophila. [Genome Res. 2008] - PubMed Result
by Klaas Vandepoele 23 Jun '08

23 Jun '08

Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole genome level. Here we unveil genome-wide patterns for the mutational mechanisms leading to new genes, and their subsequent lineage-specific evolution at different time nodes in the D. melanogaster species subgroup. We find that, *1) tandem gene duplication has generated about 80% of the nascent duplicates* that are limited to single species (D. melanogaster or D. yakuba); 2) the most abundant new genes shared by multiple species (44.1%) are dispersed duplicates, and are more likely to be retained and be functional; 3) de novo gene origination from non-coding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes; 4) retroposition is also an important mechanism, and had generated approximately 10% new genes; 5) about 30% of the new genes in the D. melanogaster species complex recruited various genomic sequences and formed chimeric gene structures, suggesting structure innovation as an important way to help fixation of new genes; and 6) the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup. Finally, we survey gene frequencies among 19 strains from all over the world for D. melanogaster-specific new genes, and reveal that 44.4% of them show copy number polymorphisms within population. In conclusion, we provide a panoramic picture for origin of new genes in Drosophila species. http://www.ncbi.nlm.nih.gov/pubmed/18550802?dopt=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/ --------------------------------------------------------- Not shy of a spark, a knife twists at the thought that I should fall short of the mark

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[Beg-evodevo] Origin and early evolution of angiosperms
by Stefanie De Bodt 23 Jun '08

23 Jun '08

http://www.ncbi.nlm.nih.gov/pubmed/18559813?dopt=Abstract -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://bioinformatics.psb.ugent.be ==================================================================

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[Beg-evodevo] Gene Ontology analysis
by Klaas Vandepoele 16 Jun '08

16 Jun '08

Two great papers: Use and misuse of the gene ontology annotations <http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2363.html>. Rhee et al., (also pointed out by Pierre); http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2363.html And an overview of 14 tools performing GO enrichment analysis Ontological analysis of gene expression data: current tools, limitations, and open problems <http://bioinformatics.oxfordjournals.org/cgi/content/full/21/18/3587>. http://bioinformatics.oxfordjournals.org/cgi/content/full/21/18/3587 Klaas -- 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/ --------------------------------------------------------- Not shy of a spark, a knife twists at the thought that I should fall short of the mark

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[Beg-evodevo] ScienceDirect - Trends in Plant Science : Adaptive evolution in invasive species
by lieven sterck 11 Jun '08

11 Jun '08

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD1-4SM7RKV-1&_u… -- ============================================================== Lieven Sterck Predoctoral fellow Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================

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[Beg-evodevo] Large-scale analysis of gene clustering in bacteria -- Yang and Sze 18 (6): 949 -- Genome Research
by Klaas Vandepoele 04 Jun '08

04 Jun '08

http://www.genome.org/cgi/content/abstract/18/6/949 -- 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/ --------------------------------------------------------- Not shy of a spark, a knife twists at the thought that I should fall short of the mark

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