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

[Beg-evodevo] PLoS Genetics: Role of Duplicate Genes in Robustness against Deleterious Human Mutations
by Klaas Vandepoele 29 Mar '08

29 Mar '08

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.100…

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[Beg-evodevo] expression divergence following duplication
by Stefanie De Bodt 25 Mar '08

25 Mar '08

http://www.ncbi.nlm.nih.gov/pubmed/18350173?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] Field & Osbourn (2008)Science,epub.pdf
by Klaas Vandepoele 25 Mar '08

25 Mar '08

Metabolic Diversification—Independent Assembly of Operon-Like Gene Clusters in Plants Ben Field and Anne E. Osbourn* -- 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/ =================================================================== I have no idea what I am talking about ===================================================================

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[Beg-evodevo] Metabolic Diversification--Independent Assembly of...[Science. 2008] - PubMed Result
by Yves Van de Peer 23 Mar '08

23 Mar '08

http://www.ncbi.nlm.nih.gov/pubmed/18356490?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] InParanoid 6: eukaryotic ortholog clusters with in...[Nucleic Acids Res. 2008] - PubMed Result
by Yves Van de Peer 23 Mar '08

23 Mar '08

http://www.ncbi.nlm.nih.gov/pubmed/18055500?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] The Dynamic Nature of Eukaryotic Genomes
by Klaas Vandepoele 19 Mar '08

19 Mar '08

A biology-oriented view on genome evolution. * The Dynamic Nature of Eukaryotic Genomes *Laura Wegener Parfrey,* Daniel J. G. Lahr,* and Laura A. Katz* *Program in Organismic and Evolutionary Biology, University of Massachusetts; and Department of Biological Sciences, Smith College, Northampton, MA Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes. Though much is known about genomes in animals, fungi, and plants, these lineages represent only 3 of the 60--200 lineages of eukaryotes. Here, we discuss diverse genomic strategies in exemplar eukaryotic lineages, including numerous microbial eukaryotes, to reveal dramatic variation that challenges established views of genome evolution. For example, in the life cycle of some members of the ''radiolaria,'' ploidy increases from haploid (N) to approximately 1,000N, whereas intrapopulation variability of the enteric parasite Entamoeba ranges from 4N to 40N. Variation has also been found within our own species, with substantial differences in both gene content and chromosome lengths between individuals. Data on the dynamic nature of genomes shift the perception of the genome from being fixed and characteristic of a species (typological) to plastic due to variation within and between species.

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[Beg-evodevo] Genes of Cyanobacterial Origin in Plant Nuclear Genomes Point to a Heterocyst-Forming Plastid Ancestor -- Deusch et al. 25 (4): 748 -- Molecular Biology and Evolution
by Klaas Vandepoele 19 Mar '08

19 Mar '08

Acquisition of cyanobacterial genes in green/red plant genomes http://mbe.oxfordjournals.org/cgi/content/abstract/25/4/748?etoc Genes of Cyanobacterial Origin in Plant Nuclear Genomes Point to a Heterocyst-Forming Plastid Ancestor * Oliver Deusch^* , Giddy Landan^{dagger} , Mayo Roettger^* , Nicole Gruenheit^* , Klaus V. Kowallik^* , John F. Allen^{ddagger} , William Martin^* and Tal Dagan^* * Plastids are descended from a cyanobacterial symbiosis which^ occurred over 1.2 billion years ago. During the course of endosymbiosis,^ most genes were lost from the cyanobacterium's genome and many^ were relocated to the host nucleus through endosymbiotic gene^ transfer (EGT). The issue of how many genes were acquired through^ EGT in different plant lineages is unresolved. Here, we report^ *the genome-wide frequency of gene acquisitions from cyanobacteria^ in 4 photosynthetic eukaryotes---/Arabidopsis/, rice, /Chlamydomonas/,^ and the red alga /Cyanidioschyzon/*---by comparision of the^ 83,138 proteins encoded in their genomes with 851,607 proteins^ encoded in 9 sequenced cyanobacterial genomes, 215 other reference^ prokaryotic genomes, and 13 reference eukaryotic genomes. The^ analyses entail *11,569 phylogenies *inferred with both maximum^ likelihood and Neighbor-Joining approaches. Because each phylogenetic^ result is dependent not only upon the reconstruction method^ but also upon the site patterns in the underlying alignment,^ we investigated how the reliability of site pattern generation^ via alignment affects our results: if the site patterns in an^ alignment differ depending upon the order in which amino acids^ are introduced into multiple sequence alignment---N- to^ C-terminal versus C- to N-terminal---then the phylogenetic^ result is likely to be artifactual. Excluding unreliable alignments^ by this means, we obtain a conservative estimate, wherein *about^ 14% of the proteins examined in each plant genome indicate a^ cyanobacterial origin *for the corresponding nuclear gene, with^ higher proportions (17--25%) observed among the more reliable^ alignments. The identification of cyanobacterial genes in plant^ genomes affords access to an important question: From which^ type of cyanobacterium did the ancestor of plastids arise? *Among^ the 9 cyanobacterial genomes sampled, /Nostoc/ sp. PCC7120 and^ /Anabaena variabilis/ ATCC29143 were found to harbor collections^ of genes which are---in terms of presence/absence and sequence^ similarity---more like those possessed by the plastid ancestor^ *than those of the other 7 cyanobacterial genomes sampled here.^ This suggests that the ancestor of plastids might have been^ an organism more similar to filamentous, heterocyst-forming^ (nitrogen-fixing) representatives of section IV recognized in^ Stanier's cyanobacterial classification. Members of section^ IV are very common partners in contemporary symbiotic associations^ involving endosymbiotic cyanobacteria, which generally provide^ nitrogen to their host, consistent with suggestions that fixed^ nitrogen supplied by the endosymbiont might have played an important^ role during the origin of plastids.^ *Key Words:* endosymbiosis . phylogenomics . multiple sequence alignment . plastid origin . nitrogen

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[Beg-evodevo] test
by Tine Blomme 10 Mar '08

10 Mar '08

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[Beg-evodevo] Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony -- Sakarya et al. 24 (5): 606 -- Bioinformatics
by Klaas Vandepoele 06 Mar '08

06 Mar '08

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/5/606?etoc -- 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/ =================================================================== = You eye each other as you pass. She looks back, you look back = ===================================================================

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[Beg-evodevo] Gene conversion in the rice genome. [BMC Genomics. 2008] - PubMed Result
by Yves Van de Peer 02 Mar '08

02 Mar '08

http://www.ncbi.nlm.nih.gov/pubmed/18298833?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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