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

[Beg-evodevo] Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
by Klaas Vandepoele 13 May '10

13 May '10

Note how in this paper synteny information is used to confirm the existence of functional gene clusters. Klaas *Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser* David A Fitzpatrick email, Peadar O'Gaora email, Kevin P Byrne email and Geraldine Butler BMC Genomics 2010, 11:290doi:10.1186/1471-2164-11-290 Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of Candida species. CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Lodderomyces elongisporus, Debaryomyces hansenii, Pichia stipitis, Candida guilliermondii and Candida lusitaniae). Saccharomyces cerevisiae is also included as a reference genome. CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C. albicans. Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie. http://www.biomedcentral.com/1471-2164/11/290/abstract

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[Beg-evodevo] evodevo share full
by Stefanie De Bodt 23 Apr '10

23 Apr '10

please clean up! Thanks, Stefanie -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://www.psb.ugent.be ==================================================================

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[Beg-evodevo] plant phys april 2010 special focus on polyploidy
by Steven Maere 22 Mar '10

22 Mar '10

http://www3.interscience.wiley.com/journal/118538954/home ================================================================== Steven Maere, PhD Group leader, Evolutionary Systems Biology group Dept. of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3805 fax: +32 9 331 3809 email: stmae(a)psb.vib-ugent.be http://www.psb.ugent.be/esb/ ==================================================================

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[Beg-evodevo] The Incredible Expanding Ancestor of Eukaryotes
by Klaas Vandepoele 15 Mar '10

15 Mar '10

-- 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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on out and change the world (around us)

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[Beg-evodevo] Extensive Divergence in Alternative Splicing Patte... [Mol Biol Evol. 2010] - PubMed result
by Klaas Vandepoele 13 Mar '10

13 Mar '10

http://www.ncbi.nlm.nih.gov/pubmed/20185454?dopt=Abstract *Extensive Divergence in Alternative Splicing Patterns After Gene and Genome Duplication During the Evolutionary History of Arabidopsis.* Zhang PG, Huang SZ, Pin AL, Adams KL. UBC Botanical Garden and Centre for Plant Research, Department of Botany, 2357 Main Mall, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada. Gene duplication at various scales, from single gene duplication to whole genome duplication, has occurred throughout eukaryotic evolution and contributed greatly to the large number of duplicated genes in the genomes of many eukaryotes. Previous studies have shown divergence in expression patterns of many duplicated genes at various evolutionary time scales and cases of gain of a new function or expression pattern by one duplicate, or partitioning of functions or expression patterns between duplicates. Alternative splicing is a fundamental aspect of the expression of many genes that can increase gene product diversity and affect gene regulation. However the evolution of alternative splicing patterns of genes duplicated by polyploidy, as well as in a sizable number of duplicated gene pairs in plants, has not been examined. Here we have characterized conservation and divergence in alternative splicing patterns in genes duplicated by a polyploidy event during the evolutionary history of Arabidopsis thaliana. We used RT-PCR to assay 104 whole genome duplicates in six organ types and in plants grown under three abiotic stress treatments to detect organ- and stress-specific patterns of alternative splicing. Differences in splicing patterns in one or more organs, or under stress conditions, were found between the genes in a large majority of the duplicated pairs. In a few cases, alternative splicing patterns were the same between duplicates only under one or more abiotic stress treatments and not under normal growing conditions, or vice versa. We also examined alternative splicing in 42 tandem duplicates and we found patterns of alternative splicing roughly comparable to the genes duplicated by polyploidy. The alternatively spliced forms in some of the genes created premature stop codons that would result in missing or partial functional domains if the transcripts are translated, which could affect gene function and cause functional divergence between duplicates. Our results indicate that alternative splicing patterns have diverged considerably after gene and genome duplication during the evolutionary history of the Arabidopsis lineage, sometimes in an organ or stress-specific manner. Alternative splicing divergence between duplicated genes may have contributed to gene functional evolution and led to preservation of some duplicated genes. PMID: 20185454 [PubMed - as supplied by publisher]

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[Beg-evodevo] Genomicus: a database and a browser to study gene ... [Bioinformatics. 2010] - PubMed result
by Yves Van de Peer 28 Feb '10

28 Feb '10

http://www.ncbi.nlm.nih.gov/pubmed/20185404?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] From elements to modules: regulatory evolution in ... [Curr Opin Genet Dev. 2009] - PubMed result
by Yves Van de Peer 14 Feb '10

14 Feb '10

http://www.ncbi.nlm.nih.gov/pubmed/19879128?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] [Fwd: Confronting Intelligent Design arguments directly in the scientific literature]
by Klaas Vandepoele 21 Jan '10

21 Jan '10

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[Beg-evodevo] Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
by Pierre Rouze 08 Jan '10

08 Jan '10

http://www.pnas.org/content/107/1/472.abstract?etoc from dear old Paterson ... -- Pierre ROUZE Bioinformatics / Senior Expert Scientist VIB Department of Plant Systems Biology Ghent University Technologie park 927, B-9052 GENT BELGIUM Tel :32.933 13694 Cell.Phone : 32.476 638 304 Fax :32.933 13809 pierre.rouze(a)psb.vib-ugent.be http://www.psb.ugent.be/bioinformatics ¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨¨ prediction is very difficult, especially about the future Niels Bohr

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[Beg-evodevo] Abstract | TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
by Klaas Vandepoele 08 Jan '10

08 Jan '10

http://www.biomedcentral.com/1471-2105/11/7/abstract TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses *Ben C Stoever* email <http://www.biomedcentral.com/logon/logon.asp?msg=ce> and *Kai F Mueller* email <http://www.biomedcentral.com/logon/logon.asp?msg=ce> /BMC Bioinformatics/ 2010, *11**:*7doi:10.1186/1471-2105-11-7 Abstract (provisional) Background Today it is common to apply multiple potentially conflicting data sources to a given phylogenetic problem. At the same time, several different inference techniques are routinely employed instead of relying on just one. In view of both trends it is becoming increasingly important to be able to efficiently compare different sets of statistical values supporting (or conflicting with) the nodes of a given tree topology, and merging this into a meaningful representation. A tree editor supporting this should also allow for flexible editing operations and be able to produce ready-to-publish figures. Results We developed TreeGraph 2, a GUI-based graphical editor for phylogenetic trees (available from http://treegraph.bioinfweb.info) It allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences. The program features versatile editing and formatting options, such as automatically setting line widths or colors according to the value of any of the unlimited number of variables that can be assigned to each node or branch. These node/branch data can be imported from spread sheets or other trees, be calculated from each other by specified mathematical expressions, filtered, copied from and to other internal variables, be kept invisible or set visible and then be freely formatted (individually or across the whole tree). Beyond typical editing operations such as tree rerooting and ladderizing or moving and collapsing of nodes, whole clades can be copied from other files and be inserted (along with all node/branch data and legends), but can also be manually added and, thus, whole trees can quickly be manually constructed de novo. TreeGraph 2 outputs various graphic formats such as SVG, PDF, or PNG, useful for tree figures in both publications and presentations.

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