February 2007 - beg-evodevo@psb.ugent.be

[Beg-evodevo] Trends in Genetics: The origins of multicellularity: a multi-taxon genome initiative
by Cindy Martens 24 Feb '07

24 Feb '07

The origins of multicellularity: a multi-taxon genome initiative * * *Iñaki Ruiz-Trillo, Gertraud Burger, Peter W.H. Holland, Nicole King, B. Franz Lang, Andrew J. Roger and Michael W. Gray* The emergence of multicellular organisms from single-celled ancestors -- which occurred several times, independently in different branches of the eukaryotic tree -- is one of the most profound evolutionary transitions in the history of life. These events not only radically changed the course of life on Earth but also created new challenges, including the need for cooperation and communication between cells, and the division of labor among different cell types. However, the genetic changes that accompanied the several origins of multicellularity remain elusive. Recently, the National Human Genome Research Institute (NHGRI) endorsed a multi-taxon genome-sequencing initiative that aims to gain insights into how multicellularity first evolved. This initiative (which we have termed UNICORN) will generate extensive genomic data from some of the closest extant unicellular relatives of both animals and fungi. Here, we introduce this initiative and the biological questions that underpin it, summarize the rationale guiding the choice of organisms and discuss the anticipated benefits to the broader scientific community. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4MYF5Y6-4&_u… -- ================================================================== Cindy Martens Tel:32 (0)9 3313822 DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:cimar@psb.ugent.be http://www.psb.ugent.be/bioinformatics ==================================================================

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[Beg-evodevo] Trends in Genetics: Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor
by Cindy Martens 24 Feb '07

24 Feb '07

Reciprocal gene loss between /Tetraodon/ and zebrafish after whole genome duplication in their ancestor * * *Marie Sémon and Kenneth H. Wolfe*^ The whole genome duplication that occurred in ray-finned fish coincided with the radiation of teleost species; consequently, these two phenomena have often been linked. Using the /Tetraodon/ and zebrafish complete genome sequences, we tested a molecular hypothesis that can relate whole genome duplication to speciation in teleosts. We estimate that thousands of genes that remained duplicated when /Tetraodon/ and zebrafish diverged underwent reciprocal loss subsequently in these two species, probably contributing to reproductive isolation between them. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4MYF5Y6-2&_u… -- ================================================================== Cindy Martens Tel:32 (0)9 3313822 DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:cimar@psb.ugent.be http://www.psb.ugent.be/bioinformatics ==================================================================

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[Beg-evodevo] Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks : Article : Molecular Systems Biology
by Klaas Vandepoele 21 Feb '07

21 Feb '07

Linking phylogenetic profiles with (prokaryotic) phenotypes & lifestyle http://www.nature.com/msb/journal/v2/n1/full/msb4100047.html

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[Beg-evodevo] nrg2063.pdf
by Klaas Vandepoele 20 Feb '07

20 Feb '07

-- ------------------------------------------------------------------ Klaas Vandepoele, PhD Tel. 32 (0)9 3313822 DEPARTMENT OF PLANT SYSTEMS BIOLOGY VIB/GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ------------------------------------------------------------------

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[Beg-evodevo] fyi :: The Regulatory Code for Transcriptional Response Diversity and Its Relation to Genome Structural Properties in A. thaliana
by Klaas Vandepoele 20 Feb '07

20 Feb '07

In fact this paper is primarily based on collecting public data, counting and comparing distributions (using statistical tests). But, it ends up in PLoS Genetics... Definitively a MUST read (contains results about expression breadth, cis-elements, paralogs & GO enrichment) http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371…

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[Beg-evodevo] FYI
by Steven Maere 16 Feb '07

16 Feb '07

Interesting... -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group Ghent University / VIB Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3692 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] DarkHorse: a method for genome-wide prediction of horizontal gene transfer
by Klaas Vandepoele 13 Feb '07

13 Feb '07

Method:: DarkHorse: a method for genome-wide prediction of horizontal gene transfer Podell S, Gaasterland T Genome Biology, 2007 8:R16 ( 2 February 2007 ) http://genomebiology.com/content/pdf/gb-2007-8-2-r16.pdf With results about plants! Klaas -- ------------------------------------------------------------------ Klaas Vandepoele, PhD Tel. 32 (0)9 3313822 DEPARTMENT OF PLANT SYSTEMS BIOLOGY VIB/GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ------------------------------------------------------------------

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[Beg-evodevo] The Gene Balance Hypothesis: From Classical Genetics to Modern Genomics
by Klaas Vandepoele 12 Feb '07

12 Feb '07

and our group is well cited (Simillion & Maere) -- ------------------------------------------------------------------ Klaas Vandepoele, PhD Tel. 32 (0)9 3313822 DEPARTMENT OF PLANT SYSTEMS BIOLOGY VIB/GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ------------------------------------------------------------------

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[Beg-evodevo] Entrez PubMed
by Yves Van de Peer 04 Feb '07

04 Feb '07

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

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