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

[Beg-evodevo] External factors accelerate expression divergence between duplicate genes (Trends in Genetics)
by Cindy Martens 31 Mar '07

31 Mar '07

1 0

[Beg-evodevo] Ostreococcus tauri: seeing through the genes to the genome (Trends in Genetics)
by Cindy Martens 31 Mar '07

31 Mar '07

/Ostreococcus tauri/: seeing through the genes to the genome * * *Patrick J. Keeling* The marine green alga /Ostreococcus tauri/ is the smallest-known free-living eukaryote. The recent sequencing of its genome extends this distinction, because it also has one of the smallest and most compact nuclear genomes. For other highly compacted genomes (e.g. those of microsporidian parasites and relic endosymbiont nucleomorphs), compaction is associated with severe gene loss. By contrast, /O. tauri/ has retained a large complement of genes. Studying /O. tauri/ should shed light on forces, other than parasitism and endosymbiosis, that result in densely packed genomes. *Trends in Genetics* <http://www.sciencedirect.com/science?_ob=PublicationURL&_cdi=5183&_pubType=…> , Volume 23, Issue 4 <http://www.sciencedirect.com/science?_ob=PublicationURL&_tockey=%23TOC%2351…> , April 2007, Pages 151-154 (http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4N55TBR-1&_u…) -- ========================================================= Cindy Martens VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: +32 (0)9 331 38 22 Fax: +32 (0)9 331 38 09 E-mail: cindy.martens(a)psb.ugent.be Website: http://www.psb.ugent.be/bioinformatics =========================================================

1 0

[Beg-evodevo] Plant Physiology: Increases in the Number of SNARE Genes Parallels the Rise of Multicellularity among the Green Plants.
by Cindy Martens 30 Mar '07

30 Mar '07

*Increases in the number of SNARE genes parallels the rise of multicellularity among the green plants* *Anton Sanderfoot* The green plant lineage is the second major multicellular expansion among the eukaryotes, arising from unicellular ancestors to produce the incredible diversity of morphologies and habitats observed today. In the unicellular ancestors, secretion of material through the endomembrane system was the major mechanism for interacting and shaping the external environment. In a multicellular organism, the external environment can be made of other cells, some of which may have vastly different developmental fates, or be part of different tissues or organs. In this context, a given cell must find ways to organize its secretory pathway at a level beyond that of the unicellular ancestor. Recently, sequence information from many green plants have become available, allowing an examination of the genomes for the machinery involved in the secretory pathway. In this work, the SNARE proteins of several green plants have been identified. While little increase in gene number was seen in the SNAREs of the early secretory system, many new SNARE genes and gene families have appeared in the multicellular green plants with respect to the unicellular plants, suggesting that this increase in the number of SNARE genes may have some relation to the rise of multicellularity in green plants. Plant Physiol., May 2007, Vol. 144, No. 1 (http://www.plantphysiol.org/cgi/rapidpdf/pp.106.092973v1) -- ========================================================= Cindy Martens VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: +32 (0)9 331 38 22 Fax: +32 (0)9 331 38 09 E-mail: cindy.martens(a)psb.ugent.be Website: http://www.psb.ugent.be/bioinformatics =========================================================

1 0

[Beg-evodevo] gene family construction
by Klaas Vandepoele 14 Mar '07

14 Mar '07

This method proposes a nice (relative-treshold based) method to select relevant homologs suitable that should work well for both fast/slowly evolving genes. For details, see Materials & Methods section & Figure 6. http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/… -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, UGent Technologiepark 927, B-9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

1 0

[Beg-evodevo] PlanTAPDB: A Phylogeny-based Resource of Plant Transcription Associated Proteins
by Stefanie De Bodt 12 Mar '07

12 Mar '07

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

1 0

[Beg-evodevo] Entrez PubMed
by Yves Van de Peer 11 Mar '07

11 Mar '07

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

1 0

[Beg-evodevo] (no subject)
by Yves Van de Peer 04 Mar '07

04 Mar '07

Dear All, Interesting paper ... We should start/try to think more how to study such particular issues (evolution of networks and gene duplication) as well ... Cheers, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant 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.ugent.be http://www.psb.ugent.be/bioinformatics/

1 0