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

[Beg-evodevo] PLoS Genetics: Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological Diversification
by Klaas Vandepoele 30 Dec '09

30 Dec '09

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.100… Kousuke Hanada1,2*, Takashi Kuromori1, Fumiyoshi Myouga1, Tetsuro Toyoda2, Kazuo Shinozaki1 1 Gene Discovery Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa, Japan, 2 Bioinformatics and Systems Engineering Division, RIKEN, Yokohama, Kanagawa, Japan The differentiation of both gene expression and protein function is thought to be important as a mechanism of the functionalization of duplicate genes. However, it has not been addressed whether expression or protein divergence of duplicate genes is greater in those genes that have undergone functionalization compared with those that have not. We examined a total of 492 paralogous gene pairs associated with morphological diversification in a plant model organism (Arabidopsis thaliana). Classifying these paralogous gene pairs into high, low, and no morphological diversification groups, based on knock-out data, we found that the divergence rate of both gene expression and protein sequences were significantly higher in either high or low morphological diversification groups compared with those in the no morphological diversification group. These results strongly suggest that the divergence of both expression and protein sequence are important sources for morphological diversification of duplicate genes. Although both mechanisms are not mutually exclusive, our analysis suggested that changes of expression pattern play the minor role (33%–41%) and that changes of protein sequence play the major role (59%–67%) in morphological diversification. Finally, we examined to what extent duplicate genes are associated with expression or protein divergence exerting morphological diversification at the whole-genome level. Interestingly, duplicate genes randomly chosen from A. thaliana had not experienced expression or protein divergence that resulted in morphological diversification. These results indicate that most duplicate genes have experienced minor functionalization.

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[Beg-evodevo] The Story behind 'A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea'
by Klaas Vandepoele 25 Dec '09

25 Dec '09

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Dongying Wu1,2, Philip Hugenholtz1, Konstantinos Mavromatis1, Rüdiger Pukall3, Eileen Dalin1, Natalia N. Ivanova1, Victor Kunin1, Lynne Goodwin4, Martin Wu5, Brian J. Tindall3, Sean D. Hooper1, Amrita Pati1, Athanasios Lykidis1, Stefan Spring3, Iain J. Anderson1, Patrik Dhaeseleer1,6, Adam Zemla6, Mitchell Singer2, Alla Lapidus1, Matt Nolan1, Alex Copeland1, Cliff Han4, Feng Chen1, Jan-Fang Cheng1, Susan Lucas1, Cheryl Kerfeld1, Elke Lang3, Sabine Gronow3, Patrick Chain1,4, David Bruce4, Edward M. Rubin1, Nikos C. Kyrpides1, Hans-Peter Klenk3 & Jonathan A. Eisen1,2 Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms1. There are now nearly 1,000 completed bacterial and archaeal genomes available2, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution3, 4, 5. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic phylogenomic efforts to compile a phylogeny-driven Genomic Encyclopedia of Bacteria and Archaea in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come. http://phylogenomics.blogspot.com/2009/12/story-behind-nature-paper-on-phyl…

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[Beg-evodevo] Heterogeneous patterns of gene expression diversif...[Mol Biol Evol. 2009] - PubMed Result
by Yves Van de Peer 20 Oct '09

20 Oct '09

http://www.ncbi.nlm.nih.gov/pubmed/19822635?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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] Gene and genome duplications: the impact of dosage...[Chromosome Res. 2009] - PubMed Result
by Yves Van de Peer 11 Oct '09

11 Oct '09

http://www.ncbi.nlm.nih.gov/pubmed/19802709?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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] /group/evodevo share almost full
by Klaas Vandepoele 06 Oct '09

06 Oct '09

>df -h /group/evodevo/ psbnas01-e0d:/vol/bioprojects/evodevo 287G 275G 12G 97% /group/evodevo Happy cleaning / archiving! Klaas Overview: *#Gb* *Location* 1.00 ./users/pepat/Gm10 1.01 ./projects/tiblo/final/plaza/PLAZA/trunk/src 1.06 ./projects/tiblo/final/plaza/PLAZA/trunk 1.06 ./projects/tiblo/final/plaza/PLAZA 1.06 ./projects/tiblo/final/plaza 1.10 ./users/sepro/TiPS 1.11 ./users/sepro/annotation/vitis 1.19 ./projects/tiblo/final/dataset2/colinearityTesting 1.20 ./projects/Plasmodium/Old/MCL/MCL_E-05_Perc70 1.28 ./users/sepro/annotation/Sorghum 1.48 ./users/pepat/Sb10 1.71 ./users/pepat/Pt11 1.74 ./users/stbod_pub 1.85 ./users/sepro_pub/new_datasets_ppi/Mint 1.90 ./users/sepro/apple/001_fail/blast 2.02 ./users/pepat/Alyrata/210808/mclblastline_nuc_ssf_b60_I25/rerun_M100 2.15 ./users/sepro/apple/002_new_attempt/blast 2.38 ./users/pepat/Pp11 2.40 ./projects/tiblo/final/dataset/cds 2.43 ./users/sepro/apple/002_new_attempt 2.75 ./users/sepro/intergenics/coords 2.75 ./users/sepro/intergenics 2.83 ./users/sepro/apple/001_fail 2.85 ./users/pepat/Os61 3.03 ./users/sepro_pub/liste_apple 3.18 ./users/pepat/Vv1 3.28 ./projects/Plasmodium/Old/MCL 3.54 ./users/sepro/annotation 3.71 ./users/pepat/Alyrata/210808/mclblastline_nuc_ssf_b60_I25 3.87 ./projects/tiblo/final/dataset 4.46 ./users/pepat/Alyrata/210808 4.46 ./users/pepat/Alyrata 4.74 ./users/sepro_pub/new_datasets_ppi 5.73 ./users/sepro/apple 6.70 ./projects/Plasmodium/Old/BLASTP 8.31 ./projects/tiblo/final/dataset2/annot/remappedtandemlists/randomlists/lists 8.32 ./projects/tiblo/final/dataset2/annot/remappedtandemlists/randomlists 8.34 ./projects/tiblo/final/dataset2/annot/remappedtandemlists 8.52 ./projects/tiblo/final/dataset2/annot 10.16 ./projects/Plasmodium/Old 10.36 ./projects/Plasmodium 10.63 ./users/sepro_pub 11.51 ./projects/tiblo/final/dataset2 15.77 ./users/sepro 16.44 ./projects/tiblo/final 19.82 ./users/pepat 30.51 ./projects/tiblo 41.01 ./projects 48.78 ./users 89.79 . -- 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] Comparative genomics of protoploid Saccharomycetaceae
by Klaas Vandepoele 29 Sep '09

29 Sep '09

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[Beg-evodevo] Abstract | PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees
by Klaas Vandepoele 25 Sep '09

25 Sep '09

http://www.biomedcentral.com/1471-2105/10/298/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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on out and change the world (around us)

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[Beg-evodevo] Molecular phylogenetics, temporal diversification and principles of evolution in the mustard family (Brassicaceae)
by Jeffrey Fawcett 14 Sep '09

14 Sep '09

de Peera... It discusses the WGD and diversification in Brassicaceae together with the ecological context and climatic changes. Jeffrey -- ================================================================== Jeffrey Fawcett Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM jeffrey.fawcett(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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[Beg-evodevo] Wiley InterScience :: JOURNALS :: The Plant Journal
by Klaas Vandepoele 10 Sep '09

10 Sep '09

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[Beg-evodevo] muscle
by Tine Blomme 05 Aug '09

05 Aug '09

Hello, There is a new version of the muscle alignment tool available (v4.0, instead of v3.7 which is now on midas). Should we ask to have the new version installed on midas? Tine °°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°° Tine Blomme Bioinformatics group VIB department of Plant Systems Biology Ghent University Technologiepark 927, B-9052 Zwijnaarde Tel: +32 (0)9 331 38 22

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