March 2010 - beg-evodevo@psb.ugent.be

[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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