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

[Beg-evodevo] Three Periods of Regulatory Innovation During Vertebrate Evolution
by Klaas Vandepoele 22 Aug '11

22 Aug '11

http://www.sciencemag.org/content/333/6045/1019.full -- Prof. Dr. Klaas Vandepoele 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/cig/ ---------------------------------------------------------

1 0

[Beg-evodevo] Reductive evolution of proteomes and protein structures
by Klaas Vandepoele 26 Jul '11

26 Jul '11

Abstract The lengths of orthologous protein families in Eukarya are almost double the lengths found in Bacteria and Archaea. Here we examine protein structures in 745 genomes and show that protein length differences between superkingdoms arise as much shorter prokaryotic nondomain linker sequences. Eukaryotic, bacterial, and archaeal linkers are 250, 86, and 73 aa residues in length, respectively, whereas folded domain sequences are 281, 280, and 256 residues, respectively. Cryptic domains match linkers (P < 0.0001) with probabilities ranging between 0.022 and 0.042; accordingly, they do not affect length estimates significantly. Linker sequences support intermolecular binding within proteomes and they are probably enriched in intrinsically disordered regions as well. Reductively evolved linker sequence lengths in growth rate maximized cells should be proportional to proteome diversity. By using total in-frame coding capacity of a genome [i.e., coding sequence (CDS)] as a reliable measure of proteome diversity, we find linker lengths of prokaryotes clearly evolve in proportion to CDS values, whereas those of eukaryotes are more randomly larger than expected. Domain lengths scarcely change over the entire range of CDS values. Thus, the protein linkers of prokaryotes evolve reductively whereas those of eukaryotes do not. http://www.pnas.org/content/108/29/11954.abstract?etoc -- Prof. Dr. Klaas Vandepoele 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/cig/ ---------------------------------------------------------

1 0

[Beg-evodevo] TATA box gain after duplication
by Stefanie De Bodt 02 May '11

02 May '11

http://www.ncbi.nlm.nih.gov/pubmed/21515810?dopt=Abstract -- ================================================================== 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 ==================================================================

1 0

[Beg-evodevo] Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
by Klaas Vandepoele 23 Mar '11

23 Mar '11

Expression evolution following WGD and fractionation in maize Klaas *Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss* James C. Schnablea, Nathan M. Springer and Michael Freeling Abstract Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5--12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars. -- Prof. Dr. Klaas Vandepoele 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/cig/ --------------------------------------------------------- Conference& Workshop Comparative& Regulatory Genomics in Plants Website: http://bioinformatics.psb.ugent.be/crg_event/ ---------------------------------------------------------

1 0

[Beg-evodevo] Ancient gene duplication provided a key molecular ... [Mol Biol Evol. 2011] - PubMed result
by Yves Van de Peer 25 Jan '11

25 Jan '11

http://www.ncbi.nlm.nih.gov/pubmed/21245414?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/ Check out! http://www.plantgenomeevolution.com/

1 0

[Beg-evodevo] Minor change, major difference: divergent function... [Development. 2011] - PubMed result
by Yves Van de Peer 25 Jan '11

25 Jan '11

http://www.ncbi.nlm.nih.gov/pubmed/21247963?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/ Check out! http://www.plantgenomeevolution.com/

1 0

[Beg-evodevo] Evolution: Young genes are essential too : Article : Nature Reviews Genetics
by Klaas Vandepoele 23 Jan '11

23 Jan '11

http://www.nature.com/nrg/journal/v12/n2/full/nrg2945.html

1 0

[Beg-evodevo] Genetic interactions reveal the evolutionary trajectories of duplicate genes
by Klaas Vandepoele 18 Nov '10

18 Nov '10

http://www.nature.com/msb/journal/v6/n1/full/msb201082.html -- 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/ --------------------------------------------------------- PLAZA, a resource for Plant Comparative Genomics http://bioinformatics.psb.ugent.be/plaza/ ---------------------------------------------------------

1 0

[Beg-evodevo] Distinct Patterns of Expression and Evolution of Intronless and Intron-Containing Mammalian Genes -- Shabalina et al. 27 (8): 1745 -- Molecular Biology and Evolution
by Klaas Vandepoele 23 Jul '10

23 Jul '10

http://mbe.oxfordjournals.org/cgi/content/abstract/27/8/1745?etoc

1 0

[Beg-evodevo] Following tetraploidy in maize, a short deletion m... [PLoS Biol. 2010] - PubMed result
by Klaas Vandepoele 11 Jul '10

11 Jul '10

http://www.ncbi.nlm.nih.gov/pubmed/20613864?dopt=Abstract PLoS Biol. <javascript:AL_get(this, 'jour', 'PLoS Biol.');> 2010 Jun 29;8(6):e1000409. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. Woodhouse MR <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Woodhouse%20MR%22%5BAuthor%5D>, Schnable JC <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Schnable%20JC%22%5BAuthor%5D>, Pedersen BS <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Pedersen%20BS%22%5BAuthor%5D>, Lyons E <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lyons%20E%22%5BAuthor%5D>, Lisch D <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lisch%20D%22%5BAuthor%5D>, Subramaniam S <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Subramaniam%20S%22%5BAuthor%5D>, Freeling M <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Freeling%20M%22%5BAuthor%5D>. Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America. Abstract Previous work in Arabidopsis showed that after an ancient tetraploidy event, genes were preferentially removed from one of the two homeologs, a process known as fractionation. The mechanism of fractionation is unknown. We sought to determine whether such preferential, or biased, fractionation exists in maize and, if so, whether a specific mechanism could be implicated in this process. We studied the process of fractionation using two recently sequenced grass species: sorghum and maize. The maize lineage has experienced a tetraploidy since its divergence from sorghum approximately 12 million years ago, and fragments of many knocked-out genes retain enough sequence similarity to be easily identifiable. Using sorghum exons as the query sequence, we studied the fate of both orthologous genes in maize following the maize tetraploidy. We show that genes are predominantly lost, not relocated, and that single-gene loss by deletion is the rule. Based on comparisons with orthologous sorghum and rice genes, we also infer that the sequences present before the deletion events were flanked by short direct repeats, a signature of intra-chromosomal recombination. Evidence of this deletion mechanism is found 2.3 times more frequently on one of the maize homeologs, consistent with earlier observations of biased fractionation. The over-fractionated homeolog is also a greater than 3-fold better target for transposon removal, but does not have an observably higher synonymous base substitution rate, nor could we find differentially placed methylation domains. We conclude that fractionation is indeed biased in maize and that intra-chromosomal or possibly a similar illegitimate recombination is the primary mechanism by which fractionation occurs. The mechanism of intra-chromosomal recombination explains the observed bias in both gene and transposon loss in the maize lineage. The existence of fractionation bias demonstrates that the frequency of deletion is modulated. Among the evolutionary benefits of this deletion/fractionation mechanism is bulk DNA removal and the generation of novel combinations of regulatory sequences and coding regions. PMID: 20613864 [PubMed - in process]

1 0