Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brainManuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona E08028, Spain
Proc Natl Acad Sci U S A 108:5319-24. 2011
..In addition, we find that tissue-specific Nova expression patterns emerged independently in other lineages, suggesting independent assembly of tissue-specific regulatory networks...
Origin of introns by 'intronization' of exonic sequencesManuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
Trends Genet 24:378-81. 2008
..Intronization is more common than the reverse process, loss of splicing of retained introns. Finally, these findings link alternative splicing with modern intron creation...
- Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
Sci Rep 2:433. 2012
..In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications...
- Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
RNA Biol 9:12-21. 2012
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- Intron mis-splicing: no alternative?
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
Genome Biol 9:208. 2008
..This striking inefficiency deepens the mystery of the proliferation and persistence of introns...
- Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
PLoS Genet 4:e1000148. 2008
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- Quantitative regulation of alternative splicing in evolution and development
Manuel Irimia
Departament de Genetica, and Institut de Biomedicina IBUB, Universitat de Barcelona, Barcelona, Spain
Bioessays 31:40-50. 2009
..We discuss the potential role of changes in developmental regulation of AS as an additional layer in complex gene regulatory networks and in the emergence of genetic novelties...
- Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures
Manuel Irimia
Department of Genetics, School of Biology, University of Barcelona, Barcelona, Spain
Genome Biol Evol 3:551-64. 2011
..These results attest to the importance of locus-specific splicing functions in differences in structural evolution across genes, as well as to commonalities of forces shaping the evolution of individual genes along different lineages...
Widespread evolutionary conservation of alternatively spliced exons in CaenorhabditisManuel Irimia
Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
Mol Biol Evol 25:375-82. 2008
..Finally, we demonstrate an inverse relationship between AS and gene duplication, suggesting that the latter may be primarily responsible for the emergence of new functional transcripts in nematodes...
- Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
Manuel Irimia
Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
BMC Evol Biol 7:188. 2007
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- Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
PLoS ONE 4:e5800. 2009
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- Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer
Manuel Irimia
Departament de Genètica and Institut de Biomedicina IBUB, Universitat de Barcelona, Barcelona, Spain
Evodevo 1:7. 2010
..These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively). To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians...
- From the American to the European amphioxus: towards experimental Evo-Devo at the origin of chordates
Jordi Garcia-Fernandez
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Spain
Int J Dev Biol 53:1359-66. 2009
..We summarise here our progress towards the dream of the experimental manipulation of the amphioxus embryo, to enter the era of Experimental Evo-Devo...
- An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
Ignacio Maeso
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona 08028, Barcelona, Spain
Genome Res 22:642-55. 2012
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- Coevolution of genomic intron number and splice sites
Manuel Irimia
Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
Trends Genet 23:321-5. 2007
..It seems that eukaryotic ancestors had relatively large intron numbers and 'weak' 5'ss, a pattern associated with frequent alternative splicing in modern organisms...
- Complex selection on 5' splice sites in intron-rich organisms
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
Genome Res 19:2021-7. 2009
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- Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus
Salvatore D'Aniello
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
Mol Biol Evol 25:1841-54. 2008
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- Internal and external paralogy in the evolution of tropomyosin genes in metazoans
Manuel Irimia
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
Mol Biol Evol 27:1504-17. 2010
..This parallel evolution of TPM genes in diverse metazoans attests to common selective forces driving divergence of different gene transcripts and represents a striking case of emergence of evolutionary novelty by alternative splicing...
- Spliceosomal introns as tools for genomic and evolutionary analysis
Manuel Irimia
Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
Nucleic Acids Res 36:1703-12. 2008
..We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions...
- Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata
Manuel Irimia
Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
Mol Biol Evol 24:1604-7. 2007
..Including the additional species paints a very different picture, with 13 remaining characters consistent with Ecdysozoa versus only 1 consistent with Coelomata...
- Rare genomic characters do not support Coelomata: intron loss/gain
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mol Biol Evol 25:620-3. 2008
..2005a. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408.). Instead, we show that our conclusions are likely to be robust to such concerns...
- Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mol Biol Evol 25:1192-8. 2008
..Finally, we find a lack of synapomorphic gene losses, suggesting a low rate of ancestral gene loss in Plasmodium...
- When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis
Scott William Roy
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
Bioessays 30:601-5. 2008
..Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html)...
- Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates
Cristian Canestro
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Av Diagonal 645, 08028 Barcelona, Spain
Semin Cell Dev Biol 24:83-94. 2013
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- Convergent evolution of clustering of Iroquois homeobox genes across metazoans
Manuel Irimia
Mol Biol Evol 25:1521-5. 2008
..Finally, we discuss the possible causes and implications of the convergent evolution of this genomic and regulatory organization throughout metazoans...
- High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae
Jakob Lewin Rukov
Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Ole Maaløes Vej 5, DK 2200 Copenhagen N, Denmark
Mol Biol Evol 24:909-17. 2007
..Moreover, our results indicate that AS contributes little to transcript variation in Caenorhabditis genes and that gene duplication may be the major evolutionary mechanism for the origin of novel transcripts in these 2 species...
- Rare genomic characters do not support Coelomata: RGC_CAMs
Scott William Roy
J Mol Evol 66:308-15. 2008
..These results indicate that the Coelomata signal is a long-branch artifact...
- Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes
Scott William Roy
Mol Biol Evol 23:1824-7. 2006
..5 billion years. Nine other predicted introns are due to annotation errors reflecting apparent mistakes in the E. histolytica genome assembly. These results underscore the massive differences in intron gain rates through evolution...
