Toni Gabaldón

Publications (90) View all

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  Available from: Toni Gabaldón

  Article: Functional and evolutionary implications of gene orthology.

  Toni Gabaldón, Eugene V Koonin
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  ABSTRACT: Orthologues and paralogues are types of homologous genes that are related by speciation or duplication, respectively. Orthologous genes are generally assumed to retain equivalent functions in different organisms and to share other key properties. Several recent comparative genomic studies have focused on testing these expectations. Here we discuss the complexity of the evolution of gene-phenotype relationships and assess the validity of the key implications of orthology and paralogy relationships as general statistical trends and guiding principles.
  Nature Reviews Genetics 04/2013; · 38.08 Impact Factor
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  Available from: Toni Gabaldón

  Article: Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida.

  Jonas Collén, Betina Porcel, Wilfrid Carré, Steven G Ball, Cristian Chaparro, Thierry Tonon, Tristan Barbeyron, Gurvan Michel, Benjamin Noel, Klaus Valentin, [......], Frédéric Partensky, Julie Poulain, Stefan A Rensing, Sylvie Rousvoal, Gaelle Samson, Aikaterini Symeonidi, Jean Weissenbach, Antonios Zambounis, Patrick Wincker, Catherine Boyen
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  ABSTRACT: Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.
  Proceedings of the National Academy of Sciences 03/2013; · 9.68 Impact Factor
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  Available from: Toni Gabaldón

  Article: Comparative transcriptomics of early dipteran development.

  Eva Jiménez-Guri, Jaime Huerta-Cepas, Luca Cozzuto, Karl R Wotton, Hui Kang, Heinz Himmelbauer, Guglielmo Roma, Toni Gabaldón, Johannes Jaeger
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  ABSTRACT: BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).
  BMC Genomics 02/2013; 14(1):123. · 4.07 Impact Factor
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  Available from: Toni Gabaldón

  Article: Measuring guide-tree dependency of inferred gaps in progressive aligners.

  Salvador Capella-Gutiérrez, Toni Gabaldón
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  ABSTRACT: MOTIVATION: Multiple sequence alignments are generally reconstructed using a progressive approach that follows a guide-tree. During this process gaps are introduced at a cost to maximize residue pairing, but it is unclear whether inferred gaps reflect actual past events of sequence insertions or deletions. It has been found that patterns of inferred gaps in alignments contain information towards the true phylogeny, but it is as yet unknown whether gaps are simply reflecting information that was already present in the guide-tree. RESULTS: We here develop a framework to disentangle the phylogenetic signal carried by gaps from that which is already present in the guide-tree. Our results indicate that most gaps are incorrectly inserted in patterns that, nevertheless, follow the guide-tree. Thus, most gap patterns in current alignments are not informative per se. This affects different programs to various degrees, being PRANK the most sensitive to the guide-tree.
  Bioinformatics 02/2013; · 5.47 Impact Factor
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  Available from: Mª del Carmen Gil Borlado

  Dataset: Pathogenic mutations in the 5 0 untranslated region of BCS1L mRNA in mitochondrial complex III deficiency

  M Carmen Gil-Borlado, Maritza González-Hoyuela, Alberto Blázquez, M Teresa García-Silva, Toni Gabaldón, Javier Manzanares, Julia Vara, Miguel A Martín, Sara Seneca, Joaquín Arenas, Cristina Ugalde
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  ABSTRACT: a b s t r a c t Mutations in the assembly chaperone BCS1L constitute a major cause of mitochondrial complex III defi-ciency. We studied the presence of BCS1L mutations in a complex III-deficient patient with metabolic aci-dosis, liver failure, and tubulopathy. A previously reported mutation, p.R56X, was identified in one BCS1L allele, and two novel heterozygous mutations, g.1181A > G and g.1164C > G, were detected in the second allele. The g.1181A > G mutation generated an alternative splicing site in the BCS1L transcript, causing a 19-nucleotides deletion in its 5 0 UTR region. Decreased BCS1L mRNA and protein levels, and a respiratory chain complex III assembly impairment, determine a pathogenic role for the novel BCS1L mutations.