Person:
Medina Bujalance, Rafael

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First Name
Rafael
Last Name
Medina Bujalance
URI
https://hdl.handle.net/20.500.14352/74313
Affiliation
Universidad Complutense de Madrid
Faculty / Institute
Ciencias Biológicas
Department
Biodiversidad, Ecología y Evolución
Area
Botánica
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2016 - 20182
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Start date: 2010 × Subject: 181.15 ×

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Now showing 1 - 2 of 2
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    HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
    (Application in Plant Sciences, 2016) G. Johnson, Matthew ; Gardner, Elliot M. ; Liu, Yang; Medina Bujalance, Rafael; Goffinet, Bernard; Shaw, A. Jonathan; Zerega, Nyree J. C.; Wickett, Norman J.
    Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of highthroughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a userfriendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.
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    Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae
    (Molecular Phylogenetics and Evolution, 2018) Medina Bujalance, Rafael; Matthew Johnson; Yang Liu; Nicholas Wilding; Terry A. Hedderson; Norman Wickett; Bernard Goffinet
    Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.