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      Transcriptome Sequences Resolve Deep Relationships of the Grape Family

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          Abstract

          Previous phylogenetic studies of the grape family ( Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

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          MRBAYES: Bayesian inference of phylogenetic trees.

          J P Huelsenbeck, F Ronquist (2001)
          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

            Alberto Casagrande (2007)
            The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
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              Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

              Brant C Faircloth, John E McCormack, Nicholas G Crawford … (2012)
              Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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                Author and article information

                Contributors
                Hector Candela: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2013
                Publication date (Electronic): 17 September 2013
                Volume: 8
                Issue: 9
                Electronic Location Identifier: e74394
                Affiliations
                [1 ]Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C., United States of America
                [2 ]BGI-Shenzhen, Shenzhen, China
                [3 ]Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
                [4 ]College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
                [5 ]UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
                [6 ]Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
                Universidad Miguel Hernández de Elche, Spain
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: JW EAZ XDF. Performed the experiments: JW ZQX ZLN LKM XZK YBZ. Analyzed the data: ZQX ZLN LKM JW. Wrote the manuscript: JW ZQX ZLN LKM JG XDF SMI EAZ.

                Article
                Publisher ID: PONE-D-13-06799
                DOI: 10.1371/journal.pone.0074394
                PMC ID: 3775763
                PubMed ID: 24069307
                SO-VID: 2a664988-aec2-43c0-bf83-4406144e03a8
                Copyright statement: Copyright @ 2013
                License:

                This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                Date received : 2 February 2013
                Date accepted : 1 August 2013
                Funding
                This study was funded by grants from the Office of the Smithsonian Undersecretary of Science, the US National Science Foundation (grant DEB 0743474 to S.R. Manchester and J. Wen, and grant DEB 0743499 to J. Gerrath), the Small Grants Program of the National Museum of Natural History of the Smithsonian Institution to JW, and trust funds generated by EAZ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article

                ScienceOpen disciplines: Uncategorized
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