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      PlnTFDB: updated content and new features of the plant transcription factor database

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          Abstract

          The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species ( sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

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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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            The Sorghum bicolor genome and the diversification of grasses.

            Andrew Paterson, John Bowers, Rémy Bruggmann … (2009)
            Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
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              The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.

              Stefan Rensing, Daniel Lang, Andreas D Zimmer … (2008)
              We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): January 2010
                Publication date (Electronic): 25 October 2009
                Publication date PMC-release: 24 October 2009
                Volume: 38
                Issue: Database issue , Database issue
                Pages: D822-D827
                Affiliations
                1Department of Molecular Biology, Institute of Biochemistry and Biology, GoFORSYS, University of Potsdam, Karl-Liebknecht-Str. 24-25, Haus 20, 14476 Potsdam-Golm, Germany, 2Colegio de Postgraduados, Km. 36.5 Carretera México, Texcoco, Montecillo, Estado de México. C.P. 56230, Mexico, 3GabiPD Team, Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, 4Cooperative Research Group, Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam - Golm and 5FRISYS, Faculty of Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg, Germany
                Author notes
                *To whom correspondence should be addressed. Tel: +49-(0)331-567-8752; Fax: +49-(0)331-567-89-8750; Email: riano@ 123456mpimp-golm.mpg.de

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

                Article
                Publisher ID: gkp805
                DOI: 10.1093/nar/gkp805
                PMC ID: 2808933
                PubMed ID: 19858103
                SO-VID: 59d16b6c-94f4-4885-abaa-aae3d7d2da1d
                Copyright © © The Author(s) 2009. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 10 July 2009
                Date accepted : 13 September 2009
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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