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    Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

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    Author
    Paiva, Jorge
    Prat, Elisa
    Vautrin, Sonia
    Santos, Mauro
    San-Clemente, Helene
    Brommonschenkel, Sergio
    Fonseca, Paulo
    Grattapaglia, Dario
    Song, Xiang
    Ammiraju, Jetty
    Kudrna, David
    Wing, Rod
    Freitas, Ana
    Berges, Helene
    Grima-Pettenati, Jacqueline
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    Affiliation
    Instituto de Investigação Científica Tropical (IICT), Centro de Florestas e dos Produtos Florestais, Tapada da Ajuda, 1349-018 Lisboa, Portugal
    Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
    INRA-CNRGV, Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
    Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID/IST), R. Alves Redol 9, 1000-029 Lisboa, Portugal
    Université de Toulouse; UPS; UMR 5546, Surfaces Cellulaires et Signalisation chez les Végétaux; BP 42617, F-31326, Castanet-Tolosan, France
    CNRS; UMR 5546; BP 42617, F-31326, Castanet-Tolosan, France
    BIOAGRO - Federal University of Viçosa, Av. P. H. Rolfs, s/n - 36570-000 - Viçosa, MG, Brasil
    EMBRAPA Genetic Resources and Biotechnology, EPqB Final W5 NOrte, 70770-910 Brasilia, DF, Brazil
    Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson AZ 85721, USA
    Issue Date
    2011
    
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    Show full item record
    Publisher
    BioMed Central
    Citation
    Paiva et al. BMC Genomics 2011, 12:137 http://www.biomedcentral.com/1471-2164/12/137
    Journal
    BMC Genomics
    Rights
    © 2011 Paiva et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
    Collection Information
    This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
    Abstract
    BACKGROUND:Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.RESULTS:We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1) digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene greater than or equal to] 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.CONCLUSIONS:The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15x), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (E. grandis BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming Eucalyptus reference genome sequence.
    EISSN
    1471-2164
    DOI
    10.1186/1471-2164-12-137
    Version
    Final published version
    Additional Links
    http://www.biomedcentral.com/1471-2164/12/137
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2164-12-137
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