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

Persistent Link:
http://hdl.handle.net/10150/610015
Title:
Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries
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
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
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

Full metadata record

DC FieldValue Language
dc.contributor.authorPaiva, Jorgeen
dc.contributor.authorPrat, Elisaen
dc.contributor.authorVautrin, Soniaen
dc.contributor.authorSantos, Mauroen
dc.contributor.authorSan-Clemente, Heleneen
dc.contributor.authorBrommonschenkel, Sergioen
dc.contributor.authorFonseca, Pauloen
dc.contributor.authorGrattapaglia, Darioen
dc.contributor.authorSong, Xiangen
dc.contributor.authorAmmiraju, Jettyen
dc.contributor.authorKudrna, Daviden
dc.contributor.authorWing, Roden
dc.contributor.authorFreitas, Anaen
dc.contributor.authorBerges, Heleneen
dc.contributor.authorGrima-Pettenati, Jacquelineen
dc.date.accessioned2016-05-20T08:56:31Z-
dc.date.available2016-05-20T08:56:31Z-
dc.date.issued2011en
dc.identifier.citationPaiva et al. BMC Genomics 2011, 12:137 http://www.biomedcentral.com/1471-2164/12/137en
dc.identifier.doi10.1186/1471-2164-12-137en
dc.identifier.urihttp://hdl.handle.net/10150/610015-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/12/137en
dc.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)en
dc.titleAdvancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC librariesen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentInstituto de Investigação Científica Tropical (IICT), Centro de Florestas e dos Produtos Florestais, Tapada da Ajuda, 1349-018 Lisboa, Portugalen
dc.contributor.departmentInstituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugalen
dc.contributor.departmentINRA-CNRGV, Chemin de Borde Rouge, 31326 Castanet-Tolosan, Franceen
dc.contributor.departmentInstituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID/IST), R. Alves Redol 9, 1000-029 Lisboa, Portugalen
dc.contributor.departmentUniversité de Toulouse; UPS; UMR 5546, Surfaces Cellulaires et Signalisation chez les Végétaux; BP 42617, F-31326, Castanet-Tolosan, Franceen
dc.contributor.departmentCNRS; UMR 5546; BP 42617, F-31326, Castanet-Tolosan, Franceen
dc.contributor.departmentBIOAGRO - Federal University of Viçosa, Av. P. H. Rolfs, s/n - 36570-000 - Viçosa, MG, Brasilen
dc.contributor.departmentEMBRAPA Genetic Resources and Biotechnology, EPqB Final W5 NOrte, 70770-910 Brasilia, DF, Brazilen
dc.contributor.departmentArizona Genomics Institute, School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson AZ 85721, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis 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.en
dc.eprint.versionFinal published versionen
All Items in UA Campus Repository are protected by copyright, with all rights reserved, unless otherwise indicated.