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Open Access Highly Accessed Research article

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

Jorge AP Paiva12*, Elisa Prat3, Sonia Vautrin3, Mauro D Santos4, Hélène San-Clemente56, Sérgio Brommonschenkel7, Paulo GS Fonseca4, Dario Grattapaglia8, Xiang Song9, Jetty SS Ammiraju9, David Kudrna9, Rod A Wing9, Ana T Freitas4, Hélène Bergès3 and Jacqueline Grima-Pettenati56

Author Affiliations

1 Instituto de Investigação Científica Tropical (IICT), Centro de Florestas e dos Produtos Florestais, Tapada da Ajuda, 1349-018 Lisboa, Portugal

2 Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal

3 INRA-CNRGV, Chemin de Borde Rouge, 31326 Castanet-Tolosan, France

4 Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID/IST), R. Alves Redol 9, 1000-029 Lisboa, Portugal

5 Université de Toulouse; UPS; UMR 5546, Surfaces Cellulaires et Signalisation chez les Végétaux; BP 42617, F-31326, Castanet-Tolosan, France

6 CNRS; UMR 5546; BP 42617, F-31326, Castanet-Tolosan, France

7 BIOAGRO - Federal University of Viçosa, Av. P. H. Rolfs, s/n - 36570-000 - Viçosa, MG, Brasil

8 EMBRAPA Genetic Resources and Biotechnology, EPqB Final W5 NOrte, 70770-910 Brasilia, DF, Brazil

9 Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson AZ 85721, USA

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BMC Genomics 2011, 12:137  doi:10.1186/1471-2164-12-137

Published: 4 March 2011

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 ≥ 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 (> 15×), 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.