A new genomic resource dedicated to wood formation in Eucalyptus.

David Rengel,Florence Servant,Hélène San Clemente,Etienne Paux,Nathalie Ladouce,Patrick Wincker,Jacqueline Grima-Pettenati,Pierre Sivadon,Arnaud Couloux

doi:10.1186/1471-2229-9-36

Abstract

BackgroundRenowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. Thus, there is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs) from genes involved in wood formation in Eucalyptus would provide a valuable resource.ResultsWe report here the normalization and sequencing of a cDNA library from developing Eucalyptus secondary xylem, as well as the construction and sequencing of two subtractive libraries (juvenile versus mature wood and vice versa). A total of 9,222 high quality sequences were collected from about 10,000 cDNA clones. The EST assembly generated a set of 3,857 wood-related unigenes including 2,461 contigs (Cg) and 1,396 singletons (Sg) that we named 'EUCAWOOD'. About 65% of the EUCAWOOD sequences produced matches with poplar, grapevine, Arabidopsis and rice protein sequence databases. BlastX searches of the Uniref100 protein database allowed us to allocate gene ontology (GO) and protein family terms to the EUCAWOOD unigenes. This annotation of the EUCAWOOD set revealed key functional categories involved in xylogenesis. For instance, 422 sequences matched various gene families involved in biosynthesis and assembly of primary and secondary cell walls. Interestingly, 141 sequences were annotated as transcription factors, some of them being orthologs of regulators known to be involved in xylogenesis. The EUCAWOOD dataset was also mined for genomic simple sequence repeat markers, yielding a total of 639 putative microsatellites. Finally, a publicly accessible database was created, supporting multiple queries on the EUCAWOOD dataset.ConclusionIn this work, we have identified a large set of wood-related Eucalyptus unigenes called EUCAWOOD, thus creating a valuable resource for functional genomics studies of wood formation and molecular breeding in this economically important genus. This set of publicly available annotated sequences will be instrumental for candidate gene approaches, custom array development and marker-assisted selection programs aimed at improving and modulating wood properties.

Highlights

Renowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly
Construction and sequencing of normalized libraries With the aim of sequencing a large number of expressed sequences tags (ESTs) representative of the set of mRNAs expressed in secondary xylem, we chose a cDNA library prepared from the differentiating secondary xylem of E. gunnii [XylcDNA] containing 1.5 × 106 clones [17], which has already proven a good source of genes expressed during wood formation [1723]
Human desmin cDNA was added at 1,000 copies to the non-normalized library whereas EgCAD2, of which 31 cDNA copies were present before normalization, served as an internal control

Summary

Introduction

Renowned for their fast growth, valuable wood properties and wide adaptability, Eucalyptus species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. There is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs) from genes involved in wood formation in Eucalyptus would provide a valuable resource. The production of wood or secondary xylem by xylogenesis is a remarkable example of terminal differentiation, producing a complex three-dimensional tissue specialized in conduction and mechanical support. This differentiation process comprises four major steps: cell division, cell expansion, deposition of lignified secondary cell wall and programmed cell death. Variations between juvenile and mature wood present within the same tree produce distinct wood properties such as density and pulp yield [3]

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Results

Conclusion