De novo assembled expressed gene catalog of a fast-growing Eucalyptus plantation tree produced by Illumina mRNA-Seq

Eucalyptus is a keystone genus for the international pulp and paper industry worth billions of dollars, and it is currently the most important hardwood fibre crop in the world. It has also been identified as a candidate source of lignocellulosic biomass for future production of bioenergy. A draft genome sequence will soon (by the end of 2010) be produced for a Eucalyptus tree species (E. grandis). Genome annotation of this valuable woody plant and genetic dissection of it superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs. Herein we present an extensive transcript-derived gene catalog for a commercially grown Eucalyptus hybrid (E. grandis x E. urophylla) genotype constructed using only Illumina mRNA-sequencing technology and de novo transcript assembly. We produced and annotated close to 19,000 transcript-derived contigs, a large proportion of which represent full-length protein coding genes including 3' and 5' UTRs. Analysis of assembly quality, contig length and diversity of genes represented show that this dataset surpasses all current publically available expressed sequence information for eucalypt species. Additionally, mRNA-Seq analysis allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions and tissue-specificity. Finally, the deep coverage of the mRNA-Seq data allowed confident identification of more than 100,000 transcript-derived SNPs which will aid in the mapping of genes and assembly of the newly sequenced E. grandis genome. This study demonstrates the benefits of ultra-high throughput short-read technology for de novo assembly of gene catalogs in non-model organisms.