"Post-genomics" research in Eucalyptus in the near future

Hibino, Takashi

doi:10.5511/plantbiotechnology.26.109

Cited by 4 publications

(1 citation statement)

References 13 publications

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“…To support the genome annotation effort, there is much value in having a dataset of genes with strong transcriptional evidence across a range of tissues and developmental stages. Until recently, limited amounts of Eucalyptus EST/unigene data were available in public databases, mainly due to the fact that commercial interests have necessitated private EST collections [ 24 ]. As of March 2010, aside from a mixed-species collection of ≈56,000 nucleotide sequences on NCBI (≈ 37,000 of which are Sanger EST sequences) and which contain extensive redundancy, the largest effort to date to generate a comprehensive catalogue of expressed genes in a single Eucalyptus species was based on 454 sequencing of cDNA fragments from E. grandis trees [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2010

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BackgroundDe novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a Eucalyptus tree species (E. grandis) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs.ResultsWe present an extensive expressed gene catalog for a commercially grown E. grandis × E. urophylla hybrid clone constructed using only Illumina mRNA-Seq technology and de novo assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any Eucalyptus tree. mRNA-Seq analysis furthermore 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.ConclusionsDe novo assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in Eucalyptus and other non-model organisms. The transcriptome resource (Eucspresso, http://eucspresso.bi.up.ac.za/) generated by this study will be of value for genomic analysis of woody biomass production in Eucalyptus and for comparative genomic analysis of growth and development in woody and herbaceous plants.

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Section: Introductionmentioning

confidence: 99%

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

et al. 2010

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The Choline Oxidase Gene codA Confers Salt Tolerance to Transgenic Eucalyptus globulus in a Semi-Confined Condition

Kikuchi

Matsunaga

et al. 2012

Mol Biotechnol

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The performance of tree species is influenced by environmental factors and growth stages. To evaluate the practical performance of transgenic tree species, it is insufficient to grow small, young trees under controlled conditions, such as in a growth chamber. Three transgenic Eucalyptus globulus lines, carrying the choline oxidase gene, were investigated for their salt tolerance and expression of the transgene at the young plantlet stage in a special netted-house. To clarify the characteristics at the young as well during the later stages, salt tolerance and the properties of the transgenic lines at large juvenile and adult stages were evaluated in the special netted-house. All transgenic lines showed high glycinebetaine content, particularly in young leaves. Trees of the transgenic line 107-1 showed low damage because of salinity stress based on the results from the chlorophyll analysis and malondialdehyde content, and they survived the high-salt-shock treatment at the large juvenile and adult stages. Only this line showed salt tolerance at all stages in the special netted-house. In this evaluation in the special netted-house, the tolerant line among young plantlets might perform better at all stages. Since evaluation in these special netted-house mimics field evaluation, line 107-1 is a potential tolerant line.

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Genomics of Trees

2014

Tree Biotechnology

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"Post-genomics" research in Eucalyptus in the near future

Cited by 4 publications

References 13 publications

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

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

The Choline Oxidase Gene codA Confers Salt Tolerance to Transgenic Eucalyptus globulus in a Semi-Confined Condition

Genomics of Trees

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