15th International Conference on Arabidopsis Research - TAIR

T10-019
Novel Gene Discovery in Arabidopsis thaliana
Beverly Underwood(1), Yongli Xiao(1), William Moskal(1), Udana Torian(1), Julia
Redman(1), Hank Wu(1), Christopher Town(1)
1-The Institute for Genomic Research; Rockville, Maryland
The latest annotation of the Arabidopsis genome estimates that there are
26,207 protein coding genes. Approximately 62% of these are represented
in GenBank by a full length cDNA and another 11% are represented only by
ESTs. The remainder has yet to be experimentally defined and only exist
based on genome analyses using modeling algorithms that predict gene
structure. At TIGR, our efforts have been focused on generating experimental
evidence for these hypothetical genes by RACE PCR, various cDNA library
construction strategies, and comparative genomics. From these studies,
we have detected many instances of alternative splicing and variations in
polyadenylation sites, as well as antisense gene expression and dicistronic
transcripts. Additionally, through comparison of Arabidopsis and Brassica
genomes, approximately 15,000 highly conserved intergenic regions have
been identified, thus suggesting the presence of non-annotated novel genes.
A pilot study with 192 of these regions confirmed expression of 52 genes
suggesting that there may be thousands of genes not yet discovered. From
these analyses, Gateway pENTR ORF clones are being produced and will be
available through the Arabidopsis Biological Resource Center. These efforts
will facilitate novel gene discovery, lead to improvements in genome annotations,
generate a set of Arabidopsis ORF clones, and ultimately contribute
to the genetic toolkit that is necessary for fulfilling goals of the Arabidopsis
2010 project.
Supported by the NSF 2010 Program
T10 Novel Tools, Techniques and Resources
T10-020
RNAi for Plant Functional Genomics
Chris Helliwell(1), Varsha Wesley(1), Anna Wielopolska(1), Louisa Matthew(1), Neil
Smith(1), Ming-bo Wang(1), David Bagnall(1), Ian Small(2), Ian Moore(3), Peter
Waterhouse(1)
1-CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
2-URGV, 2 rue Gaston Cremieux, CP 5708 91057, Evry, Cedex, France
3-Department of Plant Sciences, University of Oxford, OX1 3RB, UK
A major challenge in the post-genome era of plant biology is to determine the
functions of all the genes in the plant genome. A straightforward approach
to this problem is to reduce or knockout expression of a gene with the hope
of seeing a phenotype that is suggestive of its function. Insertional mutagenesis
is a useful tool for this type of study but is limited by gene redundancy,
lethal knockouts, non-tagged mutants and the inability to target the inserted
element to a specific gene. The efficacy of RNAi in plants using inverted
repeat transgene constructs that encode a hairpin RNA (hpRNA) has been
demonstrated and can overcome many of the deficiencies of insertional
mutagenesis listed above. We have determined design rules for using hpRNA
constructs and developed a series of vectors for dicots and monocots along
with high throughput vectors using an in vitro recombinase system. Further
developments of our RNAi vector system and its application will be described.
15 th <strong>International</strong> <strong>Conference</strong> on Arabidopsis Research 2004 · Berlin