Agriculture Reference
In-Depth Information
Plant Gene Index
The web site documents a number of animal, plant, protist and fungi species. The
site contains a number of web tools, and contains cDNA and genechip data from a
number of crop plants.
HarvEST
HarvEST software is available for 10 important agricultural crops. It originated
as an EST database with software linked to gene function, microarray design and
SNP identification. It is also available as a HarvEST BLAST search engine from an
alternative site present on the homepage.
cDNA(FullLength)
Partial cDNAs are useful for rapidly documenting and cataloguing targeted genes,
but they are not used or suitable for further study of gene function. This is because
the most popular method for preparing a cDNA library does not provide the full-
length cDNA that includes the capped site sequences. The biotinylated cap trap
method using a thermostabilised reverse transcriptase is one method for construct-
ing full-length cDNA-enriched libraries suitable for studies of gene function; and
these have become invaluable for life science projects (Maeda et al.
2006
; Tanaka
et al.
2008
; Yamasaki et al.
2008a
). The sequences derived from full-length cDNAs
can also help in identifying transcribed regions in completed or draft genomes in
other plants. In Arabidopsis and rice, full-length cDNA sequences have been used
to identify genomic structural features, such as transcription start sites (TSSs) and
transcriptional genes and variant alleles in metabolic activity (Iida et al.
2004
; Itoh
et al.
2007
; Yamamoto et al.
2009
). In species for which we have draft genomes,
such as
Physcomitrella
, soybean and poplar, full-length cDNA clones have been
used to help consolidate genomic (gene) and chromosome structure and function;
and this should also greatly contribute to discovery of new genetic information
(Nanjo et al.
2007
; Ralph et al.
2008a
; Umezawa et al.
2008
).
Full-length cDNA libraries have contributed to functional analysis using over-
expressors in reverse genetics. The full-length cDNA overexpressor (FOX) gene
hunting system, which uses full-length cDNA from transgenic plants as overex-
pressors, has introduced another approach to high-throughput analysis of functional
genes associated with phenotypic traits (Ichikawa et al.
2006
; Fujita et al.
2007
;
Kondou et al.
2009
). Full-length enriched cDNA libraries have been constructed
for non-sequenced crop or forestry species, such as wheat (
Triticum aestivum
), bar-
ley (
Hordeum vulgare
), cassava (
Manihot esculenta
), Japanese cedar (
Cryptomeria
japonica
), Sitka spruce (
Picea sitchensis
) and Lotus (Sato et al.
2008
; Kawaura
et al.
2009
; Sato et al.
2009
); as well as for plant species showing specific charac-
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