Plant Science 159 2000 87 – 95
Analysis of grape ESTs: global gene expression patterns in leaf and berry
Effie Ablett
a,
, George Seaton
b
, Kirsten Scott
a
, Dale Shelton
a
, Michael W. Graham
c
, Peter Baverstock
d
, L. Slade Lee
a
, Robert Henry
a
a
Centre for Plant Conser6ation Genetics, Southern Cross Uni6ersity, P.O.Box
157
, Lismore, NSW
2480
, Australia
b
Institute for Cell and Animal Population Biotosy, Ashworth Laborities, King
’
sBuildings, Edinburgh Uni6ersity, Edinburgh, EH
9 3
JT, UK
c
Queensland Agricultural Biotechnology Centre, Le6el
4
, Gehrmann Laboratories, Uni6ersity of Queensland, St Lucia, Qld
4072
, Australia
d
Graduate Research College, Southern Cross Uni6ersity, P.O.Box
157
, Lismore, NSW
2480
, Australia Received 9 March 2000; received in revised form 15 May 2000; accepted 3 July 2000
Abstract
Analysis of 2479 ESTs from Vitis 6inifera berry tissue and 2438 from leaf revealed that 1 of the ESTs match to known Vitis proteins, 72 to plant proteins, 11 to non-plant, and 16 had no match P[N] \ 0.5. The levels of redundancy were similar
in the leaf and berry libraries. Only 12 of the genes matched by the ESTs were common to both libraries indicating marked differences in the genes expressed in the two tissues. The abundance of transcripts with predicted cellular roles in leaf and berry
were estimated by classifying the primary BLAST matches to known proteins score \ 80 into functional categories. Thirty-six percent of the leaf transcripts were involved in photosynthesis, compared to 3 in the berry. This is a much higher proportion
of transcripts involved with a function limited to specialized cells, than was found when transcripts of 33 human tissues were compared using a similar approach, suggesting plant cells may involve their cellular machinery to a greater extent in specialized
activities than animal cells. Relatively enhanced expression of specific transcription factors, and genes involved in defense, detoxification, stress response, proteolysis, trafficing, and signal transduction, suggests berry tissue is actively engaged in
responding to environmental stimuli. © 2000 Elsevier Science Ireland Ltd. All rights reserved.
Keywords
:
Expressed sequence tags; Electronic Northern; Vitis 6inifera; Gene expression; cDNA www.elsevier.comlocateplantsci
1. Introduction
To date there have been no large-scale EST projects on fruit-bearing woody cultivars, and rel-
atively few ESTs are available from woody plant species. With the huge amount of effort that has
gone into cereal EST projects, it is surprising that so little attention has been given to woody species.
A recent assessment of dbEST listed nearly 245 000 plant ESTs. Most were from cereals, with
the only significant listings of woody plant species being 7554 ESTs from loblolly pine, 4809 from
poplar, 1251 from citrus and 430 from apple dbEST release 120399, December 3, 1999. The
grape project at the Centre for Plant Conservation Genetics, Lismore, Australia, is producing grape
Vitis 6inifera ESTs from a range of tissues and cultivars to advance gene discovery in woody
plant species, particularly in the areas of dor- mancy and budburst, berry development and vine
physiology.
ESTs were developed in 1991 as a relatively inexpensive and rapid means to identify large
numbers of expressed genes [1]. Gene functions are assigned to ESTs based on homology to known
proteins from other species. Currently about 50 of ESTs can be identified in this way. With the
number of ESTs in dbEST approaching 3.4 mil- lion, other approaches are needed to assign func-
tion to the growing numbers of unidentified ESTs.
Corresponding author. Tel.: + 61-2-66203486; fax: + 61-2- 66222080.
E-mail address
:
eablettscu.edu.au E. Ablett. 0168-945200 - see front matter © 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S 0 1 6 8 - 9 4 5 2 0 0 0 0 3 3 5 - 6
As the scope of EST projects continues to increase, EST data on large numbers of expressed genes
from a variety of tissues, cell types and develop- ment stages is becoming available. Analysis of
ESTs is now being used to identify novel genes exhibiting specific expression patterns, and to as-
sign gene function to certain cell types.
In order to analyze gene expression in specific samples from EST data, numbers of transcripts
need to be quantitated from the sampled ESTs. In an unbiased cDNA library, the number of ESTs
matching a particular gene should reflect the abun- dance of the corresponding cDNA in the library
and the level of its mRNA in the tissue from which the library was derived. EST sampling can be an
effective and quantitative measure of steady state mRNA levels [2]. This ‘electronic northern’ ap-
proach has been used to develop expression profi- les in a range of human [3], mouse, invertebrate [4],
and plant tissues [5].
Analysis of transcripts from EST data has also been used to discover novel genes only expressed in
mouse renal proximal tubule [6] and human granu- locytes [7] as well as genes expressed at different
levels in human neoplastic cells compared to their normal counterparts [8] and in cultured cells after
nerve growth factor treatment [2]. Recently re- ported methods of EST analysis [5] allow identifi-
cation of ESTs showing similar expression profiles, thereby raising the possibility of assigning function
to novel genes by virtue of their having similar expression patterns to genes related in function.
These applications will be escalated by the use of high density DNA arrays and chips for review see
[9] and methods such as SAGE [10], that allow expression levels of even larger numbers of tran-
scripts to be analyzed.
When data is available from sufficient libraries, temporal andor developmental expression profiles
can be generated. This has been demonstrated for six stages of soybean embryo development [11]. As
in conventional northerns, this data can be used to help understand more fully the function of the
corresponding gene products in biological pro- cesses, but with the EST approach this is extended
to thousands of genes. Analysis of the expression of large numbers of genes combined with knowl-
edge of their function allows us to perceive the global picture of biological processes in different
cell types. These studies have been initiated by using primary BLAST homologues to divide ESTs
matching known proteins into functional cate- gories defined for bacteria [12] and modified for
yeast [13] and plants [14]. Data for this type of analysis is available for 37 human tissues [3],
Schistosoma mansoni [4], cabbage bud flowers [15], and wood-forming tissues of poplar [16]. Here data
from the analysis of the first 5000 grape ESTs of the Centre for Plant Conservation Genetics’ grape
project are reported. Sequenced from two Char- donnay libraries, one derived from leaf tissue and
the other from berry, the grape ESTs have allowed us to look at global gene expression in two fairly
specialized types of plant cells.
2. Methods
