Biology Reference
In-Depth Information
Chapter 24
Proteome Analysis of Orphan Plant Species,
Fact or Fiction?
Sebastien C. Carpentier and Twan America
Abstract
Biological research has focused in the past on model organisms and most of the functional genomics studies
in the fi eld of plant sciences are still performed on model species or reference species that are characterized
to a great extent. However, numerous non-model plants are essential as food, feed, or energy resource.
Some features and processes are unique to these plant species or families and cannot be approached via a
model plant. The power of all proteomic and transcriptomic methods, i.e., high throughput identifi cation
of candidate gene products, tends to be lost in orphan species due to the lack of genomic information, the
complexity of the genome (protein inference problem, polyploidy) or due to the sequence divergence to a
related sequenced reference variety or to a related model organism. Nevertheless, a proteomics approach has
a great potential to study orphan species. This chapter reviews concisely orphan plants from a proteomic
angle and provides an outline of the problems encountered when initiating the proteome analysis of a non-
model organism. We discuss briefl y the problems and solutions for orphan plants associated with sample
preparation and focus further on the diffi culties associated with protein redundancy in polyploid species and
the protein inference issue which is particularly associated with a peptide based proteomics approach.
Key words
Polyploidy, Uncharacterized complex genome, Protein inference, Databases, Protein
extraction, Peptide based analysis, Protein based analysis
1
Introduction
What is a model organism? In past decades, the term “model organ-
ism” has been applied to species that facilitate experimental laboratory
research. Research communities have focused on model organisms to
gain insight into some general principles that underlie various disci-
plines. The fi rst and only classical plant model,
Arabidopsis thaliana
,
is ideal for laboratory studies. It has a short life cycle, a small size, a
good production of seeds, and a relatively small genome that is com-
pletely sequenced. Although Arabidopsis is the preeminent model
plant, to date still 48 % of the Arabidopsis genome has an unknown
molecular function, 51 % belongs to an unknown biological process
and of 48 % the cellular localization is unknown (TAIR10 genome
statistics). This illustrates the challenge to work with orphan species.
