Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 561204
Title Proteome analysis of orphan plant species, fact or fiction?
Author(s) Carpentier, Sebastien C.; America, Twan
Source In: Plant Proteomics Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781627036306 - p. 333 - 346.
DOI https://doi.org/10.1007/978-1-62703-631-3_24
Department(s) BIOS Applied Metabolic Systems
Publication type Peer reviewed book chapter
Publication year 2014
Keyword(s) Databases - Peptide based analysis - Polyploidy - Protein based analysis - Protein extraction - Protein inference - Uncharacterized complex genome
Abstract

Biological research has focused in the past on model organisms and most of the functional genomics studies in the field 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 identification 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 briefly the problems and solutions for orphan plants associated with sample preparation and focus further on the difficulties associated with protein redundancy in polyploid species and the protein inference issue which is particularly associated with a peptide based proteomics approach.

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