Related Experiment Video
Updated: Aug 13, 2026
10:10
Investigating Tissue- and Organ-specific Phytochrome Responses using FACS-assisted Cell-type Specific Expression Profiling in Arabidopsis thaliana
Published on: May 29, 2010
Assaying gene content in Arabidopsis
1Bioinformatics Department, Paradigm Genetics, 108 TW Alexander Drive, Building 1A, Research Triangle Park, NC 27709-4528, USA. kallen@paragen.com
Summary
Arabidopsis, a model plant, is broadly representative of dicot genomes but shows significant gene loss. Gene content variation appears common in angiosperm speciation.
Area of Science:
- Plant genomics
- Comparative genomics
- Evolutionary biology
Background:
- Arabidopsis thaliana is a widely used model plant in scientific research.
- The completion of the Arabidopsis genome and EST data from other dicots allow for comparative gene content analysis.
Purpose of the Study:
- To assess the representativeness of the Arabidopsis genome compared to other dicot species.
- To identify genes lost or gained during angiosperm speciation.
Main Methods:
- Comparative analysis of Arabidopsis genome with expressed sequence tags (ESTs) from three dicot species.
- Identification of homologous genes and gene loss events.
Main Results:
- Over 10% of contigs from test dicot species lacked detectable homologs in Arabidopsis.
- 154 specific cases of gene loss in the Arabidopsis lineage were identified.
- Identified genes included characterized enzymes and proteins homologous to those in Synechocystis.
Conclusions:
- Arabidopsis is generally representative of dicot genomes, but significant inter-generic variation exists.
- Gene loss and acquisition are likely features of angiosperm speciation, contributing to genomic diversity.
Related Concept Videos
02:16Light Acquisition
In order to produce glucose, plants need to capture sufficient light energy. Many modern plants have evolved leaves specialized for light acquisition. Leaves can be only millimeters in width or tens of meters wide, depending on the environment. Due to competition for sunlight, evolution has driven the evolution of increasingly larger leaves and taller plants, to avoid shading by their neighbors with contaminant elaboration of root architecture and mechanisms to transport water and nutrients.
02:34DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.