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Comparative Genome Analysis at the Sequence Level in the Brassicaceae

Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 9)

Abstract

In the world of plant genome sequencing, the cultivated Brassica species have been relatively under-resourced compared with other crop species largely due to their position in the economic hierarchy of perceived importance. Thus, with the completion of the Arabidopsis thaliana genome in the year 2000, the limited sequencing efforts undertaken in the Brassica crops and other species of the Brassicaceae have been largely restricted either to survey sequencing of various insert size clones or to finished sequences of small genomic regions, generally as bacterial artificial chromosome (BAC) clones. In this chapter, we review the sequencing efforts to date and how they have been used in comparative analysis with the Arabidopsis genome and with each other to begin to understand the genome organisation of members of the crucifer family, how they relate to one another, and how they may have evolved.

Keywords

Collinearity Comparative genome analysis Duplication Genome organisation Polymorphism Reference sequence Sequence comparison Survey sequencing 

Abbreviations

AOP

2-oxoglutarate-dependent dioxygenase

BAC

Bacterial artificial chromosome

Col

Columbia

DH

Doubled haploid

EST

Expressed sequence tag

FISH

Fluorescence in situ hybridisation

GRP

Glycine-rich pollen surface protein

InDel

Insertion/deletion

kbp

Kilo base pairs

Ler

Landsberg erecta

LRR

Leucine-rich repeat

Mbp

Mega base pairs

MITE

Miniature inverted repeat transposable elements

NB-LRR

Nucleotide-binding leucine-rich repeat

rDNA

Ribosomal DNA

R gene

Disease resistance gene

RACE

Rapid amplification of cDNA ends

RLK

Receptor-like kinase

SNP

Single nucleotide polymorphism

TAIR

The Arabidopsis Information Resource

TRIM

Terminal repeat retrotransposons in miniature

Notes

Acknowledgments

Work on Brassicaceae genomics in the authors’ laboratories has been supported by grants from the United States National Science Foundation (DBI-9813586 and DBI-0638536), the German Federal Ministry of Education and Research (BMBF), and the UK Biotechnology and Biological Sciences Research Council.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.J. Craig Venter InstituteRockvilleUSA
  2. 2.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  3. 3.John Innes Centre, Norwich Research ParkNorwichUK

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