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Comparative Genome Analysis at the Sequence Level in the Brassicaceae

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Genetics and Genomics of the Brassicaceae

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

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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.

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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

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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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Authors and Affiliations

  1. J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, 20850, USA

    Chris Town

  2. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany

    Renate Schmidt

  3. John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK

    Ian Bancroft

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  1. Chris Town
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  2. Renate Schmidt
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  3. Ian Bancroft
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Correspondence to Chris Town .

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Editors and Affiliations

  1. Kulturpflanzenforschung (IPK), Leibniz-Institut für Pflanzengenetik und, Corrensstr. 3, Gatersleben, 06466, Germany

    Renate Schmidt

  2. John Innes Institute, Norwich Research Park, Colney, Norwich, NR4 7UH, United Kingdom

    Ian Bancroft

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Town, C., Schmidt, R., Bancroft, I. (2011). Comparative Genome Analysis at the Sequence Level in the Brassicaceae. In: Schmidt, R., Bancroft, I. (eds) Genetics and Genomics of the Brassicaceae. Plant Genetics and Genomics: Crops and Models, vol 9. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-7118-0_6

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