Trends in Plant Science
Volume 11, Issue 11, November 2006, Pages 535-542
Journal home page for Trends in Plant Science

Review
The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes

https://doi.org/10.1016/j.tplants.2006.09.002Get rights and content

In this review we summarize recent advances in our understanding of phylogenetics, polyploidization and comparative genomics in the family Brassicaceae. These findings pave the way for a unified comparative genomic framework. We integrate several of these findings into a simple system of 24 conserved chromosomal blocks (labeled A–X). The naming, order, orientation and color-coding of these blocks are based on their positions in a proposed ancestral karyotype (n = 8), rather than by their position in the reduced genome of Arabidopsis thaliana (n = 5). We show how these crucifer building blocks can be rearranged to model the genome structures of A. thaliana, Arabidopsis lyrata, Capsella rubella and Brassica rapa. A framework for comparison between species is timely because several crucifer genome-sequencing projects are underway.

Section snippets

A unified comparative genomic framework for the Brassicaceae

The angiosperm family Brassicaceae (the mustard family) contains several important research and agricultural species, the foremost being the model species Arabidopsis thaliana (Arabidopsis) and the Brassica crops. In addition, several related species are the focus of active research communities, including Arabidopsis lyrata, Capsella rubella, and other genera such as Boechera, Lepidium, Thellungiella (also known as Eutrema) and Thlaspi. Comparative genomics in the Brassicaceae has largely

Comparative genomics in plants: the Crop Circle and beyond

The seminal comparative genetic mapping done in the grass family (Poaceae), which includes many important domesticated cereal and forage crops, resulted in the synthesis of the ‘Crop Circle’ 2, 3, 4, 5, 6. This approach placed the small-genome of rice at the center of the circle and then aligned the maps of larger genome grass crops (including corn, sorghum, wheat, oat, fox millet and sugar cane). A large degree of colinearity was found among genomes (however, see Ref. [7]). The rice genome

Brassicaceae: phylogeny and genome duplications

An accurate phylogeny is essential for comparative studies within the Brassicaceae. Knowledge of natural phylogenetic relationships allows estimates of: (i) derived versus ancestral states for numerous characters (morphological, cytological, biochemical), (ii) evolutionary distances and divergence times between groups and (iii) the positioning of evolutionary events to particular nodes or clades on the phylogenetic tree. Recent studies have classified the 338 genera and ∼3700 species of

Comparative mapping and genomics in the Brassicaceae

The genome sequencing of A. thaliana was a major landmark in plant biology and transformed a rather unassuming weed into the reference point for most comparative studies [20]. The reduced genome size and low chromosome number (n = 5) made Arabidopsis ideal for genome sequencing, but complicates its use in comparative studies. It is tempting to place Arabidopsis at the center of a Brassicaceae genomics circle in the same way rice was placed at the center of the Crop Circle 2, 3, 4, 5, 6. However,

ABC's: the conserved blocks of crucifer genomes

An important step toward a unified comparative genomics system across the Brassicaceae can be accomplished by integrating the colinear regions identified between B. napus and A. thaliana [31] with the concept of the n = 8 ancestral karyotype shared by A. lyrata and Capsella [33]. We propose a set of 24 genomic blocks (A–X) within the ancestral karyotype that represent an extension to the set of 21 blocks proposed for Brassica by Parkin et al. [31]. These 24 blocks represent the conserved segments

Bridging Arabidopsis thaliana and Brassica via the ancestral karyotype

Recognition of the ancestral karyotype and these genomic building blocks will facilitate comparisons between A. thaliana and Brassica and provide a basis for family-wide comparative genomics in the Brassicaceae. Although it is well known that A. thaliana and Brassica genomes differ by many rearrangements 28, 45, 46, 47, the pattern underlying these changes is less clear. In particular, the Brassica genome is less rearranged relative to the ancestral karyotype compared with that of A. thaliana.

Concluding remarks and future directions

Future research should lead to the refinement of the boundaries and definitions of many of the blocks to more precisely delineate syntenic relationships. If future studies require additional genomic subdivisions we recommend the division of the present blocks (A–X) into enumerated sub-blocks (e.g. A1 and A2). Also, there are likely to be minor species-specific differences in microcolinearity within the blocks that will become apparent from fine-mapping studies or by analyzing DNA sequence. For

Acknowledgements

We thank Tom Osborn, Isobel Parkin, Chris Pires, Ingo Shubert, Aaron Windsor and three anonymous reviewers for helpful comments on the manuscript. This work was supported by funding from Duke University to M.E.S. and T.M-O., and the Czech Ministry of Education (MSM0021622415) and a research grant from the Grant Agency of the Czech Academy of Science (KJB601630606) awarded to M.A.L.

Glossary

Acrocentric chromosomes
chromosome arms of significantly unequal length with the centromere near to one chromosome end.
Comparative Chromosome Painting (CCP)
in plant cytogenetics CCP is fluorescence in situ hybridization (FISH) of chromosome-specific large-insert DNA clones, microdissected or flow-sorted DNA probes of a reference species to chromosomes of another species.
Metacentric chromosomes
both arms are of roughly equal length with the centromere in the middle. Submetacentric chromosomes have

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