Trends in Plant Science
ReviewThe ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes
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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