1. Comparative genomics of the Brassicaceae Presented by: J. Erron Haggard To: HRT 221 May 19th, 2008

2. With four crucifer genomes undergoing sequencing (Arabidopsis lyrata, Brassica rapa, Capsella rubella, and Thellungiella halophila), Brassicaceae will soon be the most heavily sampled angiosperm family This makes comparative genomics within the family possible on a large scale

3. Comparative genomics is used to address four major areas of research: 1.Construction of robust phylogenies 2.Identification of structural changes due to rearrangements, segmental duplications, and polyploidy 3.Annotation of homologous genes and detection of conserved cis-regulatory regions 4.Understanding the evolution of novel traits

4. Accurate phylogeny allows estimates of: 1.derived versus ancestral states 2.evolutionary distances and divergence times 3.Positioning of evolutionary events to particular nodes or clades Recent studies classified the 338 genera (~3700 spp.) into 25 tribes based on nuclear- and chloroplast-encoded markers. 16 of the 25 can be grouped into one of three lineages

5. Camelineae may be paraphyletic From Schranz et al. 2007

6. Comparison of Camelineae and Brassiceae species genomes with Arabidopsis thaliana by linkage mapping and chromosome painting revealed: 1.Several derived chromosomal rearrangements are unique to A. thaliana 2.Genomic comparisons to an n=8 ancestral karyotype are easier to interpret than comparisons to A. thaliana 3.A large number of colinear blocks are conserved among the species

8. Capsella rubella and Arabidopsis lyrata (both n=8) have almost identical genome structure, presumably an ancestral state, relative to A. thaliana (n=5) Comparative studies between Brassica and A. thaliana have thus far been complicated by: 1.The derived nature of the A. thaliana genome 2.The relatively large phylogenetic distance between the two genera 3.The paleopolyploid nature of Brassiceae genomes

12. A paleopolyploid event occurred near the origin of the Brassicaceae (~40 mya), inferred from observed genome redundancy and retention of many duplicated gene pairs within the A. thaliana sequence Genome reduction in A. thaliana has been mostly due to relatively large deletions with losses of ~35% of the initial gene copies There is a bias in the types of gene duplications maintained, and most retained pairs have distinct gene- by-organ expression interactions

13. Evidence for polyploidization in A. thaliana: 1.Pairs of Mbp regions containing paralogous genes in colinear order cover ~80% on the genome 2.Estimated ages of divergence of duplicated genes are quite old and are similar between pairs of sister regions 3.Duplicated regions of similar age do not overlap each other (evidence against multiple segmental duplications)

14. Chromosomal rearrangements occurred throughout the history and protohistory of Arabidopsis Transposable elements provide homologous sites for unequal crossing-over and reciprocal translocation A. Thaliana duplicated regions contain significantly more TEs than is expected by chance

15. Present-day A. thalianaDeduced ancestral ArabidopsisHypothetical ancestor to Brassicaceae

16. Ancestral chromosome number? n=3, n=4, n=5 >37% of Brassicaceae are polyploid Polyploidy continues in the Brassicaceae: Two A. thaliana accessions are 2n=20 A. suecica (2n=26) is allotetraploid progeny of A. thaliana and A. arenosa

17. It has been hypothesized that the earliest polyploidizations and subsequent gene loss evidenced in the Arabidopsis genome may have been the driving force in early Angiosperm radiation Retention of duplicate genes is biased in favor of transcription factors, signal transducers, and developmental genes The divergence of these genes could have contributed to the increase in plant complexity seen in the origin of Angiosperm evolution and in the specialization of floral morphology to pollinating insects

18. In addition to the paleopolyploid events shared by the entire family, there is some evidence that the tribe Brassiceae underwent an additional ancient genome triplication However, there is some controversy over this supposed event, as many Arabidopsis genomic regions are present in less or more than three copies in Brassica genomes It is possible that segmental duplication, rather than polyploidy, accounts for the apparent triplication

19. Moving beyond Arabidopsis thaliana allows the investigation and exploitation of diverse developmental, physiological, and ecological phenotypes For example: Thellungiella halophila has high salt, drought, and cold tolerance Thlaspi and A. halleri are highly resistant to heavy metals Rorippa is tolerant of flooding Many pathogens affect members of the Brassicaceae, but not A. thaliana A. thaliana is not colonized by mycorrhizae, while Thlaspi can be

20. Concluding Thought We have progressed beyond the age of genomics and into the age of comparative genomics, where the pieces of the evolutionary puzzle will begin to fall into place In plants, the Brassicaceae family is a logical starting point, considering the wealth of sequence information already available and rapidly increasing in volume From there, the comparisons will expand to other families, orders, and classes as more and more sequence information becomes available What an exciting time to be a plant geneticist!

21. Schranz, EM, Song, B-H, Windsor, AJ, Mitchell-Olds, T (2007) Comparative genomics in the Brassicaceae: a family-wide perspective. Curr Opin Plant Biol 10:168-175 Schranz, EM, Lysak, MA, Mitchell-Olds, T (2006) The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends in Plant Sci 11:1360-1385 Henry Y, Bedhomme M, Blanc G (2006) History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement. Trends Plant Sci 11:267-73 References: