History, protohistory and prehistory of the Arabidopsis thaliana chromosome complement Henry Yves et al 2006, in press

Basic scenario: a reduction in chromosome number begins in the last 4-5 My from n=8 to n=5 via fusion of chromosomes. It also includes 3 ancient polyploidizations. The most recent occurred in early Brassica with n=4 about Mya. The others occurred after the mergence of Eudicots and Angiosperms. Brassica chromosome number varies 2n=8 to 2n=256 Sequencing of Arabidopsis yield unexpected results Many duplicated chromosome segments Similar to the observed 55 duplicated segments found in yeast General consensus of 3 polyploidization events Contention about ploidy of ancestor and times of divergence Difficulty lies because of sequence divergence and superimposition of younger duplications

Present day Arabidopsis thaliana (n=5) Article was review of literature Construction of maps based on this Not much in terms of methodology Phylogenetic analysis of arginine decarboxylase 13 different Brassica Placed duplication of genes (polyploidization) at A. grandiflora and Arabidopsis Most recent polyploidization within Brassica family

Deduced ancestral Arabidopsis thaliana (n=8) Reduction in chromosome number N=8 to N=5 4-5 Mya After divergence of A. thaliana and A. lyrata Lyrata genome is larger Loss of DNA from Arabidopsis Regions of Lyrata don’t match Arabidopsis Much deviation in terms of estimating divergence 2R= Mya or Mya Calibration of molecular clocks Discrepancy in dating methods Heterogenous sequence evolution

Hypothetical ancestral Brassicaceae ancestor (n=4) Flow cytometery can measure DNA copy number Polyploidization is current in Arabidopsis 2 accessions are tetraploids 2n=20 A. suecicia is allotetraploid 2n=26 Fusion of thaliana and arenosa (2n=10 & 16)

Polyploidization N=4 to N= Mya Loss of genes, “shuffling” N=8 to N=5 4-5 Mya Eudicot ancestor Polyploidization 100 Mya

Proposed Model Besides large-scale events Single gene duplication events Majority are lost after few My Models: Diversification in development and physiology depends on many genes in a pathway acquiring novel function. This is more likely to occurs if many genes are duplicated at the same time. Closing note: Polyploidy is a transitory state in evolution. These genomes eventually return to a diploid state (poorly understood), but this involves loss of majority of duplicated genes, functional diversification of the remainder and shuffling of the duplicated genomes.

Segmental Structure of the Brassica napus Genome Based on Comparative Analysis With Arabidopsis thaliana Isobel A. P. et al. 2005

Study focused on the genome of Brassica napus, an oilseed crop in relation to Arabidopsis thaliana Amphidiploid: diploid set of chromosomes from each parent N=19 Multiple fusion events between diploid B. rapa and B. oleracea A genome, n=10, B. rapa B genome, n=8, B. nigra C genome, n=9, B. oleracea Why is this important? Arabidopsis is within Brassica family of 3500 species, many of which have significant agricultural importance. By studying this model organism and exploiting already sequenced genome, candidate genes can be identified within the larger genomes of Brassica polypoids.

Inversions identified in Brassica relative to Arabidopsis are indicated by arrows B. napus populations 60 doubled halpoid lines crossed with newly resynthesized line SYN RFLP loci in B. napus 21 conserved regions Lengths as great as 50cM in B. napus (9 Mbp in A. thaliana)

359 sequenced probes detected 1232 loci and revealed 550 homologous sequences 1317 loci over 19 linkage groups Map length of 1968 cM 21 conserved regions/blocks RFLP probes 213 Brassica genomic clones 88 Arabidopsis cDNA 6 cloned Brassica or Arabidopsis genes

Block definition Minimum of 4 mapped loci 1 shared locus/5cM (napus) 1 shared locus/1Mb (thaliana) On average per block 7.8 shared loci 14.8 cM length (napus) 4.8 Mb (thaliana) All blocks combined Nearly 90% coverage of B. napus genome

With in the 21 blocks 74 translocations, fusions, or deletions 28 are common to both A and C genomes Occurred prior to divergence from common ancestor 81% of conserved segments Present in at least 6 copies Consistent with hexaploid progenitor theory

A representation of the Arabidopsis genome based on the primary location of each sequenced B. napus RFLP marker on the Arabidopsis pseudochromosomes (megabase distances are indicated to the right of the chromosomes). Blocks of markers found to be genetically linked in B. napus are indicated by shading and capital letters (A–F).

Difficulties In some instances the duplications evident within the Arabidopsis genome have made it difficult to identify the most similar region shared between the two species. For example, loci on B. napus linkage group N19 show strong homology to both chromosome 5 block C and the duplicated region on Arabidopsis chromosome 1 block D *Overall there has been conservation of gene content and gene order between Arabidopsis thaliana and Brassica napus