Download Brassica genome structure

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 24-40 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
•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
Present day Arabidopsis thaliana (n=5)
• 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=122-256 Mya or 66-109 Mya
•Calibration of molecular clocks
•Discrepancy in dating methods
•Heterogenous sequence evolution
Deduced ancestral Arabidopsis thaliana (n=8)
•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)
Hypothetical ancestral Brassicaceae ancestor (n=4)
Polyploidization
100 Mya
Eudicot ancestor
Polyploidization
N=4 to N=8
24-40 Mya
Loss of genes, “shuffling”
N=8 to N=5
4-5 Mya
•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.
Proposed Model
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.
•B. napus populations
•60 doubled halpoid lines
crossed with newly
resynthesized line SYN1
•1000 RFLP loci in B. napus
•21 conserved regions
•Lengths as great as 50cM in
B. napus (9 Mbp in A. thaliana)
Inversions identified in Brassica
relative to Arabidopsis are
indicated by arrows
•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