Download Comparative genomics of the Brassicaceae

Comparative genomics of
the Brassicaceae
Presented by:
J. Erron Haggard
To: HRT 221
May 19th, 2008
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
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
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
Camelineae
may be
paraphyletic
From Schranz et al. 2007
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
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
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 geneby-organ expression interactions
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)
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
Present-day A. thaliana
Deduced ancestral Arabidopsis
Hypothetical ancestor
to Brassicaceae
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
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
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
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
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!
References:
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