Download Arabidopsis thaliana

IB404 - 13 - Arabidopsis thaliana – Feb 29
1. This small water cress in the mustard family has become the model
system for plant biology, with major support from the NSF over the past
two decades. Mutant screens became feasible about 15 years ago, and
hence much has been learned about development and other aspects of
plant biology, eg. circadian rhythms, photo- and geotaxis, basic
photosynthetic mechanisms, water regulation, hormonal regulation,
defensive secondary metabolism, etc.
2. The genome was sequenced by an international consortium at
several labs, and there are too many major players to learn their names.
3. The project was conducted using physically-mapped large BAC and
other clones, and the euchromatin was finished in ten large segments for
the ten chromosome arms (5 metacentric chromosomes), next slide.
4. The euchromatin arms total around 115 Mbp, while the total genome
size is variously estimated as 125-150 Mbp, so there is still a lot of
centromeric heterochromatin - hence superficially this genome
resembles the Drosophila genome in organization. Indeed among plants
it is unusually small.
5. Initial annotation suggested roughly 25,000 genes, although as usual
subsequent work using more ESTs, cDNAs, and comparison with the
rice genome suggests the number of genes is higher.
6. The basic publications were in 2000, with follow up transcriptome
and knockout analyses in 2003, and functional studies on-going.
6. This overview of the
genome shows that, like
Drosophila, the roughly equal
size chromosomes have fairly
uniform gene densities on their
euchromatic arms (first two
lines below chromosome
image), but are gene-poor and
transposon- and repeat-rich in
the centromeric regions (third
line).
7. The MT/CP line (fourth)
shows the sites of recent
insertions of pieces of the
mitochondrial and
chloroplast genomes, an
ongoing process that
presumably reflects what has
happened continuously since
these two endosymbioses
occurred ~2 and ~1 BYA.
8. RNAs (last line) are tRNA
and snRNAs involved in
mRNA splicing.
9. An alternative view of chromosome 2 (right), showing
roughly uniform gene content for the chromosome arms,
but increasing transposon content (bottom two
panels)towards the unsequenced heterochromatic
centromere.
10. Sequence organization of the chromosome 5
heterochromatic knob (black blob on the previous slide)
(below). Note that the core is a 2.2 kb tandem repeat
(yellow tandem arrows). The centromeric
heterochromatin is similarly organized, except that the
major repeat is 180 bp (size of a nucleosome?).
11. Classification of the proteins into functional categories using the Gene Ontology system
shows that about 40% of the functions were unknown, not unusual for such a divergent and new
genome.
12. Comparison with other genomes showed how the proportions of the gene complement
devoted to certain roles is increased in eukaryotes. Thus the numbers of proteins involved in
energy production remain relatively constant (basically these are bacterial after all), while the
numbers involved in cell division, transcription, translation, signalling, and intracellular transport
are of course much higher in the eukaryotes.
13. In addition to the usual several hundred genes of mitochondrial origin, Arabidopsis has about
800 with best protein matches to proteins of the photosynthetic cyanobacterium Synchocystis,
presumably resulting from transfer from the chloroplast to the nuclear genome. So this is another
component of the large gene count.
14. There are several families of genes that are relatively hugely expanded in Arabidopsis,
including the p450 cytochromes with ~300 genes, compared with ~100 in Drosophila, 75 in C.
elegans and only 3 in yeast. In the animals a major role of these proteins is to detoxify the many
secondary plant chemicals that serve as defenses against herbivores, as well as other xenobiotics.
Ironically, in plants their central role appears to be in generating these many secondary chemicals
for defense.
15. Another expanded family are
the aquaporins, 8TM proteins that
form water channels (right). Water
uptake from the soil is important, as
is control of stomatal transpiration,
etc. Plants in general seem to have
up to 30 of these, compared with
fewer than 10 for animals. The 8
TM alpha helices form a channel or
pore across the cell membrane with
specificity for water, achieved by
lining it with hydrophobic aas and a
few key hydrophilic aas. The latter
act as “stepping-stones” for water.
16. Developmental biology has become a major topic in plant molecular biology as it has for
animals. The overall conclusion from these studies, supported by the genome sequence, is that
plants and animals evolved multicellularity independently because they use largely different
suites of proteins for development. For example, in contrast to the HOX family of
homeodomain-containing transcription factors that regulate pattern formation in animals, plants
use the MADS-box TF family that mediate pattern formation in flowers and other organs. The
sequences and structures of these two DNA-binding domains are quite different and presumably
evolved independently.
Homeodomain
MADS box
Some MADS box mutants - wild type is on left.
17. A major feature of the genome is the presence of large apparently duplicated regions, both
between and within chromosomes. These are thought to be the vestiges of a polyploidization
event roughly 30 Myr ago. Further analysis actually suggests another even older polyploidization
event, so the combination of these events, and differential retention of duplicated genes, explains
much of the large gene count of >25,000.
18. Polyploidization events can be detected in several ways. A
second way is to plot a histogram of the divergences of pairs of
paralogous genes within a genome, usually using the silent
substitution frequency or Ks. As shown below, this should reveal a
peak interrupting an otherwise steady decay of gene pairs and
sequence identity with time.
19. Polyploidization events can be
dated by comparing histograms of Ks
for pairs of genes within a species
(paralogs) to pairs of genes
(orthologs) between species. Splitting
the Arabidopsis gene pairs into recent
blocks of duplicates and old blocks of
duplicates allows the timing to be
estimated by comparisons with the
Ks values with other plants, e.g.
young Brassica, older Medicago and
tomato, and much older rice (a
monocot in comparison with these
dicots) (right). The vertical dotted
lines are the peaks of Ks distributions
for the younger and older
polyploidizations in Arabidopsis.
20. We’re getting ahead of ourselves,
but a current view of the history of
polyploidizations shows how
common they have been in
angiosperm (flowering plant)
evolution. Each blue dot indicates an
apparent whole genome duplication,
with the estimated age in Myr ago.
Note that this figure has the older
“Arabidopsis” event before the split
with tomato, contrary to previous
slide.
Note also that there is a really ancient
event hypothesized at the base of
angiosperms. We will see something
similar for vertebrates, and there is
endless speculation about whether
such events were pivotal in setting
the stage for angiosperm/vertebrate
evolution. Given the frequency of
these events it is unclear, plus other
equally successful groups show none,
e.g. arthropods.