Berkeley - As biologists try to tease out the finer details
of the green plant family tree, one key may lie in the cellular
organelle - the chloroplast - that makes green plants green.
As the photosynthetic factory of the plant cell, the chloroplast
contains its own complement of genes distinct from the comparably
sized mitochondrial genome in the energy center of the cell
or the much larger genome in the cell nucleus.
"The chloroplast genome can be more informative in some
ways than the complete nuclear genome, and easier to analyze
than plant mitochondrial DNA," said Brent Mishler, professor
of integrative biology at the University of California,
Berkeley, and director of the Jepson and University Herbaria.
Mishler is one of nine principal investigators on a new
project, supported by $3 million over five years from the
National Science Foundation, to isolate and sequence chloroplast
and mitochondrial genomes from 50 to 100 representative
plants, drawing on the expertise of the U.S. Department
of Energy's Joint Genome Institute (JGI) in Walnut Creek,
Calif. The grant was among the largest of seven collaborative
projects funded last month by NSF's "Assembling the Tree
of Life" program.
The biologists will compare chloroplast genomes, as well
as mitochondrial genomes and nuclear genes, along with morphological
characteristics to determine plant relationships among the
more ancient plant groups such as the mosses, algae and
ferns. Their work will complement that of on-going projects
looking at other branches of the green plant family tree,
such as the well-studied seed plants.
"The whole nuclear genome is enormous and it's very difficult
technically to get the same portions of a genome out from
a lot of different organisms," said co-PI Jeffrey L. Boore,
a scientist at the Lawrence Berkeley National Laboratory,
head of the evolutionary genomics laboratory at JGI and
an adjunct associate professor of integrative biology at
UC Berkeley. "But with organelles, either mitochondria or
chloroplasts, we can pull out this bit of DNA that is physically
separate from the nuclear genome and get this collection
of homologous genes. So we get a pretty good collection
of genes for one price."
Both chloroplasts and mitochondria originated more than
a billion years ago, when bacteria colonized early single-celled
organisms, establishing a symbiotic relationship that has
allowed plant cells to get energy from sunlight and both
plant and animal cells to produce energy efficiently.
Among the questions Mishler, Boore and their colleagues
want to answer are, how many times has land been colonized
from the sea by green algae, where did plants acquire the
adaptations essential to life on land, and how many times
did multicellular plants evolve?
To date, only two entire plant genomes have been sequenced
- a plant called Arabadopsis thalianafrom the mustard
family and rice - and JGI is at work on a third, the poplar
"Data from the already sequenced genomes have not yet been
analyzed comparatively," said Mishler, who specializes in
the study of mosses and other bryophytes. "Only about 15
green plant chloroplast genomes have been sequenced, and
even fewer mitochondrial genomes - about 10 - so our project
will be a big step forward."
The group plans to test various ways of comparing genomes
to elicit evolutionary relationships. In particular, they
want to find the best methods to use for groups of organisms
that have a long evolutionary history.
"We're going to test theories and methods for analyzing
genes comparatively," said Mishler, who was one of the leaders
of the "Deep Green" initiative that several years ago reported
the first draft of the tree of life for green plants. "Right
now we don't know the best ways to analyze the DNA once
we have it."
Typically, biologists look at the same gene in many different
species and document the sequence changes that accumulate
over time. Assuming a roughly constant rate of change as
a result of random mutations, scientists can estimate the
time since two lineages split from one another to evolve
Boore said, however, that comparing DNA sequences directly
may not be the best method, because the same mutation could
show up more than once, throwing into doubt any conclusions
about plants being from the same lineage. He has had great
success looking at gene rearrangements within the mitochondrial
genomes of animals - at genes that switch places, flip or
"When gene order rearrangements define some specific evolutionary
branching, we've judged that those are very, very powerful
characters because they are very unlikely to rearrange in
the same way in two different lineages," Boore said. "We
feel that when we find gene rearrangements, we are confident
that that part of the tree is well resolved."
Following mitochondrial gene rearrangements over time,
he and his team several years ago established convincingly
that the myriapods - millipedes and centipedes - are not
the ancestor of modern insects, as most people assumed.
Rather, these many-segmented creatures emerged from the
ocean earlier than insects. Crustaceans - crabs and lobsters
- are more closely related to insects than are millipedes
and centipedes, he said.
Boore, Mishler and other members of the collaboration hope
to find chloroplast as well as plant mitochondrial genes
that change slowly over time, and thus would be suitable
for assessing long-term evolutionary change, as well as
fast-mutating genes suitable for studying more recent evolution.
Other principal investigators on the grant are research
botanist Alan R. Smith of UC Berkeley's University Herbarium,
Charles O'Kelly of the Bigelow Laboratory for Ocean Sciences
in Maine, Paul G. Wolf of Utah State University, Karen Renzaglia
of Southern Illinois University, Dina Mandoli and Richard
Olmstead of the University of Washington and Michael Donoghue
of Yale University. Mandoli plans to construct bacterial
artificial chromosome (BAC) nuclear genome libraries for
about 50 plants representing deep-branching lineages of
green plants, for use by other researchers.
Mishler will host a Tree of Life symposium on the UC Berkeley
campus next February to discuss the structure of the green
plant family tree and how it relates to other family trees,
such as those of arthropods (insects and spiders) and vertebrate
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