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
"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 tree.
"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
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
"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 separately.
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 duplicate.
"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 animals.
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