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Tree
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(Please click
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GREEN ALGAE
Green algae are the eukaryotic base of green plant evolution.
Based on the presence of these traits in both Chlorophytes
and Charophytes, the ancestors to these clades probably
possessed basics such as mating types, plant hormones,
cell polarity, the ability to osmoregulate and retain
turgor of the central vacuole, tropisms (e.g., phototropism
and gravitropism) and circadian rhythms. Taxa in the
Chlorophytes and Charophytes that live in different
habitats (marine and freshwater), varies in thallus
size (micro- to macroalgae), morphology (simple flagellate
to complex sessile), and organization (unicellular,
colonial and true multicellular) were chosen. Having
BAC resources to compare Chlorophytes to Charophytes
is important because it will lead us to understanding
which basic traits were essential to survival and evolution
on land and which were not.
Chlorophytes: In
the Chlorophytes are the only two genetic models among
the green algae, Volvox and Acetabularia. Volvox acts
as an important counterpart to the 2 siphonous species,
Caulerpa and Acetabularia both in body habitus (colonial
versus siphonous unicells), coupling of cellular and
nuclear division (coupled in Volvox versus uncoupled
in Caulerpa and Acetabularia) and in reproductive strategy.
Whereas Volvox makes specialized reproductive cells,
Caulerpa and Acetabularia donate all of the cytoplasm
and all of the parental nuclei to their progeny. The
siphonous body plans of Caulerpa and Acetabularia beg
the question: was differentiation of cytoplasmic regions
necessary for cellularization of the multicellular vegetative
body plans of green land plants? We chose the siphonous
Chlorophytes, Acetabularia and Caulerpa, to compare
with the siphonous Charophyte, Chara.
Volvox carteri, a multicellular freshwater green alga
with fully differentiated germ and somatic cells, and
Chlamydomonas reinhardtii, the well-known unicellular
green flagellate, shared a common ancestor as recently
as 35 MYA. Together they provide a unique opportunity
to explore the genetic basis for the evolution of multicellularity
and cellular differentiation. Studies in progress (D.
Kirk, pers. comm to D.F. Mandoli) are exploring changes
in the structure and functions of orthologous gene products
that have accompanied this important transition. Although
a BAC library exists for C. reinhardtii, these comparative
studies are inhibited by the absence of a comparable
library for V. carteri.
Caulerpa species are multinucleate unicells that fascinate
plant biologists, because they bear a striking superficial
resemblance to land plants: a tube or "stolon"
grows along the sea floor differentiating root-like
structures from its lower surface, and leaves, supported
on a leaf-stem, from its upper surface. Caulerpa species
respond to gravity much as flowering plants do and,
consistent with this, they make and respond to land
plant hormones. They excel at rapid wound healing. Their
secondary biochemistry is renown, producing unusual
sequiterpenoids that act as cytoskeletal, neural and
developmental toxins. Caulerpa taxifolia is a marine
weed with potential for commercial impact. First found
in the NW Mediterranean and Italy, it quickly spread
to the SW Mediterranean and then to California. DNA
fingerprinting suggests that this weedy strain of C.
taxifolia came from an aquarium. Current studies focus
on how to eradicate this ecological pest.
Classic developmental studies in Acetabularia acetabulum
revealed the role of the nucleus and predicted the existence
of mRNA for the first time in any eukaryote. Like green
land plants, this giant, marine unicell grows by both
tip and diffuse growth even though it lacks meristems
and undergoes juvenile and adult development. It makes
a morphologically elaborate thallus (-body plan) including
a specialized reproductive structure even though it
has just one nucleus for most of its life cycle. Important
for cell biological studies, it is amenable to grafting
within and between species and graft chimeras express
intermediate morphologies. Evidence suggests that mRNAs
involved in reproductive differentiation of the apex
have a half-life of 20 days. This species shares an
alternate codon usage with the ciliates. It makes a
cell wall typical of a group of algae, "the mannan
weeds" that differs fundamentally from the cellulosic
wall of land plants. Evidence indicates that all but
one of the DNA synthesis enzymes are on the chloroplast
genome. This begs the question how the nuclear and organellar
genomes co-regulate DNA synthesis required for reproduction
(2-6 million progeny/cell/generation) and may provide
fundamental insights into different resolutions of endosymbiotic
problems. Mutants in morphology and development are
now available. Well preserved in a 570 MY fossil record
http://ifaa.port5.com/index.html,
the morphological innovations in thallus, laterals and
specialized reproductive structures in the Dasycladales
are remarkable. Interestingly, these regions may also
be physiologicallydistinct which may represent an early
drive to organogenesis. Genomic and cDNA libraries as
well as EST arrays for both juvenile and adult phases
(Mandoli et al, unpub) are available.
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Charophytes: The fossil record
indicates that relatives of the modern charaleans were
the dominant macrophytic vegetation in freshwaters for
-300 MY (http://ifaa.port5.com/index.html).
The freshwater Charophytes are considered ancestral to
land plants based on ultrastructural, biochemical and
molecular evidence of extant species. Sequence analyses
confirm the close relationship of the Charophyte algae
to land plants. Charophyte innovations, such as the division
apparatus, the "phragmoplast', were clearly built
upon by green land plants.
Based on morphological and molecular analyses, Mesostigma
viride, a scaly, freshwater flagellate in the Prasinophyceae,
is thought to be an early divergent species most closely
related to charophyceans. It is essential to understanding
the evolution of green plants. Of all the taxa discussed,
this is the most basal, retaining the most primitive features
of green plants. One key feature, a "multilayered
structure" is common to Mesostigma viride, the reproductive
cells of charophyceans and land plants. Data from mitochondrial,
chloroplast and nuclear genes support Mesostigma viride
as basal to evolution of the Charophyta. BAC library would
be invaluable because there are virtually no molecular
resources available to study this evolutionarily important
species.
Chara, which are sister to land plants, are branched,
filamentous species reaching lengths of A m. The size
of its internode cells (95 cm long) makes it ideal for
electrophysiology and many of these ion channels resemble
those in green land plants. A specialized apical cell
remains meristematic, cutting off daughters only from
its lower surface. Charalean cells use a land plant-like
phragmoplast during cell division, but differ from green
land plant division in regulation of cytokinesis. Like
Coleochaete, Chara sp. control the plane of cell division
and make plasmodesmata. Chara cells also undergo asymmetric
cell division, an ability correlated with formation of
special differentiated cells in green land plants, e.g.
stomatal complexes. They make a thick, layered cell wall
that contains cellullose. As in Coleochaete, vegetative
cells form elaborate structures which grow in coordinated
fashion to enclose sexual cells of Chara, presaging the
evolution of the embryophytes. In addition, nodal complexes
are actually tissue-like or parenchymatous. Each internode
cell contains thousands of nuclei. C. corallina internodes
contains nuclei ranging from 5.4 to 10.9 pg/nucleus (A.
Arumuganathan, M. Bisson & DF Mandoli, unpub.) which
may well reflect different stages of cell division. If
the genome of C. corallina is smaller than that of C.
aspera , it will be used instead of C. aspera. Because
Chara internode nuclei may be endoreduplicated, we will
also determine the IC value of the nucleus in the meristematic
cell of Chara sp, with confocal microscopy in order to
avoid making too large a BAC library.
Coleochaete orbicu/aris is an epiphyte that grows as a
monolayer of cells resembling tissues (the protonemata)
of the early divergent moss Sphagnum. An important morphological
innovation, Coleochaete differentiates cell types making
terminal or marginal meristems and is capable of controlling
the plane of cell division. Like charaleans and green
land plants, Coleochaete cells are interconnected by plasmodesmata.
Like Mesostigma, Coleochaete possesses a multi-layer structure.
Species with tissue-like organization tend to grow in
shallow waters and may presage evolution of green land
plant tissues. Given that this species is frequently exposed
to desiccation in its native habitat and can survive in
moist air, the evolution of physiological and physical
features for water conservation essential to survival
on land is plausible. Consistent with this, the mucilage
of this species forms ridges that have some ultrastructural
similarities to cuticles of green land plants. Grana in
Coleochaete thylakoids are organized more like those in
green land plants than in other algae. Two features of
reproduction in Coleochaete presage evolution of the embryophyta.
Unlike other algae, egg cells of Coleochaete orbicularis
are retained on the thallus. In addition, vegetative cells
surrounding the egg transfer nutrients to the embryo.
Like the pollen of land plants, Coleocheate makes sporopollenin
and phenolics using them to protect reproduction.
Alternative green algae. Construction of BAC libraries
for Chlorelia sp. (Trebouxiophyceae), K/ebsormidium flaccidum
(Klebsormidiales), and Mougeotia transeaui (Zygonematales)
would round out sampling of major lineages in the algal
phylogeny. Note that several polyphyletic groups, such
as the Prasinophytes that includes Mesostigma, are not
encompassed by our taxomonic sampling. However, the phylogenetic
data to make rational decisions are simply not yet available
in these clades. |
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Embryophytes
The extant non-seed embryophytes include three major
groups: the bryophytes (liverworts, hornworts and mosses),
lycophytes (Lycopodaceae, Selaginellaceae and Isoetaceae)
and the moniliforms (psilotophytes, equisetophytes and
the eusporangiate and leptosporangiate ferns). The embryophytes,
including seed plants, are a monophyletic group originating
from an ancestor most closely related to the charophycean
algae. The phylogenetic relationships of the extant embryophytes
and the innovations that preceded their appearance during
land plant evolution are well-documented. We will make
BAC libraries from species representing each major lineage
in the non-seed embryophytes. |
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Bryophytes: These are simple, small, rootless plants
that lack lignified vascular tissue. Their life cycle
consists of a dominant gametophytic phase and sporophytes
that are dependent, unbranched and monosporangiate. Bryophytes
are ancestral to vascular plants and are most representative
of the earliest land plants. They hold clues to understanding
the innovations necessary for the transition from life
in water to dry land. These innovations include a cuticle
to prevent water loss, stomata to enable gas exchange,
enclosure of the egg in a protective archegonium; protection
against UV and pathogens; and the beginnings of a diploid
sporophyte generation and apical meristem. Questions relating
to the evolution of the genes regulating these traits
can be addressed with BAC libraries from bryophytes. Marchantia
polymorpha (a liverwort) and Anthoceros sp, (a hornwort)
are included in this proposal because they are morphologically
very distinct and may represent independently derived
lineages. Marchantia polymorpha, a common greenhouse weed,
is particularly attractive because it can be transformed. |
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Lycophytes: Vascular plants
are thought to have followed two lines of evolution: the
Lycophytina (lycophytes) and the Euphyllophytina (all
other vascular plants). Extant lycophytes include members
of the Lycopodiaceae, Selaginellaceae and Isoetaceae;
species within each family have been included in this
proposal. Lycophytes were the first Glade to evolve stem/leaf/root
organography, reflecting an increase in the complexity
of the sporophyte generation. The lycophytes form a monophyletic
group that diverged prior to the evolution of stem/leaf/root
organography, heterosporous reproduction, secondary growth,
and complex modes of branching in the vascular plant lineage.
The lycophytes are therefore an important group for determining
if independently evolved characters in divergent groups
of plants involved the same (homologous) or different
genes and control mechanisms. Lycopodium clavatum is homosporous,
while Selaginella kraussiana and Isoetes engelmanii are
heterosporous. Although Lycopodium clavatum, has a large
genome size, it is the smallest known in this genus. Selaginella
kraussiana could become a new model plant species because
it has a small genome size [-30% that of Arabidopsis],
is easy to culture and can be crossed. Isoetes englemannii
was chosen because it has a relatively small genome and
is easy to culture. |
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Pteridophytes: Pteridophytes are a Glade including
Equisetum, Psilotum, and the ferns. Recent palaeontological
and molecular analysis indicate that pteridophytes form
a monophyletic group sister to the seed plants. Psilotum
nudum was chosen for its unique morphology, which has
caused much debate about its phylogenetic placement. Angiopteris,
one of six extant genera of the Marattiales (eusporangiate,
homosporous ferns), is related to the tree ferns that
thrived in the Carboniferous swamps; the morphology of
Angiopteris erecta has been well-characterized. Of the
leptosporangiate ferns (in which the sporangium develops
from a single cell), Ceratopteris richardii (homosporous)
and Marsilea quadrifolia (heterosporous) are choice because
they are genetically and experimentally tractable. Since
the common ancestor of pteridophytes and seed plants lacked
defined leaves and roots, the pteridophytes are also an
important group in understanding the evolution of traits
in land plants. The common ancestor of pteridophytes and
seed plants lacked defined leaves and roots, secondary
growth, bipolar growth, axillary branching, the heterosporous
life cycle, seeds and pollen. Therefore, a thorough understanding
of the comparative genomics for different pteridophytes
and seed plant groups will provide the crucial data needed
to decipher the phylogenetic and developmental origins
of these vital characters.
Alternative non-seed plants. The choice of species for
this group was simple, since there are few species to
select from, and even fewer for which all criteria (see
above) hold. Although the moss Physcomitrella patens is
amenable to reverse genetic techniques, a P. patens BAC
library is publicly available (courtesy R. Quatrano, Washington
University). Mosses were therefore excluded from this
proposal. Equisetum (the only representative of the equisetophytes)
was also excluded because the genome sizes of all species
examined to date are very large [1C>110,000 Mbp].
The genetic systems that generate flowers, fruits and
body form in angiosperms echo an evolutionary heritage
to the origins of seed plants: to non-seed plants, green
algae, and beyond. To understand the genetic complexity
of modern plants, including crops and model organisms,
one must appreciate how these systems arose evolutionarily.
We will sample taxa that occupy pivotal phylogenetic positions,
make linkages to model plants and provide sampling of
key basal lineages in the basal angiosperms, eudicots,
and outgroups. Inclusion of basal angiosperms is important
because the origins of many of the innovations elaborated
on in seed plants can be traced back to the basal angiosperms.
Hence, we include exemplars from the earliest-branching
lineages of angiosperms (i.e., Amborellaceae, Nymphaeales).
We also chose basal exemplars of the eumagnoliids (Liriodendron),
the monocots (Acorus) and the basal eudicots (Eschscholzia)
which have vast structural diversity. For linkage of these
basal seed groups to more derived and `typical' eudicot
lineages, we selected two important microevolutionary
model plants, Silene and Mimulus. |
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Gymnosperms:
Gymnosperms include the earliest living lineages with
innovations including a greatly reduced male gametophyte
(pollen), pollination, seeds, and true secondary growth
of the vascular tissues to produce "wood.".
Recent molecular phylogenetic studies indicate that the
five major lineages of extant gymnosperms (cycads, Ginkgo,
Gnetales, Pinaceae, and all other conifers) form a monophyletic
group that is sister to angiosperms, although an alternate
placement of Gnetales as sister to the angiosperms cannot
be unambiguously rejected. Because the genomes of gymnosperms
are extremely large, our priority is to build one new
library from the basal most lineage of gymnosperms, the
cycads (Zamia). Cycads represent the likely sister lineage
to all other extant gymnosperms and are consistently included
in comparative developmental and molecular systematic
studies. As a basal lineage, cycads provide exemplars
to help ascertain the generalized gymnosperm reproductive
features from which flowering plant morphology and genetic
controls were likely modified. Zamia will also be the
target of extensive sequencing and expression profiling
in the NSF Floral Genome Project. |
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Basal Angiosperm lineages:
Angiosperm innovations include the flower; double fertilization,
endosperm, "true" vessels, fibers, and great
physiological and biochemical diversity. Although most
species of angiosperms are either monocots (especially
grasses and orchids) or eudicots, the greatest diversity
of structure occurs in the basal angiosperms. Recent molecular
phylogenies have clearly identified 8-10 of the major
basal flowering plant lineages. We chose four of these
major lineages to represent this diversity so that a comprehensive
picture of the ancestral angiosperm can be developed from
the BAC library resource, and capture the genetic and
genomic changes that led to key angiosperm innovations.
The FGP will simultaneously conduct intensive EST and
gene expression studies, including in situ hybridization
on app. 300 genes and microarrays of 2,000 to 5,000 genes.
The four proposed basal angiosperms are: Amborella, Nuphar,
Liriodendron and Acorus.
Amborella trichopoda is widely recognized as the sister
to all other extant angiosperms. This species is primitively
vesselless, has unsealed carpels and has tepals rather
than distinct petal-sepal differentiation. Because of
its unique phylogenetic position, Amborella is crucial
to understanding angiosperm ancestry and development.
Amborella is endemic to New Caledonia but has recently
been brought into cultivation and is now easily maintained.
Nuphar adventa (waterlily, spatterdoc) is a second critical
basal angiosperm. Distinct petals and sepals first appeared
with the waterlilies, and they possess unusual "primitive"
vessel types. This second basal branch of angiosperms,
or perhaps the shared basal branch with Amborella [see
Amborella refs], differs morphologically and anatomically
from Amborella and thus equally important for understanding
the origin of key angiosperm innovations. Nuphar is becoming
the focus of intensive developmental, reproductive, and
evolutionary genomic study, including floral biology and
gene expression [N. Friedman, pers. comm. to C. dePamphilis].
The Eumagnoliid Glade is species rich and contains much
floral, structural, and biochemical diversity, including
oil cells, cyanogenic glycocides, terpenoids, and benzyquinaline
alkaloids. Liriodendron tulipifera (yellow or tulip poplar;
Magnoliaceae) is a valuable timber tree that is unusual
among harvested species for being relatively free from
serious pest problems, including resistance to attack
by the exotic gypsy moth. It is transformable and the
focus of intensive genetic studies. It has the lowest
chromosome number in Magnoliaceae (2n = 38) and a relatively
small genome size (784 Mbp).
Acorus gramineus (sweet flag; Acoraceae) The monocot proposed
for BAC library construction is Acorus gramineus (2n =
18) which has a very small genome (392 Mbp). A large EST
set and detailed expression studies will soon be available.
Acorus is a widely studied medicinal botanical species
producing pharmacologically active antibiotic resistance
inhibitors, essential oils, neurotransmitter sedatives,
antioxidants, and inhibitors of excitotoxic neuronal death
. Because of its unique phylogenetic position as sister
to all other monocots. Acorus gramineus will be very important
for understanding the evolution of monocot genomes as
well as morphological and developmental features. An Acorus
BAC library will enable comparisons to genomes of several
cereal grains for which BAC libraries already exist. |
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Eudicot developmental & microevolutionary model
systems: Most flowering plant diversity (outside of
the monocots) is found in two large eudicot groups, the
rosids and the asterids. Genomic resources for this group
have been driven by economic importance, not by evolutionary
significance or (except for Arabidopsis) depth of interest
in the research community. We have selected one basal
eudicot lineage and two microevolutionary model organisms
that hold key taxonomic positions in the evolution of
angiosperm diversity. BAC libraries for these plants will
be rapidly put to use by large and active research communities.
Inclusion of an early-diverging eudicot, Eschscholzia
californica (California poppy; Papaveraceae), is critical
for the broad evolutionary comparisons proposed, because
it will provide a root for all genomic-scale analysis
for more derived eudicot systems. Poppies are intensely
studied as a model for floral molecular genetics and evolution,
and for studies of the molecular basis of alkaloid (opiate)
chemistry, and latex chemistry. The California poppy has
a smaller genome
than the more widely studied opium poppy (Papaversomniferum)
and does not require research permits. We will thus also
use E. californica for FGP EST and gene expression studies.
E. californica is the most widespread poppy species in
North America and is highly variable in structure and
life history. It is transformable and a variety of floral
mutants are available.
The genus Mimulus (monkeyflower, Scrophulariaceae) is
one of the premier model systems for the study of ecological
and genetic mechanisms of evolutionary change. Several
species are the subject of genomewide studies of inbreeding
depression, mating system evolution, adaptation to toxic
soils, and different elevational habitats, divergence
of floral development and pollination hybridization and
introgression, and reproductive isolation mechanisms.
Mimulus guftatus, is easily cultivated and crossed, has
a small genome size and complete genetic map with evolutionarily
important quantitative trait loci. In addition, large
permanent mapping populations and an EST database are
being developed (Willis letter).
Silene latifolia (catch fly, Caryophyllaceae) is one of
the most intensely used wild plant models for a wide variety
of ecological and evolutionary processes including parasite-host
interactions, sex determination and development, sex ratio
evolution, and sex chromosome evolution, and metapopulation
genetics (Kesseli letter). S. latifolia (2n=24) has a
chromosomal based sex determination system in which males
(XY) and females (XX) are easily distinguished by flower
structure or by genetic markers on the sex chromosomes.
A BAC library will speed progress in all aspects of Silene
functional genomics, but will be particularly useful for
cloning of critical genes on non recombining Y-chromosome
regions.
Alternative seed plant. The following taxa in the remaining
major lineages were also carefully considered, but were
relegated to alternates for budgetary reasons. These taxa
include innovations of interest, are economically important
(e.g., floral fragrance, wood), are a model for microevolution
or a specific feature of interest (e.g., wood formation,
parasitism, ring-like anthers) and many have other resources
available.
GvmnosDerms: Welwitschia mirabilis (Genetales) (6,720
Mbp). Pinus taeda (n=12; 21,700 Mbp).
Basal Angiosperms: Yucca angustissima (n = 30; 2,500Mbp).
Eudicots: Aquilegia formosa (columbine; Ranunculales)
(n=14; 539 Mbp) (Hodges letter). Arceuthobium tsugense
(Viscaceae; Santalales). (7,154 Mbp) (Nickrent letter),
Vaccinium corymbosum (blueberries: Ericaceae) (2n = 24,
1078 Mbp) (Rowland letter). |
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