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A Gymnosperm Phylogeny
We are using genomic tools to study gymnosperms, the oldest known
seed plants. Gymnosperms have endured since the Paleozoic/Mesozoic.
Extant taxa representing the gymnosperms include the Cycadales,
Ginkgoales, Coniferales, and Gnetales. Conflicting theories regarding
the evolutionary hierarchy between these taxa leave their phylogenetic
relationship unresolved despite a number of studies using a combination
of molecular and morphological markers. Although the placement of
the Cycadales at the basal node of the gymnosperms is well accepted,
the relationship between the three remaining clades is unclear.
In particular, the placement of the Gnetales at the top of gymnosperms
supports the "Anthophyte theory", which states that the
Gnetales are a sister group to the Angiosperms, whereas recent molecular
data relegates the Gnetales as a sister group to conifers. To definitively
determine the evolutionary hierarchy among these four gymosperm
taxa, we are generating EST libraries to develop databases to provide
molecular tools for high parsimony supertree analysis. A robust
molecular definition of gymnosperm phylogeny will set the ground
work for future studies on early seed plant evolution.
Genomics in Cycads
Cycads, a once abundant plant group now greatly reduced in number
of species and geographical distribution, have long been exploited
by people as a source of food and medicine. Today, there are approximately
250 species in 11 genera existing in tropical or subtropical regions.
Cycads contrast with all other plant life in most aspects of structure
and chemical characteristics. They are the most primitive living
seed plants and are considered to be the sister group to all other
seed plants based upon morphological and molecular data. This genomic
project on cycads, will reveal insight into how the structure and
function of genes in the most primitive living seed plant compare
to modern flowering plants, such as Arabidopsis. Comparative genomics
analysis will also be used to test the evolutionary placement of
cycads as the oldest living seed plants. To do this, we are comparing
EST libraries made from cycad tissues at different stages of development
to create a comparative expression profile of gene expression. Gene
expression profiles will be further characterized using SAGE and
microarray analysis from these different tissues. Genes with known
similarity to higher plants involved with development have been
and will continue to be isolated and characterized. Comparisons
can then be made to gene expression within modern flowering plants
(e.g. Arabidopsis) to develop a basis for understanding how plants
have evolved to meet changing environmental challenges to reproduction.
Evolution of Seeds:
One intriguing characteristic of cycads is that their seeds are borne at
the margin of leaf-like sporophylls, a condition reminiscent of
the original seed plants as found in the fossil record. Hence, a
study of early seed development in cycads will further our understanding
of seed evolution. We are comparing EST libraries made from young,
developing sporophyll tissue and from young developing leaves to
create a comparative profile of gene expression between these two
tissues.
Evolution of Cones:
Cycads have evolved over millions of years from leaflike reproductive
structures to more specialized reproductive cones. The basal node
in cycad evolution is the genus Cycas, which as described above
has leaf-like sporophylls. In more evolved genera of the Cycadaceae,
such as Zamia, sporophylls have been reduced into tightly compressed
bract-like structures to form cones. Comparative genomics will also
be used to unravel the developmental molecular differences between
Cycas and Zamia.
Evolution of Vegetative Structures:
Because little is known about the genetic control of leaf development,
the Cycad Genomics Project will also examine three species of cycads
whose leaf structures vary greatly from the majority of cycad plants—Cycas
simplicipinna, Cycas micholitzii, and Cycas multipinnata. Scientists
will use a comparative genomic analysis to identify the genes controlling
leaf development. These studies may lead to the testing of hypotheses
proposing that leaves evolved from partial shoots (i.e., leaves
are highly modified naked branch systems that evolved through amalgamation
and webbing between the original branches. These original branches
are now visible as veins).
A cycad EST database:
We have generated over 4000 ESTs from Cycas rumphii Miq., which can be
downloaded below. Using BLAST analysis, 37 of these ESTs matched other gymnosperms
genes but not higher plants. To see if some of these cycad genes might be specific
to gymnosperms, we sequenced the entire clone and repeated the BLAST analysis.
The entire sequence of the 37 genes can be down loaded below:
Download cycad EST sequence below.
Cycad Leaf ESTs
Fully sequenced Cycas clones, from Cycas contigs that match only gymnosperm genes in GenBank
Evo-Devo in Gymnosperms:
Our comparative genomics approach has already uncovered a number
of genes, similar to those in higher plants, known to be important
in directing structural devolopment. We are currently testing the
spacial and temporal expression pattern of these genes in developing
cycad leaves, sporophylls and cones using in situ gene expression.
Potential for Medicinal Knowledge:
Cycads are the only plants known to produce BMAA, the neurotoxin
thought to be a cause of Guam dementia. BMAA is believed to block
the function of brain glutamate receptors (GLRs), the biochemical
mechanisms in plants and animals that prompt nerve cells in our
brains to communicate with one other. Other neurodegenerative diseases
affecting brain GLRs includes Alzheimer’s, Parkinson’s, and Lou
Gehrig’s diseases. Comparative phylogenetic analysis performed by
members of the NYU and NYBG team has shown that GLR genes are present
in plants. This surprising discovery suggests that GLRs represent
a primitive signaling pathway that existed before plants and animals
diverged. In Arabidopsis, 20 different GLR have been identified.
In our cycad GLR libraries we have identified genes with high similarity
to the Arabidopsis GLRs.
The comparative studies of GLR genes in cycads with those of Arabidopsis
and animals may allow us to understand the mechanism by which cycad
GLR genes are resistant to the BMAA neurotoxin. These studies may
lead to potential applications for new treatments or drug discoveries
for the degenerative affects of neurological disorders upsetting
GLR function in humans.
For the three components of this project, cDNA libraries made from
gymnosperm mRNA are created in NYBG’s Lewis B. and Dorothy Cullman
Program for Molecular Systematics Studies laboratory. Our cDNA libraries
are sent for sequence analysis to CSHL where large-scale, state-of-the-art,
automated sequencing technology is used to generate ESTs. Bioinformatic
analysis of this data is performed at both NYU and CSHL. We have
also have developed a collaboration with MIPS, which is developing
a user interface with the general public to access our EST database,
which is used to process ESTs into functional chategories.
Research Correspondence:
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