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 This is an electronic version of an article published in Journal of Phycology ©2005, The Phycological Society of America. This is an electronic version of an article published in Journal of Phycology ©2006, The Phycological Society of America. This is an electronic version of an article published in Journal of Phycology ©2007, The Phycological Society of America. |
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Endosymbiotic
Gene Transfer and the Evolution of the First Photosynthetic Eukaryotes (EXBO3-0000-0014) |
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| PI: | Debashish Bhattacharya | |
| Co-PI: | M. Bento Soares | |
| Key Professional Scientist : | Tom Casavant | |
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PROJECT SUMMARY: | ||
| Horizontal gene transfer, or
the introduction of genes across the "branches" of
the tree of life rather than through normal vertical evolution, has been
proven in prokaryotes but is yet to be rigorously tested in eukaryotes.
This proposal focuses on one special case of horizontal gene transfer that
has played a fundamental role in early eukaryotic evolution - endosymbiotic
gene transfer. The cyanobacterial endosymbiosis that gave rise to the first
plastid is one of the most ancient events in eukaryotic history (~1.6 billion
years ago). Endosymbiosis left a sizeable mark on the nuclear genome that
goes well beyond the lateral transfer of photosynthetic capacity. A recent
analysis (Martin et al. 2002) of Arabidopsis suggests that about 18% of this plant’s nuclear
genes, many of non-photosynthetic function (e.g., disease resistance),
originated from the cyanobacterium. Endosymbiotic gene transfer significantly
enriches nuclear genomes with foreign genes which selection can act on
to explore novel functions. To quantify this critical process in a broader context of eukaryotic genome sequences, we will
generate expressed sequence tags (ESTs) from a member of the earliest diverging
algal group, Cyanophora paradoxa (Glaucophyta). We can potentially expect to find a stronger
signal of lateral gene transfer in this ancestral alga than was evident
in the highly derived Arabidopsis genome. Normalization and subtraction protocols
will maximize the novelty of the cDNA data set. The project will rely on
initial gene identification using our high-throughput sequencing and bioinformatic
pipeline followed by complete sequencing and phylogenetic analysis of selected
cDNAs to reveal their evolutionary origin. |
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STATEMENT OF WORK |
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| This proposal has 3 specific aims that fulfill the requirements of the Astrobiology: Exobiology and Evolutionary Biology program at NASA. | |||
| Aim 1.To generate 11,000 ESTs from non-normalized and normalized cDNA
libraries from the glaucophyte alga Cyanophora paradoxa. |
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A starter (non-normalized) library will be constructed from an exponentially growing uni-algal culture of Cyanophora (available from the CCMP culture collection [CCMP329]). This library will be normalized to reduce the representation of highly expressed transcripts. Both starter and normalized will be tagged with a unique 10 bp identifier which makes identification of the source library readily apparent. We will also generate a serially subtracted normalized library that is increasingly enriched for the mRNAs of the complex frequency class (rare mRNAs). The subtracted library will be derived from an iterative process that we have developed and named Serial Subtraction of Normalized Libraries (Bonaldo et al. 1996, Soares 1997). | ||
| Aim 2. To quantify the extent of cyanobacterial (or other) gene transfer in the nuclear genome of Cyanophora. | |||
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We will develop a computer program (EndoMove) to automate genic comparisons between Cyanophora and other targeted genome sequences (e.g., Synechocystis, Arabidopsis, Porphyra, human, fly, yeast). This program will allow us to determine the phylogenetic origins of the Cyanophora genes and to identify potential candidates for gene transfer from the cyanobacterial endosymbiont. We will also generate novel sequences of target genes from poorly sampled eukaryotic lineages to account for taxonomic breadth in each of the molecular phylogenies that test for endosymbiotic gene transfer in Cyanophora. | ||
| Aim 3. To use existing nuclear genome data from green algae (e.g., Chlamydomonas), land plants (e.g., Arabidopsis), red algae (e.g., Porphyra), and Cyanophora to definitively test their monophyly, thereby assessing the support for a single origin of the plastid in their common ancestor. | |||
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We will focus on members of the red, green, and glaucophyte algae (Plantae) and use extensive concatenated data sets of vertically inherited genes (identified with specific aim 2). These data will be included in phylogenetic analyses to test the monophyly of the Plantae and their position in the tree of life. This aim will require additional sequencing of target genes in non-Plantae taxa for which no genomic data are available. | ||
Light micrograph
of the glaucophyte Cyanophora paradoxa |
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