RAUBESON, LINDA A.1*, DAVID BADER2, BERNARD M. E. MORET2, LI-SAN WANG3, TANDY WARNOW3, and STACIA K. WYMAN3. 1Biological Sciences, Central Washington University, Ellensburg WA 98926; 2Computer Science, University of New Mexico, Albuquerque NM 87131; 3Computer Science, University of Texas, Austin TX 78712. - Inferring phylogenies of photosynthetic organisms from chloroplast gene orders.
Distribution of gene order changes have been used successfully for
estimating phylogenies within and among various land plant groups.
However, such chloroplast DNA structural characters remain largely
untested for phylogenetic inference at very high taxonomic levels such
as between Chlorophytes and Streptophytes or among major lineages of
photosynthetic organisms. When chloroplast genomes of these more
distantly related organisms are compared, computational difficulties
increase dramatically. Challenges include unequal gene content and
high rates of change relative to the number of genes available as
landmarks. We have been developing and testing a variety of methods
for reconstructing phylogenies based on gene order data (see abstracts
by Jansen et al and Moret et al). Here we will compare results of our
methods when analyzing highly divergent gene orders. We have
determined gene orders, from complete genome sequence information
available in genbank, for chloroplast genomes of eleven organisms. In
our data, we represent the free-living cyanelle, Cyanophora, "red
algae" (Cyanidium, Porphyra), "green algae"
(Chlorophytes: Chlorella, Mesostigma, Nephroselmis and Streptophytes:
Marchantia and tobacco), and presumed secondary endosymbionts
(putative red algal derivatives: Guillardia, Odontella and putative
green algal derivative: Euglena). To analyze these data we have
utilized GRAPPA and other approaches based on breakpoint and inversion
distance as well as cladistic analyses using shared rearrangement
endpoints as characters.
Key words: chloroplast phylogeny, comparative genomics, gene order rearrangement, photosynthetic eukaryotes, phylogenetic methods