Phillips, Mellisa M , Raubeson, Linda A. .
Microstructural variation in the trnH-psbA region of the chloroplast genome of conifers.
In PCR experiments, we observed significant length variation in the trnH-psbA region of conifers, with size differences of more than 200%. Members of the Podocarpaceae and Araucariaceae were especially prone to this length variation. We wanted to determine what types of mutations were responsible for these variants and what sequence characteristics promoted these changes. So far, we have sequenced the region for nine Podocarpaceae and four Araucariaceae as well as twelve other conifers. We have used programs such as BLAST, ClustalW, PipMaker and Reputer in our analyses of the data. Other workers have found repeat structures to be related to the insertion and deletion events (indels) responsible for length variation. Repeats, both microsatellites and larger direct or indirect repeats, are abundant in the region. The region is variable enough that combining all of the sequences in a single alignment was not possible. So we made pairwise comparisons among more closely related species, identified each repeat and each indel, and looked for a correlation between the two. Some indels are positionally (and probably mechanistically) related to these repeats however most indels do not occur with repeats and the position of most repeats does not correspond to the position of the indels. We did find that trnI is absent from the trnH-psbA region of all Podocarpaceae and Araucariaceae that we examined; whereas the gene is present in that region of all other conifers we studied. Surprisingly, in the two Araucaria species we sequenced, we found trnY between trnH and psbA. We sequenced the trnT-psbM region where trnY usually occurs and found it to be present there as well. Thus trnY has been duplicated in the chloroplast genomes of these araucarians. It seems that the evolution of non-coding chloroplast DNA sequence can be quite complex and involves mechanisms not well understood.
1 - Central Washington University, Department of Biological Sciences, MS 7537, Ellensburg, Washington, 98926-7537, USA
noncoding chloroplast DNA.
Presentation Type: Poster
Location: Special Event Center (Cliff Lodge)
Date: Tuesday, August 3rd, 2004
Time: 12:30 PM