Abstract Detail

Systematics Section / ASPT

Raubeson, Linda A. [1], Feysa, Peter M, IV [1], Phillips, Mellisa M [1], Fine, Nichole L. Y. [1], Peery, Rhiannon [1], Fourcade, H. Matthew [2], Kuehl, Jennifer V. [2], Boore, Jeffrey [2].

Loss of the Inverted Repeat from Conifer Chloroplast Genomes, a more detailed characterization.

Various mapping studies showed that conifer chloroplast genomes have lost one copy of the large (10-25kb) rDNA-containing inverted repeat (IR), whereas the IR was retained in the chloroplast genomes of other seed plants, including Gnetales. Sequencing of the Pinus thunbergii chloroplast genome revealed a small (495bp) inverted repeat (ir). This ir was interpreted as a remnant of the large IR, i.e., the loss event was not complete, retaining a small portion at one end. That interpretation has been challenged because other repeats, direct or indirect, as large or even larger, are found in pine genomes and are not related to the former IR. The ir is composed of trnI and a 3’portion of psbA, resulting from a duplicated copy of trnI occurring between trnH and psbA, and a 3’ portion of psbA duplicated between trnI and rpl23. We have utilized a variety of PCR and sequencing approaches to examine this pattern of duplication. We have nearly complete drafts of the chloroplast genomes of Afrocarpus gracilior (Podocarpaceae) and Cryptomeria japonica (Cupressaceae); both copies of the ir are absent from the Afrocarpus genome whereas at least one ir copy is present in the Cryptomeria genome. Further work, focusing just on the two regions trnH-psbA and trnI-rpl23, shows that trnI is present in the trnH-psbA region of Gnetales, Pinaceae, Taxaceae and Cupressaceae but is absent from that region in Araucariaceae and Podocarpaceae. In addition, a 3’ portion of psbA is found in the trnI-rpl23 region of Gnetales and most Pinaceae. The simplest interpretation of these findings is that trnI-3’psbA represented one end of the ancestral IR and that the retained ir duplication in Pinus thunbergii and other Pinaceae is indeed a remnant of the IR. Part or all of the remnant ir subsequently has been lost in some lineages of conifers.

1 - Central Washington University, Department of Biological Sciences, MS 7537, Ellensburg, Washington, 98926-7537, USA
2 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA

Keywords:
conifer
chloroplast genome
gene order changes
phylogenetics.

Presentation Type: Poster
Session: 32-125
Location: Special Event Center (Cliff Lodge)
Date: Tuesday, August 3rd, 2004
Time: 12:30 PM
Abstract ID:822