Genomics / Proteomics
Peery, Rhiannon , Downie, Stephen R. , Kuehl, Jennifer V. , Boore, Jeffrey L. , Raubeson, Linda A. .
Chloroplast genome evolution in Apiaceae.
The chloroplast genome of most land plants contains two copies of a large inverted repeat (IR) separating the remainder of the genome into large and small single copy regions (LSC and SSC, respectively). The most common LSC-IR junction in angiosperms is within or near rps19. On the JLa side of the LSC-IR boundary there are usually 2-9 nucleotides between the IR and the start of trnH-GUG. Most members of the angiosperm family Apiaceae have a normal LSC-IR junction, however, some genera have contracted LSC-IR boundaries. Small expansions and contractions of the LSC-IR boundary are common, but the large contractions seen in the Apioid clade of the Apiaceae are rare. In the Apium group, within the Apioid clade, the LSC-IR junction has contracted about 1500 nucleotides and only contains 39-79 bp of rpl2. Within the Apium group we have found an anomaly around the JLa. Instead of 2-9 nucleotides between the IR and the start of trnH-GUG, we found 214-392 nucleotides of novel DNA in the examined Apium group species. The novel sequence was found in all major genera of the Apioid clade tested including: Ammi, Apium, Anethum, Conium, Foeniculum, Petroselinum, and Ridolfia. The IR boundaries in Ammi majus, Foeniculum vulgare, and Ridolfia segetum are identical. These three species have 391-393 base pairs of novel sequence that shows 92% similarity. In comparisons with other chloroplast genomes, the novel sequence does not show significant similarity to any other chloroplast sequence outside of the JLa region in the Apium group. We are currently looking further into the extent of this novel sequence within Apiaceae chloroplast genomes, working to determine at which point the sequence entered the Apium group, the source of the sequence, and whether or not the novel sequence is related to the other changes at the LSC-IR boundary.
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1 - Central Washington University, Department of Biological Sciences, 400 E University Way, Ellensburg, WA, 98926-7537, USA
2 - University of Illinois Urbana, Department of Plant Biology, 265 Morrill Hall, 505 South Goodwin Avenue, Urbana, Illinois, 61801-3707, USA
3 - DOE Joint Genome institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
Presentation Type: Oral Paper:Papers for Topics
Location: Boulevard A/Hilton
Date: Wednesday, July 11th, 2007
Time: 3:15 PM