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Systematics Section / ASPT

Raubeson, Linda A. [1], Fine, Nichole L. Y. [1], Peery, Rhiannon [1], Fourcade, H. Matthew [2], Kuehl, Jennifer V. [2], Boore, Jeffrey L. [2].

A comparison of conifer chloroplast genomes based on complete genome sequences from Pinaceae, Podocarpaceae, and Cupressaceae.

For most of the past decade only a single completely sequenced conifer chloroplast genome has been available: In 1994 Wakasugi et al (PNAS 91:9794) completed the genome sequence for Pinus thunbergii (NC_001631). In 2003 another Pinus chloroplast genome (basically identical in gene order to the Pinus thunbergii genome) was submitted to GenBank (P. koraiensis, AY228468). We now have draft sequence for two conifer chloroplast genomes, representing two additional conifer families: Podocarpaceae (Afrocarpus gracilior) and Cupressaceae (Cryptomeria japonica). In comparing the genomes from the three families, all lack the large rDNA-containing inverted repeat common to most other land plants. The podocarp lacks both copies of the remnant IR reported from Pinus thunbergii (Tsudsuki et al, 1992, MGG 232:206), whereas Cryptomeria retains at least one copy of the remnant. The Afrocarpus and Cryptomeria genomes each include all of the ndh genes, unlike the pines where those genes have been lost or inactivated. Each genome exhibits a similar number of gene order changes when compared to tobacco. However, further analysis is required to determine the exact nature of all these mutations as well as how many of these changes are shared among families and thus phylogenetically informative at that level. At this time we have more completely characterized one inversion, of atpB-E, that is absent from the Pinus genomes but common to both Afrocarpus and Cryptomeria. Using PCR and sequencing strategies, we have found this inversion to occur in all members of Podocarpaceae, Araucariaceae, Cupressaceae, and Taxaceae that we have screened to date. We are continuing to work at characterizing the other gene order changes.

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

Gene order
chloroplast DNA

Presentation Type: Paper
Session: 58-10
Location: Cottonwood B (Snowbird Center)
Date: Wednesday, August 4th, 2004
Time: 4:00 PM
Abstract ID:692

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