Genomics / Proteomics
Karol, Kenneth G. , Banks, Jo Ann , Roper, Jessie M. , Hansen, S. Kellon , Wolf, Paul G. , Kuehl, Jennifer V. , Boore, Jeffrey , Everett, Karin , Mandoli, Dina F. , Olmstead, Richard G .
Plastid genome evolution in lycophytes.
THE plastid genome (cpDNA) of land plants is generally conserved with respect to gene content and architecture. Complete cpDNA sequences have increased our understanding of land plant phylogeny and cpDNA evolution. However, robust phylogenies using only one or a few plastid-encoded genes from Selaginella have been recalcitrant because of the apparent accelerated rate of evolution in this lineage. We compared complete plastid genome sequences from three lycophyte lineages (Huperzia, Isoetes, and Selaginella) with representative plastid genomes from bryophytes, ferns, and seed plants to better characterize cpDNA evolution of this early-diverging vascular plant lineage. Plastids were isolated using Fluorescence Activated Cell Sorting (FACS) and amplified with Rolling Circle Amplification (RCA). The RCA products were cloned and shotgun sequenced to an average of 8x coverage for each genome. PCR was used to confirm regions of poor coverage. Analyses of gene content and order identified Selaginella as an extremely divergent plastid genome. Protein coding gene content in Selaginella is similar to other land plant cpDNA however ~21 tRNAs have been lost relative to most land plant lineages. Also, a sizable region of the Selaginella large single copy (LSC), including psaA/B, rps4/14, psbC/D/Z and ycf3, has been transferred to the small single copy (SSC) region. Codon usage and base composition are significantly different in Selaginella than other lycophytes. Genome structure, content and codon usage will be compared with other land plastid genomes.
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1 - University of Washington, Department of Biology, Box 355325, Seattle, Washington, 98195-5325, USA
2 - Purdue University, Department of Botany and Plant Pathology, West Lafayette, Indiana, 47907-1155, USA
3 - Utah State University, Department of Biology, College of Science, 5305 Old Main Hill, Logan, Utah, 84322, USA
4 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA
5 - University of Maryland, Department of Biology, Box 355325, Seattle, Washington, 98195-5325, USA
6 - University of Washington, Department of Biology & Center for Developmental Biology, Box 355325, Seattle, Washington, 98195, USA
Presentation Type: Oral Paper:Papers for Topics
Date: Tuesday, August 1st, 2006
Time: 4:00 PM