Abstract Detail

Systematics Section / ASPT

Wolf, Paul G. [2], Kuehl, Jennifer V. [6], Mishler, Brent D. [1], Mandoli, Dina F. [3], Arumuganathan, K. [4], Olmstead, Richard [3], Renzaglia, Karen S. [5], Manne, Ashwin Kumar [2], Ellis, Mark W. [2], Karol, Kenneth G. [3], Boore, Jeffrey L. [6].

The complete chloroplast genome sequence of the lycopod, Huperzia lucidula (Lycopodiaceae): implications for land plant phylogeny.

We made organellar-enhanced DNA extractions of the lycopod, Huperzia lucidula (Michx.) Trevis. using Fluorescence Activated Cell Sorting (FACS). We amplified the chloroplast genome with rolling-circle amplification, sheared DNA into approximately 3kb fragments, and then shotgun subcloned. We then sequenced to 8x depth coverage to obtain the complete chloroplast genome sequence. The genome is 154,360 bp, with an inverted repeat of 15,314 bp, a large single-copy region of 104,088 bp and a small single-copy region of 19,644 bp. Gene order is more similar to that of mosses, liverworts and hornworts, than those known for vascular plants. For example, the Huperzia chloroplast genome possesses the bryophyte gene order for a previously characterized 30 kb inversion, thus supporting the hypothesis that lycopods are sister to all other extant vascular plants. Acquisition of the first chloroplast genome sequence of a lycopod also provides a better reconstruction of the basal tracheaophyte genome, which is useful for inferring relationships among bryophyte lineages. Several unique characters are observed in Huperzia, such as movement of the gene ndhF from the short single copy region into the inverted repeat. The results are discussed in relation to a growing comparative database of genomic and morphological data across the green plants. (Supprted by the Green tree of Life grant from NSF: http://ucjeps.berkeley.edu/TreeofLife/)

Related Links:
Green Tree of Life Project

1 - University of California, Berkeley, Integrative Biology, University and Jepson Herbaria, 1001 Valley Life Sciences Building, Berkeley, California, 94720-2465, USA
2 - Utah State University, Department of Biology, College of Science, 5305 Old Main Hill, Logan, Utah, 84322-0305, United States
3 - University of Washington, Biology, Seattle, Washington, 98195-5325
4 - Virginia Mason, Benaroya Research Institute, Seattle, Washington, 98101
5 - Southern Illinois University, Department of Plant Biology, 1125 Lincoln Drive, Carbondale, Illinois, 62901-6509, USA
6 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA

Keywords:
phylogenomics
phylogeny
chloroplast
chloroplast DNA
Annotation
Gene order
Inversion
Land Plant Evolution
land plants
Vascular plants.

Presentation Type: Poster
Session: 32-124
Location: Special Event Center (Cliff Lodge)
Date: Tuesday, August 3rd, 2004
Time: 12:30 PM
Abstract ID:423