The Giardia Genome Project: Production Pipeline and Assembly of LI-COR Bi-Directional Sequence Data

Hilary G. Morrison, Andrew G. McArthur, Julie E.J. Nixon, Nora Q.E. Passamaneck, Ulandt Kim, Melissa K. Crocker, Gregory Hinkle, Michael E. Holder, Rebecca Farr, Claudia I. Reich, Gary J. Olsen, Lorena A. Fierro, Stephen B. Aley, Rodney D. Adam, Frances D. Gillin and Mitchell L. Sogin
The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
The Marine Biological Laboratory, Woods Hole, MA 02543
E-mail: morrison@mbl.edu, sogin@mbl.edu

Introduction

Giardia lamblia is an environmentally transmitted, waterborne, human pathogen. We have selected G. lamblia as a model organism for genome analysis because of its well-recognized impact on human health, its relatively small genome containing approximately 12 million base pairs, and the insights it will provide about the origins of nuclear genome organization. Previous comparisons between several gene families have demonstrated Giardia's basal position in molecular phylogenies. Since the divergence of Giardia lies close to the transition between eukaryotes and pro-karyotes in universal ribosomal RNA phylogenies, it is a valuable model for gaining basic insights into the genetic innovations that led to the formation of eukaryotic cells.

In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. Sequence analyses of the Giardia lamblia genome will address several important questions related to human health, including the number, gene organization and regulation of variant-specific surface protein coding regions. The Giardia genome project at the Marine Biological Laboratory in Woods Hole is part of an NIH Investigator-Initiated Interactive Research Project Grant (IRPG). The genome sequencing component is a collaborative effort between the laboratories of Mitchell L. Sogin (Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the MBL), Stephen Aley (University of Texas at El Paso), Rodney Adam (University of Arizona at Tucson), and Gary Olsen (University of Illinois at Urbana-Champaign). The Giardia sequencing effort is complemented by its IRPG functional genomics unit, directed by Frances D. Gillin at the University of California at San Diego.