@article{opperman_bird_williamson_rokhsar_burke_cohn_cromer_diener_gajan_graham_et al._2008, title={Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism}, volume={105}, ISSN={["1091-6490"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54149092490&partnerID=MN8TOARS}, DOI={10.1073/pnas.0805946105}, abstractNote={
            We have established
            Meloidogyne hapla
            as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence. At 54 Mbp,
            M. hapla
            represents not only the smallest nematode genome yet completed, but also the smallest metazoan, and defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. The
            M. hapla
            genome encodes significantly fewer genes than does the free-living nematode
            Caenorhabditis elegans
            (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous genes suspected to be involved in adaptations to parasitism. In some cases, amplification and tandem duplication have occurred with genes suspected of being acquired horizontally and involved in parasitism of plants. Although
            M. hapla
            and
            C. elegans
            diverged >500 million years ago, many developmental and biochemical pathways, including those for dauer formation and RNAi, are conserved. Although overall genome organization is not conserved, there are areas of microsynteny that may suggest a primary biological function in nematodes for those genes in these areas. This sequence and map represent a wealth of biological information on both the nature of nematode parasitism of plants and its evolution.
          }, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Opperman, Charles H. and Bird, David M. and Williamson, Valerie M. and Rokhsar, Dan S. and Burke, Mark and Cohn, Jonathan and Cromer, John and Diener, Steve and Gajan, Jim and Graham, Steve and et al.}, year={2008}, month={Sep}, pages={14802–14807} }
 @article{diener_houfek_kalat_windham_burke_opperman_dean_2005, title={Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system}, volume={6}, journal={BMC Bioinformatics}, author={Diener, S. E. and Houfek, T. D. and Kalat, S. E. and Windham, D. E. and Burke, M. and Opperman, C. and Dean, R. A.}, year={2005} }
 @article{charles_carbone_davies_bird_burke_kerry_opperman_2005, title={Phylogenetic analysis of Pasteuria penetrans by use of multiple genetic loci}, volume={187}, ISSN={["1098-5530"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-23644445501&partnerID=MN8TOARS}, DOI={10.1128/JB.187.16.5700-5708.2005}, abstractNote={ABSTRACT
          
            Pasteuria penetrans
            is a gram-positive, endospore-forming eubacterium that apparently is a member of the
            Bacillus-Clostridium
            clade. It is an obligate parasite of root knot nematodes (
            Meloidogyne
            spp.) and preferentially grows on the developing ovaries, inhibiting reproduction. Root knot nematodes are devastating root pests of economically important crop plants and are difficult to control. Consequently,
            P. penetrans
            has long been recognized as a potential biocontrol agent for root knot nematodes, but the fastidious life cycle and the obligate nature of parasitism have inhibited progress on mass culture and deployment. We are currently sequencing the genome of the
            Pasteuria
            bacterium and have performed amino acid level analyses of 33 bacterial species (including
            P. penetrans
            ) using concatenation of 40 housekeeping genes, with and without insertions/deletions (indels) removed, and using each gene individually. By application of maximum-likelihood, maximum-parsimony, and Bayesian methods to the resulting data sets,
            P. penetrans
            was found to cluster tightly, with a high level of confidence, in the
            Bacillus
            class of the gram-positive, low-G+C-content eubacteria. Strikingly, our analyses identified
            P. penetrans
            as ancestral to
            Bacillus
            spp. Additionally, all analyses revealed that
            P. penetrans
            is surprisingly more closely related to the saprophytic extremophile
            Bacillus haladurans
            and
            Bacillus subtilis
            than to the pathogenic species
            Bacillus anthracis
            and
            Bacillus cereus
            . Collectively, these findings strongly imply that
            P. penetrans
            is an ancient member of the
            Bacillus
            group. We suggest that
            P. penetrans
            may have evolved from an ancient symbiotic bacterial associate of nematodes, possibly as the root knot nematode evolved to be a highly specialized parasite of plants.
          }, number={16}, journal={JOURNAL OF BACTERIOLOGY}, author={Charles, L and Carbone, I and Davies, KG and Bird, D and Burke, M and Kerry, BR and Opperman, CH}, year={2005}, month={Aug}, pages={5700–5708} }