Latest documents http://publikationen.ub.uni-frankfurt.de/index/index/ Wed, 19 Dec 2012 12:36:03 +0100 Wed, 19 Dec 2012 12:36:03 +0100 http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/27141 Background: In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila. Results: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished. Conclusion: Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly. Phil Latreille; Stacie Norton; Barry S. Goldman; John Henkhaus; Nancy Miller; Brad Barbazuk; Helge Björn Bode; Creg Darby; Zijin Du; Steve Forst; Sophie Gaudriault; Brad Goodner; Heidi Goodrich-Blair; Steven Slater article http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/27141 Wed, 19 Dec 2012 12:36:03 +0100 http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/23734 Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points. John M. Chaston; Garret Suen; Sarah L. Tucker; Aaron W. Andersen; Archna Bhasin; Edna Bode; Helge Björn Bode; Alexander Oliver Brachmann; Charles E. Cowles; Kimberly N. Cowles; Creg Darby; Limaris de Léon; Kevin Drace; Zijin Du; Alain Givaudan; Erin E. Herbert Tran; Kelsea A. Jewell; Jennifer J. Knack; Karina C. Krasomil-Osterfeld; Ryan Kukor; Anne Lanois; Phil Latreille; Nancy K. Leimgruber; Carolyn M. Lipke; Renyi Liu; Xiaojun Lu; Eric C. Martens; Pradeep R. Marri; Claudine Médigue; Megan L. Menard; Nancy M. Miller; Nydia Morales-Soto; Stacie Norton; Jean-Claude Ogier; Samantha S. Orchard; Dongjin Park; Youngjin Park; Barbara A. Qurollo; Darby Renneckar Sugar; Gregory R. Richards; Zoé Rouy; Brad Slominski; Kathryn Slominski; Holly Snyder; Brian C. Tjaden; Ransome van der Hoeven; Roy D. Welch; Cathy Wheeler; Bosong Xiang; Brad Barbazuk; Sophie Gaudriault; Brad Goodner; Steven C. Slater; Steven Forst; Barry S. Goldman; Heidi Goodrich-Blair article http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/23734 Wed, 28 Dec 2011 11:32:45 +0000