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      Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea

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          ABSTRACT

          Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with ∼47% transcribed from one strand and ∼53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO 2 and NH 3 assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.

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          Consed:A Graphical Tool for Sequence Finishing

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            Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.

            The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.
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              Base-calling of automated sequencer traces using phred. II. Error probabilities.

              Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data. These error probabilities are shown here to be valid (correspond to actual error rates) and to have high power to discriminate correct base-calls from incorrect ones, for read data collected under several different chemistries and electrophoretic conditions. They play a critical role in our assembly program phrap and our finishing program consed.
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                Author and article information

                Journal
                Journal of Bacteriology
                J Bacteriol
                American Society for Microbiology
                0021-9193
                1098-5530
                May 2003
                May 2003
                : 185
                : 9
                : 2759-2773
                Affiliations
                [1 ]Joint Genome Institute, Walnut Creek, California 94598
                [2 ]Lawrence Livermore National Laboratory, Livermore, California 94550
                [3 ]Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
                [4 ]University of Minnesota, Minneapolis, Minnesota 55455
                [5 ]University of Louisville, Louisville, Kentucky 40208
                [6 ]Utah State University, Logan, Utah 84322
                [7 ]Oregon State University, Corvallis, Oregon 97331
                Article
                10.1128/JB.185.9.2759-2773.2003
                154410
                12700255
                c60d2f02-e7a3-4e06-a7cb-58a3122a901f
                © 2003

                https://journals.asm.org/non-commercial-tdm-license


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