ABSTRACT
While sequencing methods were available in the late 1970s, it was not until the human genome project and a significant influx of funds for such research that this technology became high throughput. The fields of microbiology and microbial ecology, among many others, have been tremendously impacted over the years, to such an extent that the determination of complete microbial genome sequences is now commonplace. Given the lower costs of next-generation sequencing platforms, even small laboratories from around the world will be able to generate millions of base pairs of data, equivalent to entire genomes worth of sequence information. With this prospect just around the corner, it is timely to provide an overview of the genomics process: from sample preparation to some of the analytical methods used to gain functional knowledge from sequence information.
Subject(s)
Bacteria/genetics , Genome, Bacterial , Genomics/methods , Molecular Sequence Annotation/methods , Nitrification/genetics , Nitrogen Cycle/genetics , Sequence Analysis, DNA/methods , Bacteria/metabolism , Nitrosomonas europaea/genetics , Nitrosomonas europaea/metabolismABSTRACT
Caldicellulosiruptor obsidiansis OB47(T) (ATCC BAA-2073, JCM 16842) is an extremely thermophilic, anaerobic bacterium capable of hydrolyzing plant-derived polymers through the expression of multidomain/multifunctional hydrolases. The complete genome sequence reveals a diverse set of carbohydrate-active enzymes and provides further insight into lignocellulosic biomass hydrolysis at high temperatures.
Subject(s)
DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Genome, Bacterial , Gram-Positive Bacteria/genetics , Anaerobiosis , Cellulose/metabolism , Gram-Positive Bacteria/metabolism , Hot Temperature , Hydrolases/genetics , Hydrolases/metabolism , Molecular Sequence Data , Sequence Analysis, DNAABSTRACT
Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003).
Subject(s)
Bacillus thuringiensis/genetics , Genome, Bacterial , Base Sequence , Molecular Sequence Data , Sequence Analysis, DNAABSTRACT
The HYDIN gene located in human chromosome band 16q22.2 is a large gene encompassing 423 kb of genomic DNA that has been suggested as a candidate for an autosomal recessive form of congenital hydrocephalus. We have found that the human HYDIN locus has been very recently duplicated, with a nearly identical 360-kb paralogous segment inserted on chromosome 1q21.1. The duplication, among the largest interchromosomal segmental duplications described in humans, is not accounted for in the current human genome assembly and appears to be part of a greater than 550-kb contig that must lie within 1 of the 11 sequence gaps currently remaining in 1q21.1. Both copies of the HYDIN gene are expressed in alternatively spliced transcripts. Elucidation of the role of HYDIN in human disease susceptibility will require careful discrimination among the paralogous copies.
Subject(s)
Chromosomes, Human, Pair 16/genetics , Chromosomes, Human, Pair 1/genetics , Gene Duplication , Hydrocephalus/genetics , Microfilament Proteins/genetics , Animals , Computational Biology , Genome, Human , Humans , In Situ Hybridization, Fluorescence , Mice , Physical Chromosome MappingABSTRACT
Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains of B. anthracis reveal conspicuous sequence homogeneity, environmental isolates of B. cereus and B. thuringiensis exhibit extensive genetic diversity. Here we report the sequencing and comparative analysis of the genomes of two members of the B. cereus group, B. thuringiensis 97-27 subsp. konkukian serotype H34, isolated from a necrotic human wound, and B. cereus E33L, which was isolated from a swab of a zebra carcass in Namibia. These two strains, when analyzed by amplified fragment length polymorphism within a collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis isolates, appear closely related to B. anthracis. The B. cereus E33L isolate appears to be the nearest relative to B. anthracis identified thus far. Whole-genome sequencing of B. thuringiensis 97-27and B. cereus E33L was undertaken to identify shared and unique genes among these isolates in comparison to the genomes of pathogenic strains B. anthracis Ames and B. cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus ATCC 14579. Comparison of these genomes revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms.
