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New species from old data - By searching genome sequences of several Drosophila species researchers have identified new bacterial species that live inside fruit flies.
February 18, 2005Researchers have discovered three previously unknown species of a bacterium by scanning a publicly available data bank, reveals a study published today in the journal Genome Biology. The finding highlights the value of making unanalysed data from large-scale genome sequencing projects openly available online.
Steven Salzberg from The Institute for Genomic Research in Maryland and colleagues identified three new species of the bacterium Wolbachia from the genome sequences of the fruit fly Drosophila that are stored in the Trace Archive.
The Trace Archive is a public repository of raw genomic data from sequencing projects. When the genome of an organism is sequenced, the genome of endosymbiotic bacteria that live inside the organism can get incorporated into the data, contaminating the final genomic sequence of the host organism. Scanning raw sequences can therefore lead to the identification of previously unknown endosymbionts.
Salzberg and colleagues scanned through the newly sequenced genomes of seven different Drosophila species, using the genome of the bacterium Wolbachia pipientis wMel as a probe. From D. ananassae, they retrieved 32,720 sequences that matched the wMel strain. This yielded a new genome of 1,440,650 bp, which they identified as the new species Wolbachia wAna. Using the same technique, they identified Wolbachia wSim in the genome of D. simulans and Wolbachia wMoj in the genome of D. mojavensis.
"The discovery of these three new genomes demonstrates how powerful the public release of raw sequencing data can be" write the authors, who have deposited their findings in Genbank, another open repository of genomic sequences.
The team compared the new Wolbachia genomes with the wMel genome and found a number of new genes - up to 464 new genes in wAna - as well as a sign of extensive rearrangement between wMel and wAna, indicating that the two strains have diverged significantly since they first infected the two Drosophila species. The two most closely related strains are wAna and wSim, which have nearly identical genomes. wMel and wMoj share about 97% of their genomes with wAna and wSim but are a bit more distant from one another.
These findings might help shed light on the evolution of bacterial endosymbionts and on the mechanisms these organisms use to alter the cell cycle of the host in order to reproduce.
BioMed Central Limited
Salzberg and colleagues scanned through the newly sequenced genomes of seven different Drosophila species, using the genome of the bacterium Wolbachia pipientis wMel as a probe. From D. ananassae, they retrieved 32,720 sequences that matched the wMel strain. This yielded a new genome of 1,440,650 bp, which they identified as the new species Wolbachia wAna. Using the same technique, they identified Wolbachia wSim in the genome of D. simulans and Wolbachia wMoj in the genome of D. mojavensis.
"The discovery of these three new genomes demonstrates how powerful the public release of raw sequencing data can be" write the authors, who have deposited their findings in Genbank, another open repository of genomic sequences.
The team compared the new Wolbachia genomes with the wMel genome and found a number of new genes - up to 464 new genes in wAna - as well as a sign of extensive rearrangement between wMel and wAna, indicating that the two strains have diverged significantly since they first infected the two Drosophila species. The two most closely related strains are wAna and wSim, which have nearly identical genomes. wMel and wMoj share about 97% of their genomes with wAna and wSim but are a bit more distant from one another.
These findings might help shed light on the evolution of bacterial endosymbionts and on the mechanisms these organisms use to alter the cell cycle of the host in order to reproduce.
BioMed Central Limited
Genome Current Events and Genome News RSSTime of day matters to thirsty trees, U of T researcher discovers
The time of day matters to forest trees dealing with drought, according to a new paper produced by a research team led by Professor Malcolm Campbell, University of Toronto Scarborough's vice-principal for research and colleagues in the department of cell and systems biology at the St. George campus.
Genetic analysis helps dissect molecular basis of cardiovascular disease
Using highly precise measurements of plasma lipoprotein concentrations determined by nuclear magnetic resonance spectroscopy (NMR), researchers led by Daniel Chasman at Brigham and Women's Hospital and Harvard Medical School in Boston, MA, the Framingham Heart Study in Framingham, and the PROCARDIS consortium in Stockholm, Sweden and Oxford, England performed genetic association analysis across the whole genome among 17,296 women of European ancestry from the Women's Genome Health Study.
Gene mismatch influences success of bone marrow transplants
A commonly inherited gene deletion can increase the likelihood of immune complications following bone marrow transplantation, an international team of researchers reports in the November 22 advance online issue of Nature Genetics.
Scientists at UA, collaborating institutions decode maize genome
Scientists from the University of Arizona led by Arizona Genomics Institute director Rod A. Wing and from collaborating institutions have deciphered the complete genetic code of the maize plant for the first time.
Ancestry attracts, but love is blind
People preferentially marry those with similar ancestry, but their decisions are not necessarily based on hair, eye or skin colour.
WPI Researchers Take Aim at Hard-to-Treat Fungal Infections
A team of researchers at the Worcester Polytechnic Institute (WPI) Life Sciences and Bioengineering Center at Gateway Park has developed a new model system to study fungal infections.
Technique finds gene regulatory sites without knowledge of regulators
A new statistical technique developed by researchers at the University of Illinois allows scientists to scan a genome for specific gene-regulatory regions without requiring prior knowledge of the relevant transcription factors.
Causative gene of a rare disorder discovered by sequencing only protein-coding regions of genome
For the first time, scientists have successfully used a method called exome sequencing to quickly discover a previously unknown gene responsible for a mendelian disorder.
New research into the mechanisms of gene regulation
A team led by Penn State's Ross Hardison, T. Ming Chu Professor of Biochemistry and Molecular Biology, has taken a large step toward unraveling how regulatory proteins control the production of gene products during development and growth.
Maize cell wall genes identified, giving boost to biofuel research
Purdue University scientists have helped identify and group the genes thought to be responsible for cell wall development in maize, an effort that expands their ability to discover ways to produce the biomass best suited for biofuels production.
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