While finishing sequencing the genomes of seven species of Drosophila last year, a team of researchers at the University of California, Berkeley, inadvertently sequenced the genes of several bacteria that secretly live in fruit fly embryos.
These bacteria, which belong to the Wolbachia genus, reside in the Drosophila gene database, where they lived quietly, and, until now, unnoticed, according to Michael Eisen, a Berkeley assistant professor of molecular and cell biology and a faculty scientist at Lawrence Berkeley National Laboratory.
“The sequencers who did the Drosophila species didn’t even notice this because this is just a very small fraction of the total sequence and it was sort of tossed into the garbage,” Eisen said in a statement released by his university. “In every genome there is always stuff that doesn’t make sense, and people weren’t looking for it. We thought this was interesting as much for the novelty of the way the bacterial genomes were sequenced than what we learned about the bacteria themselves.”
After his discovery — and largely because he’s a Drosophila geneticist and “not an expert on bacteria” — Eisen sought the help of The Institute for Genomic Research, and soon hooked up with Steven Salzberg, TIGR’s director of bioinformatics.
“The discovery of these three new genomes demonstrates how powerful the public release of raw sequencing data can be,” the authors wrote in their study describing the discovery, which appears in the February 22 issue of Genome Biology. The authors have deposited their data in Genbank.
According to Eisen, these bacterial species live inside the fruit fly genome database because of the way the fly was sequenced: Researchers ground up embryos and extracted their DNA, “meaning that any endosymbionts ... would have had their DNA intermixed with fly DNA before sequencing,” according to the statement.
— Kirell Lakhman
US Patent 6,865,491. Method for sequencing poly-nucleotides. Assignee: Ramot at Tel-Aviv University. Inventors: Itzhak Peer, Ron Shamir. Issued: March 8, 2005.
This patent covers “a method for obtaining a nucleotide sequence that is indicative of the sequence of a target poly-nucleotide molecule T. The method makes use of hybridization data obtained by incubating T with nucleotide probes. A score is assigned to each of a plurality of candidate nucleotide sequences based upon the hybridization data and upon at least one reference nucleotide sequence,” according to the abstract. The sequence is selected based on the best score.
US Patent 6,863,791. Method for in situ calibration of electrophoretic analysis systems. Assignee: SpectruMedix. Inventors: Changsheng Liu, Hequan Zhao. Issued: March 8, 2005.
This patent covers an electrophoretic system with several separation lanes that each has its own automatic calibration feature. “For each lane, the calibration coefficients map a spectrum of received channel intensities onto values reflective of the relative likelihood of each of a plurality of dyes being present,” according to the abstract. “The system … thus permits one to use different dye sets to tag DNA nucleotides in samples which migrate in separate lanes, and also allows for in situ calibration with new, previously unused dye sets.”
New organisms slated for sequencing, according to an NHGRI announcement in March. The lucky species include: marmoset, sea slug, pea aphid, and a free-living soil amoeba, among others.
The J. Craig Venter Institute completed the sequence of Erythrobacter litoralis, a sea-living microbe. The sequence is the first of a large-scale project by the institute to sequence the genomes of more than 100 marine microbes stored in culture collections around the world. The Gordon and Betty Moore Foundation contributed $8.9 million in grants to fund the project.
Solexa and Lynx Therapeutics officially completed their merger. The combined public company, which will use the name Solexa, also announced that it used its own technology to sequence the 5,000-base genome of the Phi-X 174 virus.
A team of British researchers has sequenced the Bacteroides fragilis genome to better understand this human colon-dwelling pathogen. The genome consists of about 5.2 million base pairs coding for some 4,200 genes.
Scientists in Italy and the US have sequenced the 6.4 megabase genome of Photobacterium profundum, a bacterium that lives in the deep sea under high pressure.
An international research team led by the Max Planck Institute for Evolutionary Anthropology has extracted and sequenced fossil protein from an approximately 75,000-year-old Neanderthal. The protein is the oldest ever sequenced, the team said.