What's New - The TIGR Brugia malayi Genome Project

Genome assembly The B. malayi genome has been sequenced to more than eight-fold redundancy and close to 75 Mb of the genome has been assembled into 8236 scaffolds. From the assembly data the genome has been estimated at 85-95 Mb. The assembly is presently in the first phase of gap closure. The closing of gaps is ongoing and represents a combination of automated and manual closure efforts. A first-pass annotation was performed using gene finding algorithms trained on B. malayi genes and ESTs available in the public databases. Close to 11,000 genes were predicted.

The NIAID-funded Brugia malayi genome project at TIGR has reached its first milestone: The ~165,000 sequences generated to date constitute 1X coverage of the 110 Mb haploid genome. These whole genome shotgun reads have been assembled and while most sequences at this stage remain as singletons, the entire dataset is available for searching and downloading.

In a collaboration between TIGR, Dr. Jeremy Foster (NEB), and Children's Hospital Oakland Research Institute (CHORI), a new BAC library, CHORI-106, and a Fosmid library, CHORI-1106, were recently constructed by Drs. Chung-Li Shu and Kazutoyo Osoegawa in Dr. Pieter de Jong's laboratory, BACPAC Resources, CHORI. CHORI-106 was generated from MboI partial genomic digests and is comprised of 4,500 clones with an average insert size of 125 kb and 4,500 clones with an average insert size of 85 kb. The Fosmid library was prepared from sheared DNA with an average insert size of 35 kb. The total of 18,000 clones from both libraries provides ~10X haploid genome coverage. The entire CHORI-106 and CHORI-1106 libraries, as well as individual clones and high density filters, will be available for distribution within the next few weeks through BACPAC resources. End-sequences from 10,000 clones will be determined by early next year. These will be essential in the assembly of the genome as they allow ordering of the groups of contiguous sequences (contigs) as well as the linking of adjacent contigs separated by repetitive sequences.

We are pleased to announce that the National Institute of Allergy and Infectious Diseases (NIH/NIAID) has awarded the Institute for Genomic Research (TIGR) a 2-year grant to initiate the sequencing of the Brugia malayi genome. The sequencing strategy we plan to use is whole genome shotgun and we expect to achieve, at current costs, a 3.5 fold coverage of the estimated 110Mb genome.

This grant is great news. It will be of enormous benefit to the Brugia and filarial communities. We will provide the research community with complete access to the genomic sequences and the sequence analysis through our World Wide Web server and submissions to GenBank. Sheared DNA plasmid libraries will be constructed within the next few weeks with adult worm genomic DNA that will be provided by Drs. Slatko and Foster of New England Biolabs. At the latest, we expect the first batches of sequences to be available in early 2002.

The TIGR Brugia malayi web page will allow the scientific community to read a detailed description of our sequencing strategy, view status reports, follow the progress of the project, retrieve sequence data in batches or search the sequence database with a variety of algorithms. In the meantime, I invite you to visit our website where you will find the TIGR Brugia malayi Gene Index (BmGI) which integrates research data from international B. malayi EST sequencing and gene research projects. The ultimate goal of the BmGI is to represent a non-redundant view of all B. malayi genes, data on their expression patterns, cellular roles, functions, and evolutionary relationships.

A new BAC library, which is the result of a collaboration between TIGR, Barton Slatko and Jeremy Foster at New England Biolabs, and Pieter de Jong's group at the Children's Hospital Oakland Research Institute (CA), will be ready soon and will also be a major substrate for our sequencing efforts here at TIGR.