What's New - The TIGR Schistosoma mansoni Genome Project

Dear Colleagues,
This is an update on the progress of the NIAID-funded Schistosoma mansoni genome project at TIGR. Phase I of the project, which aimed at generating about 13 Mb of discontinuous single-pass sequence, is now completed. This was implemented by the end-sequencing of about 9,000 clones from a segment of the Sm1 BAC library, and about 13,000 clones from CHORI-103, a new S. mansoni BAC library. The total number of end sequences generated is now 31,441 adding up to 20 Mb of discontinuous sequence. You can examine a summary of the progress. The purpose of this first phase is to enhance early gene discovery and to provide paired-markers that are crucial for almost any sequencing strategy, including BAC-based map-as-you-go or whole genome shotgun. The entire dataset is available for searching or downloading.

In a collaboration between TIGR, Dr. Phillip LoVerde, and Children's Hospital Oakland Research Institute (CHORI), a new BAC library, CHORI-103 was recently constructed by Drs. Chung-Li Shu and Kazutoyo Osoegawa in Dr. Pieter de Jong's laboratory, BACPAC Resources, CHORI. CHORI-103 was generated from MboI partial genomic digests with average insert size of 145 kb. A total of ~ 34,000 clones provide ~19X haploid genome coverage. The entire CHORI-103 library as well as individual clones and high density filters are available for distribution through BACPAC resources.

We are pleased to bring you a brief update of the progress of the NIAID-funded Schistosoma mansoni genome project at The Institute for Genomic Research (TIGR)  and to announce the release of TIGR's new web site http://www.tigr.org/tdb/e2k1/sma1.

Phase I of the project, which consists of generating about 13 Mb of discontinuous single-pass sequence,  is well underway.  This is being implemented by end-sequencing of about 9,000 clones from a segment of the Sm1 BAC library.  The purpose of this first phase was to enhance early gene discovery and to provide paired-markers that are crucial for our map-as-you-go sequencing strategy. The S. mansoni end sequence database is continuously being updated and is available for retrieval and homology searching at  http://www.tigr.org/tdb/e2k1/sma1/gene.shtml.  In addition, a BAC end sequence mapping tool is being made available http://www.tigr.org/tdb/e2k1/sma1/map_ends.shtml.  This program allows searches with large DNA fragments against the BAC ends database. The results are presented in graphical format with candidate minimal overlapping BAC clones suggested. We have recently deposited 12,305 sequences in the dbGSS division of Genbank [Accession numbers BH199420-BH211620], representing about 7.2 Mbases of discontinuous sequence data.  A new BAC library, which is the result of a collaboration between TIGR,  Phil LoVerde's group at SUNY-Buffalo (NY) 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.

We have also simultaneously initiated Phase II of the Schistosoma mansoni project at TIGR, which consists of sequencing about 8 Mbases of chromosomes over the next two years using a clone-by-clone strategy. A number of 'seed' BAC clones from different chromosomes have been identified as entry points for sequencing.  As of August 2001, we have started depositing S. mansoni BAC sequences at various stages of completion to the High Throughput Genome (HTG) sequences database at NCBI. You may view the status of our contiguous sequencing progress at http://www.tigr.org/tdb/e2k1/sma1/genome.shtml.  This page provides a summary of our progress, allows viewing the progress of our sequencing project as BAC clones progress through closure and complete annotation, and provides links to sequence data for all our unfinished BAC clones as submitted to the HTGS division of Genbank.

The Web site also provides access to pages describing our sequencing strategy, the TIGR S. mansoni gene index,  and our data release policy, among other things.  We invite you to visit it and as always, your comments are welcome. We thank Hean Koo and Lowell Umayam for their important contributions to the functionality of this new web site.