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A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics
Authors:Whitton Claire  Daub Jennifer  Quail Mike  Hall Neil  Foster Jeremy  Ware Jennifer  Ganatra Mehul  Slatko Barton  Barrell Bart  Blaxter Mark
Affiliation:Ashworth Laboratories, Institution of Cell, Animal and Polulation Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh EH9 3JT, UK.
Abstract:
Comparative nematode genomics has thus far been largely constrained to the genus Caenorhabditis, but a huge diversity of other nematode species, and genomes, exist. The Brugia malayi genome is approximately 100 Mb in size, and distributed across five chromosome pairs. Previous genomic investigations have included definition of major repeat classes and sequencing of selected genes. We have generated over 18,000 sequences from the ends of large-insert clones from bacterial artificial chromosome libraries. These end sequences, totalling over 10 Mb of sequence, contain just under 8 Mb of unique sequence. We identified the known Mbo I and Hha I repeat families in the sequence data, and also identified several new repeats based on their abundance. Genomic copies of 17% of B. malayi genes defined by expressed sequence tags have been identified. Nearly one quarter of end sequences can encode peptides with significant similarity to protein sequences in the public databases, and we estimate that we have identified more than 2700 new B. malayi genes. Importantly, 459 end sequences had homologues in other organisms, but lacked a match in the completely sequenced genomes of Caenorhabditis briggsae and Caenorhabditis elegans, emphasising the role of gene loss in genome evolution. B. malayi is estimated to have over 18,500 protein-coding genes.
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