The canine hookworm genome: analysis and classification of Ancylostoma caninum survey sequences

Abstract

Hookworms infect nearly a billion people. The Ancylostoma caninum hookworm of canids is a model for studying human infections and information from its genome coupled with functional genomics and proteomics can accelerate progress towards hookworm control. As a step towards a full-scale A. caninum genome project, we generated 104,000 genome survey sequences (GSSs) and determined the genome size of the canine hookworm. GSSs assembled into 57.6 Mb of unique sequence from a genome that we estimate by flow cytometry of isolated nuclei to be 347 +/- 1.2 Mb, substantially larger than other Rhabditina species. Gene finding identified 5538 genes in the GSS assembly, for a total of 9113 non-redundant A. caninum genes when EST sequences are also considered. Functional classifications of many of the 70% of genes with homology to genes in other species are provided based on gene ontology and KEGG associations and secreted and membrane-bound proteins are also identified.

Figure 1

The number of nuclei scored at differing levels of red fluorescence. The red fluorescence corresponds to binding of propidium iodide to the DNA of 2C nuclei in: A. Co-prepared heads of female D. melanogaster Iso-1 (1C = 175 Mb) and female D. virilis (1C = 333.5 Mb); B. Co-prepared heads of female D. melanogaser, and D. virilis with A. caninum. C. A single female A. caninum (1C = 347.2 Mb). Small differences in PMT voltage shift means to slightly higher or lower channels in the three histograms. The DNA estimate is based on the ratio of co-prepared sample and standard as in 1B and 1C.

Figure 2

Distribution of Ancylostoma caninum BLAST matches by database. Caenorhabditis spp., represents C. elegans, C. briggsae and C. remanei; Other nematodes, all nematode beyond Caenorhabditis and Ancylostoma; and Non-nematoda, all species beyond nematodes. Databases were built 06/09/06, e-value scores ≤ 1e-05 are considered.