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The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task.  Haemonchus contortus  is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism  Caenorhabditis elegans , making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the  H. contortus  genome and undertook detailed annotation and comparative analysis with  C. elegans . The adult  H. contortus  transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in  C. elegans  of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in  H. contortus  than in  C. elegans , with annotated  H. contortus  genes being an average of two-to-three times larger than their putative  C. elegans  orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent.  C. elegans  operons appear to be partially conserved in  H. contortus . Our findings suggest that a combination of RNA-seq and comparative analysis with  C. elegans  is a powerful approach for the annotation and analysis of strongylid nematode genomes.

Annotation of Two Large Contiguous Regions from the Haemonchus contortus Genome Using RNA-seq and Comparative Analysis with Caenorhabditis elegans