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Background  Hookworms infect nearly 700 million people, causing anemia and developmental stunting in heavy infections. Little is known about the genomic structure or gene regulation in hookworms, although recent publication of draft genome assemblies has allowed the first investigations of these topics to be undertaken. The transcription factor DAF-16 mediates multiple developmental pathways in the free living nematode  Caenorhabditis elegans , and is involved in the recovery from the developmentally arrested L3 in hookworms. Identification of downstream targets of DAF-16 will provide a better understanding of the molecular mechanism of hookworm infection.    Methods  Genomic Fragment 2.23 containing a DAF-16 binding element (DBE) was used to identify overlapping complementary expressed sequence tags (ESTs). These sequences were used to search a draft assembly of the  Ancylostoma caninum  genome, and identified two neighboring genes,  snr-3 and lpp-1 , in a tail-to-tail orientation. Expression patterns of both genes during parasitic development were determined by qRT-PCR. DAF-16 dependent  cis -regulatory activity of fragment 2.23 was investigated using an  in vitro  reporter system.    Results  The  snr-3  gene spans approximately 5.6 kb in the genome and contains 3 exons and 2 introns, and contains the DBE in its 3′ untranslated region. Downstream from  snr-3  in a tail-to-tail arrangement is the gene  lpp-1 . The  lpp-1  gene spans more than 6 kb and contains 10 exons and 9 introns. The  A. caninum  genome contains 2 apparent splice variants, but there are 7 splice variants in the  A. ceylanicum  genome. While the gene order is similar, the gene structures of the hookworm genes differ from their  C. elegans  orthologs. Both genes show peak expression in the late L4 stage. Using a cell culture based expression system, fragment 2.23 was found to have both DAF-16-dependent promoter and enhancer activity that required an intact DBE.    Conclusions  Two putative DAF-16 targets were identified by genome wide screening for DAF-16 binding elements.  Aca - snr -3 encodes a core small nuclear ribonucleoprotein, and  Aca-lpp-1  encodes a lipid phosphate phosphohydrolase. Expression of both genes peaked at the late L4 stage, suggesting a role in L4 development. The 3′-terminal genomic fragment of the  snr-3  gene displayed  Ac -DAF-16-dependent  cis -regulatory activity.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-014-0609-0) contains supplementary material, which is available to authorized users.

parasites and vectors

Two potential hookworm DAF-16 target genes, SNR-3 and LPP-1: gene structure, expression profile, and implications of a cis-regulatory element in the regulation of gene expression