Bioinformatic analysis of abundant, gender-enriched transcripts of adult Ascaris suum (Nematoda) using a semi-automated workflow platform q C. Cantacessi a, 1 , F.C. Zou b,1 , R.S. Hall a , W. Zhong a, c , A.R. Jex a , B.E. Campbell a , S. Ranganathan d , P.W. Sternberg c , X.Q. Zhu e, ** , R.B. Gasser a, * a Department of Veterinary Science, The University of Melbourne, Werribee, Victoria 3030, Australia b College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province 650201, PR China c Biology Division, California Institute of Technology, Pasadena, CA 91125, USA d Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia e College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China article info Article history: Received 27 January 2009 Accepted 16 March 2009 Available online 8 April 2009 Keywords: Ascaris suum Gender-enriched Suppressive-subtractive hybridization Caenorhabditis elegans Bioinformatics Gene ontology Genetic interactions abstract Expressed sequence tag (EST) data representing transcripts with a high level of differential hybridization in suppressive-subtractive hybridization (SSH)-based microarray analysis between adult female and male Ascaris suum were subjected to detailed bioinformatic analysis. A total of 361 ESTs clustered into 209 sequences, of which 52 and 157 represented transcripts that were enriched in female and male A. suum, respectively. Thirty (57.7%) of the ‘female’ subset of 52 sequences had orthologues/homologues in other parasitic nematodes and/or Caenorhabditis elegans, 13 (25%) exclusively in other parasitic nematodes and nine (17.3%) had no match in any other organism for which sequence data are currently available; the C. elegans orthologues encoded molecules involved in reproduction as well as embryonic and gamete development, such as vitellogenins and chitin-binding proteins. Of the ‘male’ subset of 157 sequences, 73 (46.5%) had orthologues/homologues in other parasitic nematodes and/or C. elegans, 57 (37.5%) in other parasitic nematodes only, and 22 (14.5%) had no significant similarity match in any other organism; the C. elegans orthologues encoded predominantly major sperm proteins (MSPs), kinases and phosphatases, actins, myosins and an Ancylostoma secreted protein-like molecule. The findings of the present study should support further genomic investigations of A. suum. Ó 2009 Elsevier Ltd. All rights reserved. 1. Introduction Diseases caused by parasitic nematodes (¼roundworms) are of major socioeconomic importance worldwide. For example, Ascaris sp. (or Ascaris lumbricoides) infects hundreds of millions of people globally and causes the disease ascariasis, which particularly affects children [1]. Similarly, ascariasis of pigs due to Ascaris suum infec- tion can cause major production and financial losses linked to reduced feed conversion efficiency and losses to the meat industry associated with the condemnation of ‘milk-spot’ livers [2]. In addition to the socioeconomic impact of such parasites in animals, genetic resistance in a range of nematode groups against all the main classes of anthelmintics (drugs) has become a major problem globally [3]. Therefore, there is a need to discover new methods of intervention against parasitic nematodes. Gaining an improved understanding of fundamental, molecular aspects of parasite development and reproduction provides a possible avenue to assist this discovery effort. Compared with the free-living nematode Caenorhabditis elegans (see WormBase; www.wormbase.org), there is a paucity of infor- mation on the molecular biology of development and reproduction in parasitic nematodes [4–7]. The entire genome sequence of C. elegans is known [8], the functions of more than 96% of the C. elegans genes have been assessed [9–13] by double-stranded RNA interference (RNAi, or gene silencing; Ref. [14]), and microarray analyses have explored developmental and gender-enriched gene expression [15,16]. Current evidence indicates that w50–70% of genes in parasitic nematodes have orthologues in C. elegans (see [17,18]), and there is similarity in other features (such as moulting and basic body plan) between C. elegans and parasitic nematodes, indicating that some molecular pathways are conserved [6,19]. Understanding the pathways linked to basic nematode biology and q Note: New nucleotide sequence data used in this paper have been deposited in the GenBank database under accession numbers GO254595–GO254953. * Corresponding author. Tel.: þ61 3 97312000; fax: þ61 3 97312366. ** Corresponding author. E-mail addresses: xingquanzh@scau.edu.cn (X.Q. Zhu), robinbg@unimelb.edu.au (R.B. Gasser). 1 Equal contributions. Contents lists available at ScienceDirect Molecular and Cellular Probes journal homepage: www.elsevier.com/locate/ymcpr 0890-8508/$ – see front matter Ó 2009 Elsevier Ltd. All rights reserved. doi:10.1016/j.mcp.2009.03.003 Molecular and Cellular Probes 23 (2009) 205–217