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A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans

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Abstract

Plant-parasitic nematodes are important and cosmopolitan pathogens of crops. Here, we describe the generation and analysis of 1928 expressed sequence tags (ESTs) of a splice-leader 1 (SL1) library from mixed life stages of the root-lesion nematode Pratylenchus penetrans. The ESTs were grouped into 420 clusters and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. Approximately 80% of all translated clusters show homology to Caenorhabditis elegans proteins, and 37% of the C. elegans gene homologs had confirmed phenotypes as assessed by RNA interference tests. Use of an SL1-PCR approach, while ensuring the cloning of the 5′ ends of mRNAs, has demonstrated bias toward short transcripts. Putative nematode-specific and Pratylenchus -specific genes were identified, and their implications for nematode control strategies are discussed.

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Acknowledgements

Plant parasitic nematode genome research at Washington University was supported by NSF Plant Genome award 0077503 to D.M.B. and S.W.C. J.P.M. was supported by a Helen Hay Whitney/Merck postdoctoral fellowship. A.A.E. was supported by the Iowa Agriculture and Home Economics Experiment Station, Ames, IA and by Hatch Act and State of Iowa funds as well as by a Storkan-Hanes-McCaslin Foundation fellowship. We thank Merry McLaird, Brandi Chiapelli, Claire Murphy, and the GSC EST Group for their role in library generation and sequencing, Todd Wylie and John Martin for bioinformatics analysis, and Robert H. Waterston for project guidance. J.P.M. and A.P.K. are employees and equity holders of Divergence Inc.

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Mitreva, M., Elling, A.A., Dante, M. et al. A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans. Mol Genet Genomics 272, 138–148 (2004). https://doi.org/10.1007/s00438-004-1054-0

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