Computational and Systems Biology Summer Institute
Iowa State University

Introduction

• The root-knot nematode ( Meloidogyne incognita ) parasitizes a wide range of plants and is responsible for approximately 5% of global crop loss (Sasser and Carter,1985).

• M. incognita secretes a large set of parasitism proteins to help it enter and feed on the roots of plants. • Using traditional Sanger sequencing, we have previously sequenced ~3000 ESTs from a gland cell library, leading to the discovery of many new, and novel, parasitism proteins.

• Using Roche 454 deep sequencing of a newly created gland cell library, we hope to identify new parasitism proteins expressed in the secretory gland cells of M. incognita .

• Identification of transcripts involved in parasitism could lead to the development of new management techniques to mitigate the damage caused by M. incognita.

We Need a Bioinformaticist to:

• Align 454 sequencing data with known genomic sequence of M. incognita to identify the complete coding sequences.

• Run BLAST to search for protein homology.

• Run Signal P analysis to find proteins that have the potential to be secreted .

The Summer student will work with Dr. Xuefeng Zhao of L H Baker Center, ISU to analyze the 454 sequencing data.

Sasser JN, Carter CC: Overview of the International Meloidogyne Project 1975–1984. In An Advanced Treatise on Meloidogyne . Edited by: Sasser JN, Carter CC. Raleigh: North Carolina State University Graphics; 1985:19-24.

Huang G, Allen R, Davis EL, Baum TJ, Hussey RS. Engineering broad root-knot resistance in transgenic plants by RNAi silencing of a conserved and essential root-knot nematode parasitism gene. Proceedings of the National Academy of Sciences, USA (2006b) 103:14302–14306