Construction of an annotated sequence database to advance molecular genetic investigations of Triphysaria versicolor, a parasitic angiosperm

Parasitic plant species invade tissues of neighboring host plants in order to rob them of water and essential nutrients. The invasive organ of parasitic plants is the haustorium. Parasitic plants in the Orobanchaceae develop haustoria on their roots in response to molecular signals released from the host plant. The Yoder Lab is investigating host plant recognition and early haustorium development in the parasite Triphysaria versicolor . The lab constructed a normalized and subtracted cDNA library from root-tips harvested soon after treatment with the chemical haustorium inducing factor 2,6-dimethoxy-p-benzoquinone. Our group initially sequenced ∼2500 ESTs from a cDNA library enriched for transcripts co-regulated during early haustorium development. The goal of my work was to clean and process the sequence data and put it into a searchable format accessible for use by lab members.; Following an evaluation of available options, I used phred software to generate basecalls, lucy to mask vector and adaptor, the DNA assembler cap3 to build contigs, and BLAST to identify similarity with publicly available sequence databases, and InterProScan to identify protein domain signatures. I further clustered these contigs to gene families and putative functional classes using PEDANT classifications and Gene Ontology terms. All data was entered into a relational database called EDITdb and implemented with MySQL. I used phpMyAdmin, a suite of PHP scripts to render the interface for SQL queries of EDITdb (at URL http://pscroph.ucdavis.edu). Using the functional classes, I synthesized a model for early haustorium formation based on a literature survey of the putative transcript classes.