Yoder Lab - Databases

 

Databases

Subtractive and full length cDNA libraries from Triphysaria

We are taking a transcription profiling approach to identify genes associated with host plant recognition and early haustorium development. cDNA libraries were made from roots of Triphysaria seedlings that had been in contact with host roots or host root factors for several hours prior to RNA extraction. The phenotypes of Triphysaria roots during this time period are shown in the figure below. We used suppressive subtractive hybridization to enrich for transcripts regulated during early haustorium development. These were Sanger sequenced in 2006 by the DOE Joint Genome Institute as a Community Science Project.

 

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FASTA files of Sanger sequenced cDNA libraries

Treatment

SSH library

Triphysaria root extracts Forward library

CBAA

Triphysaria root extract Reverse library

CBAB

Host root exudates Forward library

CBAC

Host root exudates Reverse library

CBAF

Peonidin Forward library

CBAG

Peonidin Reverse library

CBAH

Root tip Specific library

CBAI

DMBQ Forward library

TvD1

Host root Forward library

TvH1

Host root Reverse library

TvH2

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The Parasitic Plant Genome Project

The Parasitic Plant Genome Project is funded by the NSF Plant Genome Research Program to carry out comparative functional genomic analysis of parasitic plants in order to discover the genome-wide changes that led to the establishment of the parasitic lifestyle and the changes that resulted as a consequence of adoption of the parasitic life-style. This is a collaborative project between the labs of Jim Westwood (Virginia Tech), Michael Timko (University of Virginia), Claude DePamphilis (Penn State) and John Yoder (UC Davis). We are comparing the transcriptomes of three parasitic genera from the Orobanchaceae- Triphysaria, Striga, and Orobanche, and one closely related non parasite- Mimulus. These species are derived from the same evolutionarily event leading to haustorium development yet span the full range of parasitic ability from free-living to completely heterotrophy. We have sequenced developmental stage-specific cDNAs from Triphysaria versicolor, Striga hermonthica, and Orobanche aegyptiaca using 454 and Illumina Technologies. Sequences have been assembled and annotated and are available at the project website: http://ppgp.huck.psu.edu/