Saturday, September 26, 2015

Date: Dec 7, 2015. Susan Strickler: Long read assembly and annotation strategies for complex plant genomes

Susan Strickler is a Research Associate in the Mueller lab at the Boyce Thompson Institute on Cornell University campus.

Plant genome assembly can be notoriously difficult due to such challenges as heterozygosity, polyploidy, and repeats.  The long read technology provided by PacBio sequencing can help to overcome some of these obstacles to result in more complete and accurate assembly and annotation.  In this talk, I will discuss de novo genome assembly tools and methods for processing PacBio genome and transcriptome data to generate high quality plant genomes and gene models.

Date: Dec 07, 2015
Time: 11:00 AM
Location: Weill hall, Room 221


Date: Oct 19, 2015. Katie Wilkins: Population Diversity of Xanthomonas oryzae pv oryzicola TAL Effectors and their Candidate Targets

Katie Wilkins is a Computational Biology PhD Candidate in the Bogdanove lab in the Plant Pathology and Plant-Microbe Biology section of the School of Integrative Plant Science at Cornell University.

Xanthomonas oryzae pv oryzicola is the causal agent of bacterial leaf streak of rice, a disease that can lead to up to 30% yield loss in this staple crop. Disease progression is mediated in part by the secretion of transcription activator-like (TAL) effectors that upregulate host genes by binding to corresponding promoter regions. Genes upregulated by TAL effectors can confer host resistance or enhance host susceptibility. Knowledge of these important TAL effector-target pairs informs breeding of resistant rice varieties. To determine the distribution of TAL effectors and their candidate targets at the population level, we sequenced 10 strains of Xanthomonas oryzae pv oryzicola and performed RNA-Seq of rice inoculated with each strain. We also used population level conservation to evaluate potential importance of the identified TAL effectors and their candidate targets.

Date: Oct 19, 2015
Time: 11:00 AM
Location: Weill hall, Room 221