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
Slides
Showing posts with label RNAseq. Show all posts
Showing posts with label RNAseq. Show all posts
Saturday, September 26, 2015
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
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
Tuesday, January 27, 2015
Date: Feb 2, 2015. Zehong Ding: Comparison of leaf gradient transcriptomics in multiple C3 and C4 species
Zehong Ding is a Postdoctoral Associate at the BRC Bioinformatics Facility on campus.
Transferring C4 photosynthesis into C3 crops has been proposed as one of the most promising ways to increase the yield ceiling and hence global productivity. To better understand the function of C4 photosynthesis, and to identify candidate genes that associated with C4 pathway, comparative transcriptomes were conducted along a leaf developmental gradient in maize, viridis, sorghum and rice. In total 478 C4 candidate genes were identified. Besides the classical C4 genes, many function well characterized genes that associated with light reaction, starch and sucrose metabolism, hormone, TFs, and transporters were included. These findings will provide important insights into the gene differentiation between C3 and C4 species. In addition, the C4 candidate genes that identified in our approach would be a useful gene resource that could be used for C4 engineering of C3 crops.
Date: Feb 2, 2015
Time: 11:00 AM
Location: Weill hall, Room 321
Slides
Transferring C4 photosynthesis into C3 crops has been proposed as one of the most promising ways to increase the yield ceiling and hence global productivity. To better understand the function of C4 photosynthesis, and to identify candidate genes that associated with C4 pathway, comparative transcriptomes were conducted along a leaf developmental gradient in maize, viridis, sorghum and rice. In total 478 C4 candidate genes were identified. Besides the classical C4 genes, many function well characterized genes that associated with light reaction, starch and sucrose metabolism, hormone, TFs, and transporters were included. These findings will provide important insights into the gene differentiation between C3 and C4 species. In addition, the C4 candidate genes that identified in our approach would be a useful gene resource that could be used for C4 engineering of C3 crops.
Date: Feb 2, 2015
Time: 11:00 AM
Location: Weill hall, Room 321
Slides
Subscribe to:
Posts (Atom)