Monday, October 9, 2017

Date: Oct 27, 2017. Mark Daly: Dovetail Genomics – Building the Best Genomes on Earth

Mark Daly is the Director of Sales at Dovetail Genomics LLC

A contiguous and accurate genome assembly is a crucial first step in fully understanding the biology of any organism.  A high-quality genome assembly will make any downstream analyses, like gene annotation, synteny, comparative genomics and population genetics far easier and more reliable.

Dovetail Genomics is the leading service provider for high quality genome assemblies. To date, they have completed more than 400 projects, spanning many classes of organisms from plants to reptiles, amphibians, fish, mammals, birds, insects and more.

Using two complementary scaffolding methods, Chicago and Dovetail Hi-C, they are dramatically increasing the contiguity and accuracy of genome assemblies, enabling true, full-chromosome-length scaffolding. This talk will provide an update on their most current technologies.  Mark will profile several customer projects and discuss how improvements in their assemblies led to better science and new discoveries.

Date: Oct 27, 2017
Time: 10:00 AM
Location: Weill hall, Room 226

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

Tuesday, April 28, 2015

Date: May 4, 2015. Kevin Panke-Buisse: Rhizosphere Microbiome: Manipulation and Investigation

Kevin Panke-Buisse is a PhD Candidate in the Kao-Kniffin Lab in the Horticulture section of the School of Integrative Plant Science at Cornell University.

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. This talk will outline some of the ways we can manipulate the rhizosphere microbiome and look at shifts across treatments via 16s sequencing.

Date: May 04, 2015
Time: 10:30 AM
Location: Weill hall, Room 321

Monday, April 13, 2015

Date: Apr 20, 2015. Jeff Glaubitz: The Maize Rare Alleles Project: Biology & Bioinformatics

Jeff Glaubitz is a Senior Research Associate and the Project Manager of Panzea - the NSF Maize Diversity Project.

The NSF project Biology Of Rare Alleles In Maize And Its Wild Relatives (Ed Buckler, PI) is combining the power of population genetic and molecular models with quantitative genetics to elucidate the relative contributions of rare versus common alleles to phenotypic variation and evolution. We are taking advantage of recent advances in high-throughput genotyping and phenotyping methodologies to identify the key biological attributes of variants (genome annotations) that will allow us to better predict the functional effects of rare alleles in Zea. This information will then be used to accelerate crop improvement either through more accurate genomic selection or via future genome editing approaches. We hope to enhance the effectiveness of plant breeding by improving our ability to identify, predict, and select on the effects of rare variants, both deleterious and beneficial. In this talk I will give an overview of the biological goals of this project and the various bioinformatic tools that are being developed to achieve these goals, with an emphasis on TASSEL.

Date: April 20, 2015
Time: 11:00 AM
Location: Weill hall, Room 321

Thursday, February 26, 2015

Date: Mar 2, 2015. Minghui Wang: Genome-wide crossover distribution in the population of maize B73 and Mo17

Minghui Wang is a Postdoctoral Associate at the BRC Bioinformatics Facility on campus.

Crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. However, CO are not evenly distributed across genome. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in maize, in male and female meiosis.

Date: Mar 2, 2015
Time: 11:00 AM
Location: Weill hall, Room 321

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