Veronica Mankinen, Vice President Commercial Operations, Dovetail Genomics, will present a seminar The Use of Confirmation Capture Technology for Genome Assembly, Genome Wide Structural Variation and TAD Analysis

The Use of Confirmation Capture Technology for Genome Assembly, Genome Wide Structural Variation and TAD Analysis

Tue 24 Apr 2018 2:30pm3:30pm

Venue

QBP Bldg #80
UQ St Lucia campus
Room: 
Small Seminar Room 3.146

Presenting Speakers:

Veronica Mankinen - Vice President, Commercial Operations, Dovetail Genomics

Confirmation Capture Technology: Overview and applications

Proximity ligation, a library prep technique that enables visualization of regions of the genome that although distant in genomic space are in close proximity when the genome is in its native 3-dimensional state, can be used for a variety of applications including Scaffolding of de novo genome assemblies up to full chromosomes, visualization of genome wide Structural Variation and evaluation of TADs, Topologically Associated Domains.
Dovetail Genomics is focused on the use of Proximity Ligation in all of these applications through our services and our new kits. During this seminar we will present an overview of the techniques and case studies of each of these applications for use in human, agricultural and evolutionary biology applications.

Elizabeth Ross - Queensland Alliance for Agriculture and Food Innovation

The Story of the Brahman Genome: from contigs to chromosomes

Just 15 years after the massive undertaking that was the Human Genome Project, we have now reached a point where technological advances make it possible to sequence and assemble a de-novo genome in under one year to a reference standard. This may be the tipping point where it is now viable for economically important species to have a reference quality genome sequence. Sequencing of a Brahman genome (Bos indicus) for use a reference was identified as an industry goal, to ensure that cattle with B. indicus genomic content can fully benefit from the full suite of genomics technologies (e.g. GWAS) that are available for trait improvement and understanding. Here we present the Brahman reference genome. In total 195GB of sequence data was obtained from the PacBio Sequel. The sequence reads were error corrected using the DAZZler scrubber suite and then assembled with the Falcon assembler. The assembly yielded 1867 contigs, with an N50 of 6MB. The assembled contigs were error corrected with Arrow, and then scaffolded using Hi-C and Chicago data. After scaffolding the assembly consisted of 843 scaffolds with an N50 of 62MB, and L50 of 13 with 1106 gaps. The scaffolds then underwent several rounds of gap filling using PBJelly and Arrow. After gap filling and polishing the assembly consists of 835 scaffolds, which contain only 443 gaps in total. Eighteen of the 30 chromosomes are present at >95% length in a single scaffold, including the notoriously hard to assemble X chromosome. The X chromosome scaffold contains 83 gaps and shows a high level of agreement with other recent cattle assemblies. By using independent scaffolding methods it will be possible to compare the B. indicus and Bos taurus genomes with the aim of identifying structural variation and other genomic differences.