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Interview: Transcriptome of an agricultural pest delineated by Oxford Nanopore RNA-Seq

Fri 25th January 2019

Anthony Bayega at NCM 2018

Webinar date: Thursday 14th February

Time: 12pm EST/5pm GMT/9am PST

Speaker: Anthony Bayega, McGill University, Canada

Anthony Bayega is currently completing a PhD at McGill University in Canada, studying transcriptional dynamics in early embryo development of the olive fruit fly (Bactrocera oleae), a pest that costs the olive fruits industry an estimated $200 million annually. In this interview, we talked to Anthony about his research and how long-read sequencing is benefitting his work.

Anthony will be presenting Transcriptome of an agricultural pest delineated by Oxford Nanopore RNA-Seq on Thursday 14th February 2019 5pm GMT/12.00pm EST/9.00am PST with Genome Web.

What are your current research interests?

We are currently studying transcriptional events that shape early embryo development in insects of agricultural importance, using long-read sequencing technologies, such as the Oxford Nanopore full-length RNA-Seq technology. We also use long-read sequencing to sequence and obtain de novo genome assemblies to improve genomic characterisation of these organisms as part of the i5k consortium.

What first got you interested in the field of genomics and transcriptomics?

I first got interested in genomics back in 2011 whilst I was a Master’s student at King’s College London. Until then, researchers had used array comparative genomic hybridisation and other low-resolution genomic technologies to identify aberrant genomic regions in Cutaneous T-cell Lymphomas (CTCL) and I was intrigued by the use of exome sequencing to identify mutations that play a role in the pathogenesis of CTCL. Fast-forward to my current project, I now work with organisms that are not well characterised, which poses a genomics challenge. It was clear that using long-read sequencing technologies, combined with short-read sequencing, enables better characterisation of these organisms.

How is long-read sequencing changing the study of genomics and transcriptomics? How has it benefited your work?

The current standard of high-throughput transcriptome analysis uses short-read sequencing technologies, particularly Illumina. The challenge with this approach is the reconstruction of gene structures and accurate determination of isoform abundancies, and long-read sequencing offers a solution to both problems. Although long-read RNA-Seq has been used in well characterised organisms like humans, a clear advantage is in poorly characterised organisms, where the structure of genes is not well curated. Working with the olive fruit fly, we have been able to identify the full length of genes expressed in our samples and expand the isoform diversity by 4-fold using long-read RNA-Seq. Long-reads also enables us to obtain a highly contiguous genome of the olive fly and improve the assembly of the Y-chromosome.

What impact could a deeper understanding of the transcriptional dynamics in early embryo development have?

Embryo development is a very intriguing phenomenon. From a single cell, a complex multicellular organism develops and so understanding the early events that shape this process has long been a very interesting research area. Working with the olive fruit fly, the most important pest in the olives agribusiness industry, we aimed to identify the gene that determines male sex during development. This gene is known to reside on the Y chromosome and is activated in the first 6 hours of embryo development. Identifying this gene could provide avenues of biological sterile insect technique to control the populations of the fly where olives trees are grown.

What have been the main challenges in your research and how have you approached them?

Being a relatively new technology with a smaller community of users, there are far less bioinformatic tools to analyse long-read data compared to tools currently available for short-read data. We are constantly on the lookout for new tools; developing our own and collaborating with bioinformatics software developers. However, as the genomics field increasingly adopts long-read technologies, the bioinformatic tools are now increasingly available.

What’s next for your research?

We have so far explored the transcriptional dynamics of early embryo development in the olive fly. We would like to extend this work to another agriculturally important pest, the Mediterranean fruit fly. We would like to perform sexed single embryo multiplexed long-read RNA-Seq for an extended period into development to capture more dynamics of development. We also plan to extend our experience to identify pathogenic fusion genes in cancer.

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Anthony is currently a PhD candidate in the Department of Human Genetics at McGill University in Canada under the supervision of Professor Ioannis Ragoussis. His work is focused on using long-read technologies, particularly from Oxford Nanopore, to characterize genomes and transcriptomes of organisms.

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