CIE Seminar Series 2017 – Functional annotation of avian genomes and the emergence of avian phylogenomics

SPEAKER: Prof David Burt, Department of Genomics and Genetics, The Roslin Institute and Royal School of Veterinary Studies, University of Edinburgh

DATE: Friday, 21st April 2017
LOCATION: Geelong Campus at Waurn Ponds – room ka4.207
TIME: 1:30pm
Seminar will also be video linked to the following campuses: Melbourne Campus at Burwood – Burwood Corporate Centre (attendees-please report to reception on the day); and Warrnambool Campus – room B3.03

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ABSTRACT: Our knowledge of avian genomes has increased rapidly, starting with the publication of the chicken genome in 2004, a milestone for avian and evolutionary biology. Advances in DNA sequencing now make it possible to produce draft sequences of any vertebrate genome, quickly and cheaply. We have seen the completion of draft genomes of more than 50 other birds, with plans to sequence all 10,000 by the B10K Consortium.

With advances in long read sequencing and optical mapping, we are seeing chromosome level genome assemblies with N50 contigs of 20-30Mb.  The annotation of genomes has also been under continuous improvement, taking advantage of transcriptome data generated both by short and long read RNA sequencing technologies.

Recently, we sequenced normalised full-length chicken cDNA libraries with Pacific Bioscience Iso-Seq. From these Iso-Seq sequencing projects, over 60K transcripts and 29K genes were defined within the chicken transcriptome. Of these, more than 20K are novel long non-coding RNA (lncRNA) transcripts with approx. 3K classified as sense-exonic overlapping lncRNA, which is a class that is underrepresented in all other vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes.

Our results indicate that the chicken transcriptome is similar in complexity (with multiple starts and stops, and alternative isoforms) compared to human. Our improved methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of the transcriptomes of any complex organism. Recently, the analysis of 44 bird genomes by the Avian Phylogenomics Consortium created new opportunities. For individual species, the sequences coupled with the initial annotations, can serve as a vehicle for basic research. On the other hand generating a multiple genome sequence alignment can enable comparative studies, which benefits all these species. Such studies broaden our understanding of genome evolution and the evolution of traits or can help to disentangle phylogenetic relationships.

Our main aim is to integrate these and other data sources (transcripts, CAGE-seq, ChIP-seq, ATAC-seq, etc. for example as part of the FAANG initiative) with a focus on creating a detailed functional map relevant to birds. Such a map can be used to drive the identification of novel protein-coding and non-coding genes, binding sites for transcription factors, enhancers or other functional elements.

I will review the current status of avian genome annotation and open up the discussion on future possibilities using phylogenomics in the study of species diversity and the evolution of avian traits.

BIOProfessor David W. Burt, FRSB, FLS received his B.Sc. in Molecular Biology at Edinburgh University (1977), a PhD in molecular genetics from Leicester University (1980) and MSc modules in Bioinformatics from Manchester University (2002). His post-doctoral training included research on molecular genetics of a wide range of species (bacteriophage lambda, bacteria, mouse, rat and human) and research areas (transcription circuits, cDNA cloning of growth factors, renin-angiotensin system and hypertension, QTL mapping, bioinformatics, phylogenetics and avian genomics). He has worked with AstraZeneca at Leicester University (UK), Harvard Medical School (USA), MRC Clinical Research Centre (UK) and Roslin Institute/Edinburgh University (UK). He was appointed Head of Avian Genomics Group (1988), Director of ARK-Genomics (2000), Director of the National Avian Research Facility (2014), convener of Institute Strategic Program (Genomics, 2016) and Personal Chair in Comparative Genomics, University of Edinburgh (2009).

In 2017, Professor David W. Burt was appointed Director of the UQ Genomics Initiative  a virtual network that aims to facilitate partnerships and engagement across all genomics researchers at UQ and beyond. UQ genomics research has the potential for strong synergies with The Roslin Institute and we hope to develop this relationship over the coming years. To facilitate this Professor Burt will continue to work closely with The Roslin Institute in his new capacity at UQ and will hold an honorary Chair in Comparative Genomics at Edinburgh University.

He has obtained over $70m in competitive funding to support his research activities and has published over 300 articles, books and chapters (h-index 57) including in high impact journals such as Nature, Science, Nature Genetics, Current Biology and Genome Research. His current research is focused on comparative genomics and applications in poultry and other livestock species.  He has served on many scientific committees, including the BBSRC Animal Science Committee, the Scottish Branch Council of the Royal Society of Biology, the Board for Edinburgh Genomics and several editorial boards. He is active in promoting avian genomics as co-chair in various consortia and international meetings, including the International Chicken Genome Consortium, International Society for Animal Genetics (ISAG), Bird10K, Avian Model Systems, Plant & Animal Genome workshop on Avian Genomes and theInternational Functional Annotation of Animal Genomes (FAANG) Steering Committee.

The UQ Genomics Initiative offers a clear point of entry to UQ’s collective genomic capabilities, including its interactions with government and industry. The Director ensures that the UQ Genomics Initiative facilitates interdisciplinary interactions in fundamental and applied research, education, training and consulting across all faculties and institutes. It is my goal to build synergies throughout Australasia to promote and enhance a regional Genomics Community.

Appointments with guest speaker may be made via Kate Buchanan.