Genome assembly. chromosomal organization and comparative genomics of multiple bird species: beyond "catalogues of genes"

Lead Research Organisation: University of Kent
Department Name: Sch of Biosciences

Abstract

Imagine trying to navigate through a town with only the index from your A-Z to guide you and not the street map. In essence, this is what happens when the genome of a new species is sequenced. Old fashioned technology used to "sketch the outline of the streets" first before filling in the gaps with the gene sequence. The new technology (so called "Next Generation Sequencing") is much cheaper and quicker but is quite poor at sorting out where the genes are in relation to one another. Essentially, Next Generation Sequencing assemblies are little more than catalogues of genes with little structure of the overall genome apparent. Fortunately this problem can be rectified using a technique called "FISH" that can take the data from next generation sequencing projects and visualise directly the genes as they appear in their rightful place in the genome. In this project we intend to do this with 25-30 recently completed genome sequences from birds. Birds are among the most diverse animals with around 10,000 living species. Many are models for human disease and development and are critical to agriculture (both meat and eggs). Others are threatened or endangered and, with impending global warming, molecular tools for the study of ecology and conservation of birds are essential. It is also possible to compare the overall structure of one genome with another, somewhat like comparing the maps of towns with similar layouts. We have developed online tools that can directly visualize the similarities and differences between the genomes of several birds at a time. Of course the differences between these bird genomes came about through changes that happened during evolution. One of the main aims of this project is to find out how and why this occurred. We have a number of ideas such as we think there may be different "gene signatures" at the places in the genome where evolutionary rearrangements are more or less likely to occur. We think that the whole process may be related to the mechanisms by which our genes recombine in our germ cells. We also think there may be a role for small pieces of DNA that "float around" these bird genomes. Finally, we have received overwhelming support from numerous laboratories all over the world, all of whom are interested in bird genomics and who would wish to use our online resource to ask biological questions of their own. For this reason we feel that this project not only will help us understand evolution in birds but also establish the UK as a central international hub for work of this kind.

Technical Summary

Every genome sequence needs a good map however modern next generation sequencing (NGS) technologies struggle fully to assemble whole genomes de-novo. This is disappointing as mapping information on a chromosomal basis brings the opportunity to address many fundamental biological questions of genome evolution. Modern genomic research generally focuses on the role of individual genes but the role of chromosomes and homologous synteny blocks (HSBs) is often disregarded. This is despite the ubiquity of HSBs and the phenotypic consequences/evolutionary implications of chromosome rearrangement. In mammals, there are sufficient assembled reference genomes to make assembly by comparative analysis. For birds however only three such reference genomes exist and chromosomal assembly needs to be achieved by other means. Classical approaches involving karyotyping and FISH coupled with comparative genomics browser technology provide a straightforward solution for the many avian genomes that are assembled to the point of 100+ large scaffolds. The aim of the project will thus be to generate a freely available comparative genomic resource that can be used to compare the genome structures of 25-30 bird species. HSBs and Evolutionary Breakpoint Regions (EBRs) will be displayed using the "Evolution Highway" browser. We will anchor each of the scaffolds physically to chromosomes by FISH. We will address at least four fundamental questions pertaining to genome evolution: We will test the hypotheses that HSB lengths are non-randomly distributed in birds, that there are specific gene ontology signatures of HSBs and EBRs, that EBRs coincide with recombination hotspots in birds (but not in mammals) and that transposable element density in increased in EBRs. The extensive letters of support from potential users indicate that this will be a widely used resource addressing a myriad of further biological questions in this most diverse and biologically important group of vertebrates.

Planned Impact

Exploitation and Application.
Technology Transfer activity at both Universities is administered by Enterprise offices. Collaborative agreement already exist with Digital Scientific and CytoCell. These separately capture exploitation and collaborative output issues going forward. Cytocell, Aviagen and Digital Scientific UK see benefit to this project either through the identification of commercially important traits or through the sales of products and have thus offered generous in kind support. A specific strategic advisory board has been established to identify potential impact issues from this and other projects.

Communications and engagement with the identified beneficiaries.
The main beneficiaries of this grant will be the avian genomics community in industry, third sector and academia. In 2002 the Kent lab was set up as a resource centre for avian molecular cytogenetics (FARMACRHOM). Through these activities we developed a mature and functioning collaborative network with most of the major players in avian genomics and biology many of whom have attached letters of support. Evolution Highway the "industry standard" for browser comparative genomics in the mammalian chromosome world with over ~50 regular users 16,000 hits from academia, industry and third sector in the last year. Inherently used for collaborative research it is, in itself, a tool to facilitate communication and engagement. Another beneficiary is the poultry breeding industry through which the Kent lab is, and has been, supported and funded through BBSRC grants and PhD CASE studentships. In the past we have provided genome maps for the species of interest (turkey and duck). A local zoo (Wingham Wildlife Park) was engaged as another and benefitted by subsequent broadcast media coverage and by provision of a display on the collaborative work performed (this is currently on display to the general public). We will participate in company-managed events and community activities with specialist audiences and the general public to disseminate findings and will develop as a CPD module for delivery to outside engagers. We will contribute to the Bioscience KTN newsletter, to "BBSRC business," newsletters published by individual companies and by the Departments/Universities and to media coverage as well as online activities. Bioscience KTN provide further help and advice on collaboration and their website has >3,000 registered members working in industry and academia The PI's have a healthy relationship with the University press offices and are regular contributor to public engagement activities including "Café Scientifique," Science Fairs and public lectures. Thus far, this work has led to several press releases in addition to appearances in the national and local broadcast media (BBC's "Big Questions," "The World Tonight", Radio 2 Simon Mayo show" BBC radio Kent etc.). Both Universities have active outreach programmes to which the PIs will contribute.

Capacity and Involvement
The two PIs will be the primary participants in impact activities aided by by PhD students and post-doctoral researchers. Professor Griffin has extensive training and experience in communication activities and commercial exploitation of research. The communications and development office in both Universities provide technical expertise and help in writing publications, web pages and user-friendly interfaces and it is expected that post-docs and PhD students will be provided with significant training in both dissemination and exploitation activities through Departmental, University and Bioscience KTN related activities. In conclusion therefore, this project has a range of expertise and ambitious, but achievable plans for impact at local, regional national and international levels.

See complete impact plan (attached) for further details

Publications

10 25 50

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Farré M (2016) Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. in Genome biology and evolution

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Griffin DK (2015) 20th International Chromosome Conference (ICCXX) : 50th Anniversary, University of Kent, Canterbury, 1st-4th September 2014. in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

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Ishishita S (2014) Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric repetitive sequences in New World quails. in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

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Lithgow PE (2014) Novel tools for characterising inter and intra chromosomal rearrangements in avian microchromosomes. in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

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Schmid M (2015) Third Report on Chicken Genes and Chromosomes 2015. in Cytogenetic and genome research

 
Description In the first year of the project we have made considerable progress toward the objective of the project. Being part of the genome effort to sequence 50 or so avian genomes - submitting a paper to Genome Biology (sadly rejected) and editing/contributing to a special issue of Chromosome Research.


1: Salomonsen J, Chattaway JA, Chan AC, Parker A, Huguet S, Marston DA, Rogers
SL, Wu Z, Smith AL, Staines K, Butter C, Riegert P, Vainio O, Nielsen L, Kaspers
B, Griffin DK, Yang F, Zoorob R, Guillemot F, Auffray C, Beck S, Skjødt K,
Kaufman J. Sequence of a complete chicken BG haplotype shows dynamic expansion
and contraction of two gene lineages with particular expression patterns. PLoS
Genet. 2014 Jun 5;10(6):e1004417. doi: 10.1371/journal.pgen.1004417. eCollection
2014 Jun. PubMed PMID: 24901252; PubMed Central PMCID: PMC4046983.


2: Lithgow PE, O'Connor R, Smith D, Fonseka G, Al Mutery A, Rathje C, Frodsham R,
O'Brien P, Kasai F, Ferguson-Smith MA, Skinner BM, Griffin DK. Novel tools for
characterising inter and intra chromosomal rearrangements in avian
microchromosomes. Chromosome Res. 2014 Apr;22(1):85-97. doi:
10.1007/s10577-014-9412-1. PubMed PMID: 24696127.


3: Ishishita S, Tsuruta Y, Uno Y, Nakamura A, Nishida C, Griffin DK, Tsudzuki M,
Ono T, Matsuda Y. Chromosome size-correlated and chromosome size-uncorrelated
homogenization of centromeric repetitive sequences in New World quails.
Chromosome Res. 2014 Apr;22(1):15-34. doi: 10.1007/s10577-014-9402-3. PubMed
PMID: 24532185.


4: Skinner BM, Al Mutery A, Smith D, Völker M, Hojjat N, Raja S, Trim S, Houde P,
Boecklen WJ, Griffin DK. Global patterns of apparent copy number variation in
birds revealed by cross-species comparative genomic hybridization. Chromosome
Res. 2014 Apr;22(1):59-70. doi: 10.1007/s10577-014-9405-0. PubMed PMID: 24570127.


5: Nishida C, Ishishita S, Yamada K, Griffin DK, Matsuda Y. Dynamic chromosome
reorganization in the osprey ( Pandion haliaetus , Pandionidae, Falconiformes):
relationship between chromosome size and the chromosomal distribution of
centromeric repetitive DNA sequences. Cytogenet Genome Res. 2014;142(3):179-89.
doi: 10.1159/000358407. Epub 2014 Feb 7. PubMed PMID: 24513810.


6: Nishida C, Ishijima J, Ishishita S, Yamada K, Griffin DK, Yamazaki T, Matsuda
Y. Karyotype reorganization with conserved genomic compartmentalization in
dot-shaped microchromosomes in the Japanese mountain hawk-eagle (Nisaetus
nipalensis orientalis, Accipitridae). Cytogenet Genome Res. 2013;141(4):284-94.
doi: 10.1159/000352067. Epub 2013 Jul 2. PubMed PMID: 23838459.


7: Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J,
Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L,
Tafer H, Vignal A, Lee T, Kim KW, Sheng Z, An Y, Searle S, Herrero J, Groenen MA,
Crooijmans RP, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S,
Kehr S, Marz M, Stadler PF, Smith J, Kraus RH, Zhao Y, Ren L, Fei J, Morisson M,
Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N. The duck genome and
transcriptome provide insight into an avian influenza virus reservoir species.
Nat Genet. 2013 Jul;45(7):776-83. doi: 10.1038/ng.2657. Epub 2013 Jun 9. PubMed
PMID: 23749191; PubMed Central PMCID: PMC4003391.


8: Griffin D, Burt DW. All chromosomes great and small: 10 years on. Chromosome
Res. 2014 Apr;22(1):1-6. doi: 10.1007/s10577-014-9413-0. PubMed PMID: 24700106.


In the second year, progress has continued apace. We have been part of another community effort in the avian genome world.

Schmid et al. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res.2015;145(2):78-179.

We have reconstructed 2 further genomes (Pigeon and Peregrine), developed high throughput methods of processing our data, provided insight in tot the chromosomes of dinosaurs and are in the process of mapping numerous other genomes.
Exploitation Route The project is ongoing and we have several collaborators
Sectors Agriculture, Food and Drink,Education

URL http://www.bbsrc.ac.uk/news/fundamental-bioscience/2017/170105-pr-complete-animal-genomes-become-easier-to-map/
 
Description The project is in progress (just over three years old) but I continue to get several invitations to give public and academic lectures based around the work.
First Year Of Impact 2014
Sector Education
Impact Types Cultural

 
Description List of collaborators 
Organisation Central Veterinary Research Laboratory
Country United Arab Emirates 
Sector Public 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Digital Scientific UK
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Hokkaido University
Country Japan 
Sector Academic/University 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Illumina
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation University of Cambridge
Department Department of Pathology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006