Evolutionary dynamics of genome obesity

Lead Research Organisation: Queen Mary, University of London
Department Name: Sch of Biological and Chemical Sciences

Abstract

The central dogma in genetics is that 'DNA codes for RNA which makes proteins'. Why then do similar and closely related organisms often have widely different amounts of DNA in their nuclei? Even in organisms with a small amount of DNA, the fraction that comprises genes is frequently very small. What is the extra DNA doing and how did it get there? These are important questions because we know that organisms with large genomes are at greater risk of extinction, are less adaptable to living in polluted soils, and are less able to tolerate extreme environmental conditions. Clearly the total amount of DNA has ecological consequences which shape the distribution and persistence of biodiversity. In fact an analysis of many thousands of species reveals that genome size varies enormously. In plants alone it can vary nearly 2000-fold. The non-genic component of DNA is usually composed of highly repeated sequences of two types, (i) dispersed repetitive sequences and (ii) tandem repeated sequences. Together these give the chromosomes a particular character, such as their size. Chromosome size is important in the evolution and diversification of all organisms because large chromosomes (or more accurately the total sum of all chromosomes = the genome) often come at a cost, including long generation times, slow development and restrictions on the type of habitat occupied by the organism. There may nevertheless be advantages to having large genomes in some circumstances because some organisms do have particularly large amounts of DNA. In the last 20 years there has been an enormous effort expended by the science community to increase our understanding of plant genomes for three main reasons: (i) to improve the efficiency, versatility and value of agriculture; (ii) to harness resources for medical research, and (iii) to stimulate new discoveries through fundamental research. To achieve this end several plants were selected to have their genomes completely sequenced, so that we could discover in detail the nature and occurrence of genic and non-genic DNA. This was an expensive and time-consuming task involving labs from around the world. To minimise the scale of the task, plants with small genomes, like the weed Arabidopsis thaliana and the crop rice, were selected for analysis. Our current thinking is that over many thousands or millions of years, DNA in the genome can expand through amplification of some repetitive DNA and shrink through small bite-like loses. Nevertheless, this fascinating view of the dynamic nature of plant genomic DNA is flawed because we only understand the dynamics of plants with small to medium-sized genomes, i.e. those genomes chosen for DNA sequencing. Is this picture of genome evolution true for organisms with large genomes? To address this we have selected the plant genus Fritillaria for analysis, since it includes species with truly giant genomes including the largest so far reported for any plant. The problem is how to tackle the Herculean task of determining the nature and evolution of so much DNA in Fritillaria. Fortunately a powerful new method to sequence huge amounts of DNA cost-effectively has been developed that enables us to get a handle on genome evolution in organisms with giant genomes. These methods use sophisticated DNA handling and analytical approaches for studying DNA. When coupled with microscopical studies of the chromosomes themselves, and a detailed understanding of how the species are related to each other, we can build a picture of the evolutionary events that occurred in the formation of giant genomes. We will address what DNA sequences are involved in genome enlargement, why particular sequences became so abundant, and if genome enlargement happened suddenly in evolution, or slowly over time. Thus our study will provide the community with fundamental knowledge of the processes occurring in plant genome evolution.

Publications

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Dodsworth S (2015) Genomic repeat abundances contain phylogenetic signal. in Systematic biology

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Dodsworth S (2015) Genome size diversity in angiosperms and its influence on gene space. in Current opinion in genetics & development

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Garcia S (2017) Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. in The Plant journal : for cell and molecular biology

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Kelly L (2012) Why size really matters when sequencing plant genomes in Plant Ecology & Diversity

 
Description Our findings have provided new fundamental insights into the organization and evolution of the giant genomes of Fritillaria, which contain more than 30 times as much DNA in each nucleus as humans. By analysing the most repetitive fraction of some of the largest known genomes for diploid species, the research has shown that genomic expansion in Fritillaria has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of their immense genomes is composed of highly heterogeneous, relatively low abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our research thus indicates that a lack of deletion, and low turnover, of repetitive DNA is a major contributor to the evolution of extremely large genomes and that their size cannot simply be accounted for by the activity of a small number of high abundance repeat families. An additional key finding of the research is that the giant genomes of Fritillaria cannot be explained by a catastrophic failure of the epigenetic machinery as signatures of epigenetic regulation have been uncovered (see Becher et al. 2014). This therefore has overturned one frequently suggested explanation as to why the genomes of Fritillaria have undergone such genome expansion.
These novel findings have now opened up new areas of research including (i) investigating the nature of the epigenetic machinery and processes underpinning the reduced rates of DNA elimination that have been identified in the Fritillaria genomes, (ii) determining whether the genomic repeat landscape and underlying genomic processes responsible that we have uncovered in Fritillaria are typical of all species with giant genomes (e.g. similar approaches are being used to analyse the giant genomes in the plant family Melanthiaceae as part of an EU-funded Beatriu de Pinós fellowship), (iii) the role of DNA as a metabolic drag.

In addition to these findings focused on understanding genomic processes, the research has also led to the development of novel uses of the large amounts of repetitive sequence data generated by next generation sequencing (NGS) approaches. We have demonstrated that the repetitive fraction of the genome contains a signature of evolutionary relationships and hence can be used to build phylogenetic trees. This novel methodology, published in Dodsworth et al. (Systematic Biology 2014; doi: 10.1111/nph.13107) may well prove to be especially useful in groups where there is little genetic differentiation with standard phylogenetic markers. Thus, rather than discarding such NGS data, as many researchers do in their focus on genes, these findings highlight the potential for them to deliver a wealth of novel data for phylogenetic inference.
Exploitation Route The findings have laid the foundation to understanding the composition and evolutionary processes responsible for generating the giant genomes encountered in Fritillaria. Already the data are being used by our research group (i) to investigate the epigenetics of genome obesity, (ii) to uncover whether the mechanisms responsible for generating giant genomes are homologous between different lineages of plants, both within angiosperms as well as with other land plant groups such as gymnosperms, and (iii) in collaboration with Dr Jiri Macas (named collaborator on NERC grant) and his team, the data are being used to test whether there is a fundamental shift in the genomic processes operating once genomes get beyond a certain size. In addition, an increasing number of visitors are asking to be trained in the analysis of the repetitive fraction of the genome so that similar approaches can be applied to other plant systems.
Sectors Agriculture, Food and Drink,Education,Environment

URL https://evolve.sbcs.qmul.ac.uk/leitch/
 
Description The work undertaken with this grant generated fundamental research and therefore its major outcome are listed under key findings. The overall economic and societal impacts have yet to be fully realised, nevertheless the research on Fritillaria has led to detailed understanding of evolutionary relationships between Fritillaria species, and these are likely to lead to societal impact and be exploited in agricultural and environmental settings, since the work is leading to a better understanding of the metabolic costs of genome size. We have contributed data leading to publications, attracting PhD students and Marie Curie Fellows to the UK using EU Framework 7-derived resources, CSC scholarships and Science without Borders Scholarships.
First Year Of Impact 2006
Sector Agriculture, Food and Drink,Education
 
Description Richard Nichols coordinating a successful Marie Curie ITN and Leitch a participant
Geographic Reach Asia 
Policy Influence Type Influenced training of practitioners or researchers
Impact Training 13 PhD students over 4 years into advanced plant breeding and nature conservation approaches
 
Description Richard Nichols invited to chair Steering committee of NERC bimolecular analysis facility
Geographic Reach National 
Policy Influence Type Membership of a guidance committee
Impact guidance on how to spend NERC money in bioinformatics
 
Description Marie Curie IEF
Amount € 209,033 (EUR)
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 10/2012 
End 10/2014
 
Description Marie Curie ITN
Amount € 3,582,732 (EUR)
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 09/2011 
End 08/2015
 
Description NERC consortium grant;The role of lateral exchange in modulating the seaward flux of C, N, P
Amount £3,000,000 (GBP)
Funding ID NE/J012106/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start  
 
Title Illumina sequence datasets for RdDM 
Description Illumina sequences for Fritiallaria species with giant genomes 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact New understanding of plant genome evolution 
URL https://goo.gl/PrNKfB
 
Title Illumina sequence for giant genomes paper 
Description 454 sequence data for Fritillaria 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Data on evolution of giant genomes 
 
Description Collaboration with Dr Ales Kovarik 
Organisation Academy of Sciences of the Czech Republic
Department Institute of Biophysics
Country Czech Republic 
Sector Public 
PI Contribution Provided data for numerous joint publications
Collaborator Contribution Provided data for numerous joint publications
Impact 1. Dadejova, M., Lim, K.Y., Souckova-Skalicka, K., Matyasek, R., Grandbastien, M.A., Leitch, A. and Kovarik, A. (2007) Transcription activity of rRNA genes correlates with a tendency towards intergenomic homogenization in Nicotiana allotetraploids. New Phytologist, 174, 658-668. 2. Koukalova, B., Fojtova, M., Lim, K.Y., Fulnecek, J., Leitch, A.R. and Kovarik, A. (2005) Dedifferentiation of tobacco cells is associated with ribosomal RNA gene hypomethylation, increased transcription, and chromatin alterations. Plant Physiology, 139, 275-286. 3. Koukalova, B., Moraes, A.P., Renny-Byfield, S., Matyasek, R., Leitch, A.R. and Kovarik, A. (2010) Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years. New Phytologist, 186, 148-160. 4. Kovarik, A., Dadejova, M., Lim, Y.K., Chase, M.W., Clarkson, J.J., Knapp, S. and Leitch, A.R. (2008) Evolution of rDNA in Nicotiana allopolyploids: A potential link between rDNA homogenization and epigenetics. Annals of Botany, 101, 815-823. 5. Kovarik, A., Lim, K.Y., Souckova-Skalicka, K., Matyasek, R. and Leitch, A.R. (2012a) A plant culture (BY-2) widely used in molecular and cell studies is genetically unstable and highly heterogeneous. Bot. J. Linn. Soc., 170, 459-471. 6. Kovarik, A., Pires, J.C., Leitch, A.R., Lim, K.Y., Sherwood, A.M., Matyasek, R., Rocca, J., Soltis, D.E. and Soltis, P.S. (2005) Rapid concerted evolution of nuclear ribosomal DNA in two tragopogon allopolyploids of recent and recurrent origin. Genetics, 169, 931-944. 7. Kovarik, A., Renny-Byfield, S., Grandbastien, M.-A. and Leitch, A. (2012b) Evolutionary implications of genome and karyotype restructuring in Nicotiana tabacum L. In Polyploidy and Genome Evolution (Soltis, P.S. and Soltis, D.E. eds): Springer Berlin Heidelberg, pp. 209-224. 8. Leitch, A.R., Kovarik, A., Matyasek, R., K., S.-S., Chase, M.W., Clarkson, J.J., Leitch, I.J., Knapp, S., Grandbastien, M.A. and Lim, K.Y. (2007) Polyploid-diploid cycle in the genus Nicotiana (abstract for International Chromosome Conference Amsterdam 2007). Chromosome Research, 15, 8. 9. Lim, K.Y., Kovarik, A., Matyasek, R., Chase, M.W., Clarkson, J.J., Grandbastien, M.A. and Leitch, A.R. (2007a) Sequence of events leading to near-complete genome turnover in allopolyploid Nicotiana within five million years. New Phytologist, 175, 756-763. 10. Lim, K.Y., Kovarik, A., Matyasek, R., Chase, M.W., Knapp, S., McCarthy, E., Clarkson, J.J. and Leitch, A.R. (2006a) Comparative genomics and repetitive sequence divergence in the species of diploid Nicotiana section Alatae. Plant Journal, 48, 907-919. 11. Lim, K.Y., Matyasek, R., Kovarik, A., Fulnecek, J. and Leitch, A.R. (2005) Molecular cytogenetics and tandem repeat sequence evolution in the allopolyploid Nicotiana rustica compared with diploid progenitors N. paniculata and N. undulata. Cytogenetic and Genome Research, 109, 298-309. 12. Lim, K.Y., Matyasek, R., Kovarik, A. and Leitch, A. (2007b) Parental origin and genome evolution in the allopolyploid Iris versicolor. Annals of Botany, 100, 219-224. 13. Lim, K.Y., Matyasek, R., Kovarik, A. and Leitch, A.R. (2004) Genome evolution in allotetraploid Nicotiana. Biological Journal of the Linnean Society, 82, 599-606. 14. Lim, K.Y., Souckova-Skalicka, K., Sarasan, V., Clarkson, J.J., Chase, M.W., Kovarik, A. and Leitch, A.R. (2006b) A genetic appraisal of a new synthetic Nicotiana tabacum (Solanaceae) and the Kostoff synthetic tobacco. American Journal of Botany, 93, 875-883. 15. Matyasek, R., Fulnecek, J., Leitch, A.R. and Kovarik, A. (2011) Analysis of two abundant, highly related satellites in the allotetraploid Nicotiana arentsii using double-strand conformation polymorphism analysis and sequencing. New Phytologist, 192, 747-759. 16. Matyasek, R., Fulnecek, J., Lim, K.Y., Leitch, A.R. and Kovarik, A. (2002) Evolution of 5S rDNA unit arrays in the plant genus Nicotiana (Solanaceae). Genome, 45, 556-562. 17. Matyasek, R., Lim, K.Y., Kovarik, A. and Leitch, A.R. (2003) Ribosomal DNA evolution and gene conversion in Nicotiana rustica. Heredity, 91, 268-275. 18. Matyasek, R., Renny-Byfield, S., Fulnecek, J., Macas, J., Grandbastien, M.-A., Nichols, R., Leitch, A. and Kovarik, A. (2012) Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics, 13. 19. Petit, M., Lim, K., Julio, E., Poncet, C., Dorlhac de Borne, F.o., Kovarik, A., Leitch, A., Grandbastien, M.-A.l. and Mhiri, C. (2007) Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Molecular Genetics and Genomics, 278, 1-15. 20. Renny-Byfield, S., Ainouche, M., Leitch, I.J., Lim, K.Y., Le Comber, S.C. and Leitch, A.R. (2010) Flow cytometry and GISH reveal mixed ploidy populations and Spartina nonaploids with genomes of S. alterniflora and S. maritima origin. Annals of Botany, 105, 527-533. 21. Renny-Byfield, S., Chester, M., Kovarík, A., Le Comber, S.C., Grandbastien, M.-A., Deloger, M., Nichols, R.A., Macas, J., Novák, P., Chase, M.W. and Leitch, A.R. (2011) Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Mol. Biol. Evol., 28, 2843-2854. 22. Renny-Byfield, S., Kovarik, A., Chester, M., Nichols, R.A., Macas, J., Novak, P. and Leitch, A.R. (2012) Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum. PLoS ONE, 7, e36963. 23. Renny-Byfield, S., Kovarik, A., Kelly, L.J., Macas, J., Novak, P., Chase, M.W., Nichols, R.A., Pancholi, M.R., Grandbastien, M.A. and Leitch, A.R. (2013) Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences. Plant Journal, 74, 829-839. 24. Skalicka, K., Lim, K.Y., Matyasek, R., Matzke, M., Leitch, A.R. and Kovarik, A. (2005) Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. New Phytologist, 166, 291-303. 25. Yang, Q., Hanson, L., Bennett, M.D. and Leitch, I.J. (1999) Genome structure and evolution in the allohexaploid weed Avena fatua L. (Poaceae). Genome, 42, 512-518. 26. Ma L, Hatlen A, Kelly L, Becher H, Wang W, Kovarik A, Leitch I, Leitch A. 2015. Angiosperms are unique amongst land plants for the occurrence of key genes in the RNA-Directed DNA methylation (RdDM) pathway. Genome biology and evolution 7: 2648-2662.
 
Description Collaboration with Drs J. Macas and P. Novak 
Organisation Green Living Movement (GLM)
Country Zambia 
Sector Charity/Non Profit 
PI Contribution Ongoing collaboration with Drs J Macas and P Novak (Ceske Budejovice, Czech Republic) in the analysis of NGS data resulting in publication (Kelly et al. 2012) (see Publications).
Collaborator Contribution Providing bioinformatics Know how
Impact Please see: Dodsworth et al 2015 and Kelly et al 2015
 
Description Collaboration with Professor Jonathan Wendel 
Organisation University of Iowa
Country United States 
Sector Academic/University 
PI Contribution Discussions leading to a Sabbatical in the UK
Collaborator Contribution Collaborative discussion
Impact None yet
Start Year 2017
 
Description Conference talk Evolutionary Dynamics Between Angiosperm and Mammalian Genomes". Plant and Animal Genome Conference, San Diego 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk sparked questions and discussion afterwards

Talk formed part of a new COST consortium developed at conference
Year(s) Of Engagement Activity 2013
 
Description Conference talk, Plant Genome Dynamics 2013, Banyuls, France. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact talk sparked questions and discussion afterwards

Stimulated experiments that now form part of an ERC grant application in 2014
Year(s) Of Engagement Activity 2013
 
Description Kew Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This involved the preparation of an interactive display entitled "what is genome size and why do we care" including demonstrating the diversity of genome sizes encountered in plants and what impact it can have on the plant. It also included opportunities for hand on demonstration of how genome size is estimated to over 150 people aged 3 to old age.
Year(s) Of Engagement Activity 2017
URL https://www.kew.org/about-our-organisation/press-media/press-releases/kew-science-festival-2017
 
Description Kew Science Festival "unearth the world of plants and Fungi held over three days 5-9 August 2016, to showcase Botanical and mycological sciences 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 15,000 additional new visitors came to Kew Gardens for this science festival, which sparked interest from people from 3 years upwards. Indeed our youngest scientists, extracting nuclei to measure genome size in plants was 3 years old. Amongst scientists, several wanted further information, and one will purchase a flow cytometer based on this display. A local MP also visited the exhibition.
Year(s) Of Engagement Activity 2016
URL http://science.kew.org/strategic-output/science-gardens
 
Description Lecture given at international conference, Plant Genomics Congress, May 2014, London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk sparked questions and discussion afterwards,

New and ongoing collaborations and further talk invitations
Year(s) Of Engagement Activity 2014
 
Description Open day to showcase research acivities and programme opportunities 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Open-days are attended by undergraduate and graduate students and their parents, who question all aspects of university and research life, and want detail of training programmes available.
Year(s) Of Engagement Activity 2014,2015
URL http://www.qmul.ac.uk/postgraduate/meet-us/openevents/
 
Description conference talk, Plant and Animal Genome Conference 2014, San Diego, USA. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact talk sparked questions and discussion afterwards

New collaboration and experimental ideas, plus asked to run a workshop at same conference series in the following year
Year(s) Of Engagement Activity 2014
 
Description workshop talk;Genome size divergence in polyploid Nicotiana; Ohio, USA 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Workshop describing how to conduct cytogenetic methods in plant breeding, and an application for an NSF-BBSRC joint fund (Unsuccessful)

New USA-UK collaborations
Year(s) Of Engagement Activity 2012