The evolutionary genomics of sexual recombination

Lead Research Organisation: University of Hull
Department Name: Biological Sciences

Abstract

The puzzling predominance of sexual reproduction amongst animals has been repeatedly identified as one of the major outstanding questions in biology and has received an enormous amount of study. Meiotic recombination is one of the fundamental forces of evolution and plays a very significant role in both generating and mixing the genetic diversity present in sexual organisms. Recombination is also suggested to be instrumental in shaping the content of eukaryotic genomes.

Here we propose to study the role of breeding system and recombination in shaping the content and diversity of animal genomes using an exceptionally powerful natural system- the Root Knot Nematodes. We will, for the first time, be able to take a comparative genomic view of radically different reproductive modes in a phylogenetic design. Together these studies will give us a novel and powerful understanding of the role sexual reproduction plays in shaping genome content.

Planned Impact

The principal users of this work will be the academic community interested in evolutionary biology, genomics, nematology, reproduction and diversity. The immediate outputs from this grant will be basic scientific understanding concerning the nature of genome change. The enormous agricultural importance of these species will also ensure that the impact of this work, production of genetic markers and characterising genes associated with attack of their plant hosts, will have lasting impacts.

This project will be published in open-access peer reviewed journals wherever possible, to give scientists, applied researchers, and the public maximum access.

The genomics age, and the interaction of this new technology with basic biology and agriculture will additionally be highlighted to school children taking GCSE and A-level science courses (and their parents). This will be accomplished by extending the interactions we already have in place. These include tours of the DNA labs, practical sessions investigating DNA, discussions of the science relating to genome with school children of ages 13-17, and presentation of our work at open days at both universities.

We will develop a dynamic web presence including blog and news feeds, and also prepare promotional materials for dissemination to schools, colleges and fellow institutions.

Publications

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Lunt DH (2014) The complex hybrid origins of the root knot nematodes revealed through comparative genomics. in PeerJ

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Szitenberg A (2016) Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements. in Genome biology and evolution

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Szitenberg A (2017) Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change. in Genome biology and evolution

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Szitenberg A (2015) ReproPhylo: An Environment for Reproducible Phylogenomics. in PLoS computational biology

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Szitenberg A (2014) The evolution of tyrosine-recombinase elements in Nematoda. in PloS one

 
Description Root Knot Nematodes (RKN) are among the world's most important plant pathogens, and cause a 5% loss in world agriculture per annum. We have investigated the origins of this group using genomics. We have shown that some of the key RKN species are double hybrids, with very complex matings between 'parental' species. This double hybridisation was likely the origin of highly diverse genomes of the pathogenic RKN.
In addition we have begun a program to better characterise the genomes of nematodes more broadly. Our characterisation of transposons, a major component of all genomes, has revealed that the diversity of nematode genomes is best understood by broad sampling of species, and that relying on single species in the past has lead to misleading conclusions.
Exploitation Route We have three major research directions:
1. The characterisation of diversity in plant parasitic nematode genomes
2. Understanding the origins of plant parasitic nematode species
3. Understanding the way in which reproductive mode influences genome content and diversity
The first and second will have direct relevance to understanding and ultimately control of a major global crop threat. The third is a biologically fundamental question, of relevance to all biologists interested in basic questions such as 'what is in a genome and why?'
Sectors Agriculture, Food and Drink
URL http://www.nematodes.org/nematodegenomes
 
Description Our findings have been used via citation of our publications.
 
Title ReproPhylo 
Description ReproPhylo is a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale genomic data for phylogenetics, and to assist methodological experimentation. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact The ReproPhylo pipeline and approach was incorporated into grant proposal for future funding by the Cipres science gateway https://www.phylo.org/ and was fundamental to the design and completion of metaBEAT https://github.com/HullUni-bioinformatics/metaBEAT 
URL http://hulluni-bioinformatics.github.io/ReproPhylo/