We are sequencing the genomes of a variety of bdelloid rotifers, fungi and bacteria in order to understand the role of selection, gene flow and horizontal gene transfer in shaping diversity among organisms. We also use metagenomics and targeted sequencing of genomes from historical collections to track evolutionary change through time, and transcriptomics in order to search for functionally important genes in challenging non-model organisms.

Bdelloid genomics

Bdelloid rotifers are microscopic invertebrates with incredibly interesting genomes. They are degenerate tetraploid, meaning that most of their genes come in 4 copies (as in A1,A2, B1,B2), with a much larger divergence between the A's and the B's (homoeologous divergence) than within either A or B (homologous divergence). However, the homologous divergence varies substantially both within a species (i.e. along a chromosome) and between species (averaged across the genome). Bdelloid genomes also encode a surprising variety of transposable elements (TEs) of all shapes and sizes, including DNA transposons, LTR and non-LTR retrotransposons and enigmatic Penelope-like elements, which may play some role in telomere maintenance. Finally, bdelloid genomes appear to encode a remarkably high proportion of "foreign" genes, acquired from a variety of non-metazoan organisms (mostly bacteria) presumably via horizontal gene transfer (HGT). In combination with the truly remarkable life-history and physiological characteristics of bdelloids (i.e. asexuality and anhydrobiosis), these features put bdelloid genomes in a unique position among metazoa, from which we can leverage insights into the evolution of sex and the genomic causes and consequences of "extremotolerance" phenotypes such as desiccation tolerance.

Active research questions include:

• Can we find conclusive genetic and genomic evidence as to the true nature of bdelloid reproduction? In other words, are bdelloids really anciently and obligately asexual?
• What might explain the uniquely large proportion of HGT genes in bdelloids?
• Deleterious TEs are not expected to survive for long evolutionary periods in asexuals. What might explain the presence of a diverse array of TEs in bdelloids?
• What are the molecular and evolutionary drivers of variation in homologous divergence within and between bdelloid species?

References

Nowell, R.W., Almeida, P., Wilson, C.G., Smith, T.P., Fontaneto, D., Crisp, A., Micklem, G., Tunnaclife, A., Boschetti, C., Barraclough, T.G. 2018. Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PLoS Biology 16: e2004830

Eyres, I., Bochetti, C., Crisp, A., Fontaneto, D., Tunnacliffe, A. and Barraclough. T.G. 2015. Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats. BMC Biology. 13:90 DOI 10.1186/s12915-015-0202-9

Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, Lubzens E, Barraclough TG, Micklem G and Tunncliffe A. 2012. Biochemical diversification through foreign gene expression in bdelloid rotifers. PLoS Genet 8: e1003035 2.