Research Interests

The evolution of C4 photosynthesis

With over 60 independent origins, C4 photosynthesis is one of the most remarkable examples of convergent evolution. Multiple studies have identified a large repertoire of genes that are differentially expressed between closely related C3 and C4 species, and within C4 species, thousands of genes have been implicated in biochemical and anatomical development. While the catalogue of genes that is associated with C4 biology continues to increase, the mechanisms that regulate C4-specific gene expression remain largely unknown.

We are interested in identifying the gene expression regulators that control C4 gene expression and understanding how these regulators have evolved from their C3 ancestors. We hope that by understanding this we can help engineer advantageuos C4 traits into C3 plants.

Hughes, T.E., Langdale, J.A., and Kelly, S. (2014). The impact of widespread regulatory neofunctionalisation on homeolog gene evolution following whole genome duplication in maize. Genome ResearchPDF

Aubry, S., Kelly, S., Kümpers, B.M.C., Smith-Unna, R.D., Hibberd, J.M., (2014).Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLoS GeneticsPDF

Christin, P.A., Arakaki, M., Osborne, C.P., Bräutigam, A., Sage, R.F., Hibberd, J.M., Kelly, S., Covshoff, S., Wong, G.K., Hancock, L., Edwards, E.J. (2014) Shared origins of a key enzyme during the evolution of C4 and CAM metabolism Journal of Experimental BotanyPDF

Kelly, S., Wang, P., Fouracre, J.P. and Langdale, J.A., (2013). Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy. The Plant JournalPDF

Wang, P., Fouracre, J., Kelly, S., Karki, S., Gowick, U., Aubry, S., Shaw, M.K., Westhoff, P., Slamet-Loedin, I.H., Quick, W.P., Hibberd, J.M., and Langdale, J.A. (2012). Evolution of GOLDEN2-LIKE gene function in C(3) and C (4) plants. PlantaPDF

The structure/function relationship of the genome

Genomes are not just libraries of information they are dynamic storage-machines which temporally control access to information through a variety of different mechanisms. It is clear that long-range physical interactions between discrete chromosomal regions play an important role in how that information is accessed and expressed across the “tree-of-life”. Evidence for this comes from a variety of sources and experiments; from the earliest observations on isolated bacterial “nucleoids” to recent experiments mapping the entire 3D structure of the Human genome using parallel sequencing. All of these lines of evidence indicate that genome function is controlled at multiple different levels and scales of organisation, from the linear sequence of the genome itself through nucleosome structure to large-scale chromosome arrangement in the nucleus. We are interested in understanding how 3D genome organisation influences how the genome works. We are particularly interested in the genomes of plants. Plant genomes can be very large, they are often characterised by massively paralogous gene families and they exploit all manner of regulatory mechanisms to control their function. So there is lots to study and understand and a whole manner of mechanisms that can be exploited to meet future food production demands.

Holden, J.M., Koreny, L., Obado, S., Ratushny, A.V., Chen, W.M., Chiang, J.H., Kelly, S., Chait, B.T., Aitchison, J.D., Rout, M.P. and Field, M.C (2014) Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity. Molecular Biology of the CellPDF

Kelly, S., Kramer, S., Schwede, A., Maini, P.K., Gull, K., and Carrington, M. (2012). Genome organization is a major component of gene-expression control in response to stress and during the cell-division cycle in trypanosomes. OpenBiologyPDF

Tiengwe, C., Marcello, L., Farr, H., Dickens, N., Kelly, S., Swiderski, M., Vaughan, D., Gull, K., Barry J.D., Bell, S.D. and McCulloch, R. (2012). Genome-wide Analysis Reveals Extensive Functional Interaction between DNA Replication Initiation and Transcription in the Genome of Trypanosoma brucei. Cell reportsPDF

Building better bioinformatic tools

We are interested in developing improved methods for both multiple sequence alignment, phylogenetic inference, genome annotation, orthologue detection, high throughput sequence analysis genome analysis … well just about everything you could call bioinformatics!

Collingridge, P.W. and Kelly, S. (2012). MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. BMC BioinformaticsPDF

Kelly, S. and Maini P.K. (2013). DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments. PLoS OnePDF