Blaxter, Mark

Rambaut, Andrew

Koutsovoulos, Georgios D.

Biotechnology and Biological Sciences Research Council (BBSRC)

2015-09-11T14:25:02Z

2015-09-11T14:25:02Z

2015-06-29

Nematoda is a very diverse animal phylum. Within Nematoda, species display a multitude of life styles, different reproductive strategies and parasitism has arisen independently several times. Furthermore, morphological conservation and a high rate of homoplasy have impeded the resolution of nematode systematics. To address these issues, single gene (usually the nuclear ribosomal small subunit gene) and mitochondrial gene phylogenies have been used, but the information contained within the sequence of these genes is not enough to resolve the topological relationships between clades that emerged during rapid cladogenesis. Next generation sequencing data have been shown to produce high quality genomic and transcriptomic assemblies at low cost, as a result more and more nematode species are being sequenced. Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. These sequences were screened for orthologous gene clusters, which were concatenated into a supermatrix with thousands of aminoacid sites. The analysis of the supermatrix with maximum likelihood and Bayesian inference methods sheds light into the early splitting clades of the phylogenetic tree of nematodes and the derived clades III, IV and V. Furthermore, the phylogenetic relationships within the parastitic family Onchocercidae were resolved, unveiling the evolutionary history of these important taxa. Finally, data produced in this work will be useful for subsequent evolutionary studies of the phylum Nematoda.

http://hdl.handle.net/1842/10558

en

The University of Edinburgh

M. Blaxter and G. Koutsovoulos, "The evolution of parasitism in Nematoda," Parasitology, pp. 1-14, 2014.

S. Kumar, M. Jones, G. Koutsovoulos, M. Clarke, and M. Blaxter, "Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots," Frontiers in genetics, vol. 4, 2013.

G. Koutsovoulos, B. Makepeace, V. N. Tanya, and M. Blaxter, "Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode," PLoS genetics, vol. 10, no. 6, p. e1004397, 2014.

P. H. Schi er, M. Kroiher, C. Kraus, G. D. Koutsovoulos, S. Kumar, J. I. Camps, N. A. Nsah, D. Stappert, K. Morris, P. Heger, et al., "The genome of Romanomermis culicivorax : revealing fundamental changes in the core developmental genetic toolkit in nematoda," BMC genomics, vol. 14, no. 1, p. 923, 2013.

J. Wang, M. Mitreva, M. Berriman, A. Thorne, V. Magrini, G. Koutsovoulos, S. Kumar, M. L. Blaxter, and R. E. Davis, "Silencing of germline-expressed genes by DNA elimination in somatic cells," Developmental cell, vol. 23, no. 5, pp. 1072-1080, 2012.

C. Godel, S. Kumar, G. Koutsovoulos, P. Ludin, D. Nilsson, F. Comandatore, N. Wrobel, M. Thompson, C. D. Schmid, S. Goto, et al., "The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets," The FASEB Journal, vol. 26, no. 11, pp. 4650-4661, 2012.

F. Comandatore, D. Sassera, M. Montagna, S. Kumar, G. Koutsovoulos, G. Thomas, C. Repton, S. A. Babayan, N. Gray, R. Cordaux, et al., "Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes," Genome biology and evolution, vol. 5, no. 9, pp. 1668-1674, 2013.

D. H. Lunt, S. Kumar, G. Koutsovoulos, and M. L. Blaxter, "The complex hybrid origins of the root knot nematodes revealed through comparative genomics," PeerJ, vol. 2, p. e356, 2014.

S. Kumar, G. Koutsovoulos, G. Kaur, and M. Blaxter, "Toward 959 nematode genomes," in Worm, vol. 1, pp. 42-50, Landes Bioscience, 2012.

M. Blaxter, G. Koutsovoulos, M. Jones, S. Kumar, and B. Elsworth, Next- Generation Systematics, ch. Phylogenomics of Nematoda. Cambridge University Press, Cambridge, UK, 2014.

nematodes

evolution

bioinformatics

phylogenomics

Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes

Thesis or Dissertation

Doctoral

PhD Doctor of Philosophy