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MBE Advance Access published online on October 19, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj041
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted September 21, 2005

Research Article

Dense Taxonomic EST Sampling and its Applications for Molecular Systematics of the Coleoptera (beetles)

Joseph Hughes 1* *, Stuart J. Longhorn 1 *, Anna Papadopoulou 2, Kosmas Theodorides 1, Alessandra de Riva 1, Monica Mejia-Chang 1, Peter G. Foster 3, and Alfried P. Vogler 1

1 Department of Entomology, The Natural History Museum, London SW7 5BD, UK; Department of Biological Sciences, Imperial College London, Silwood Park Campus, Ascot Sl5 7PY
2 Department of Entomology, The Natural History Museum, London SW7 5BD, UK
3 Department of Zoology, The Natural History Museum, London SW7 5BD, UK

* To whom correspondence should be addressed.
Joseph Hughes, E-mail: j.hughes{at}bio.gla.ac.uk


  Abstract

EST sequences can provide a wealth of data for phylogenetic and genomic studies, but the utility of these resources is restricted by poor taxonomic sampling. Here, we use small EST libraries (<1000 clones) to generate phylogenetic markers across a broad sample of insects, focusing on the species rich Coleoptera (beetles). We sequenced over 23,000 ESTs from 34 taxa, which produced 8728 unique sequences after clustering non-redundant sequences. Between taxa, the sequences could be grouped into 731 gene clusters, with the largest corresponding to mtDNA transcripts and gene families chymotrypsin, actin, troponin and tubulin. While levels of paralogy were high in most gene clusters, several mid-sized clusters including many ribosomal protein genes appeared to be free of expressed paralogs. To evaluate the utility of EST data for molecular systematics, we curated available transcripts for 66 ribosomal protein genes from representatives of the major groups of Coleoptera. Using super-tree and super-matrix approaches for phylogenetic analysis, the results were consistent with the emerging phylogenetic conclusions about basal relationships in Coleoptera. Numerous small EST libraries from a taxonomically densely sampled lineage can provide a core set of genes that together act as a scaffold in phylogenetic reconstruction, comparative genomics, and studies of gene evolution.

Keywords: phylogenomics; Gene Ontology; Shallow genomics; Expressed Sequence Tag.

*These authors contributed equally to the work


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