Gene discovery in the horned beetle Onthophagus taurus

Jeong-Hyeon Choi, Teiya Kijimoto, Emilie Snell-Rood, Hongseok Tae, Youngik Yang, Armin P. Moczek, Justen Andrews

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Background: Horned beetles, in particular in the genus Onthophagus, are important models for studies on sexual selection, biological radiations, the origin of novel traits, developmental plasticity, biocontrol, conservation, and forensic biology. Despite their growing prominence as models for studying both basic and applied questions in biology, little genomic or transcriptomic data are available for this genus. We used massively parallel pyrosequencing (Roche 454-FLX platform) to produce a comprehensive EST dataset for the horned beetle Onthophagus taurus. To maximize sequence diversity, we pooled RNA extracted from a normalized library encompassing diverse developmental stages and both sexes.Results: We used 454 pyrosequencing to sequence ESTs from all post-embryonic stages of O. taurus. Approximately 1.36 million reads assembled into 50,080 non-redundant sequences encompassing a total of 26.5 Mbp. The non-redundant sequences match over half of the genes in Tribolium castaneum, the most closely related species with a sequenced genome. Analyses of Gene Ontology annotations and biochemical pathways indicate that the O. taurus sequences reflect a wide and representative sampling of biological functions and biochemical processes. An analysis of sequence polymorphisms revealed that SNP frequency was negatively related to overall expression level and the number of tissue types in which a given gene is expressed. The most variable genes were enriched for a limited number of GO annotations whereas the least variable genes were enriched for a wide range of GO terms directly related to fitness.Conclusions: This study provides the first large-scale EST database for horned beetles, a much-needed resource for advancing the study of these organisms. Furthermore, we identified instances of gene duplications and alternative splicing, useful for future study of gene regulation, and a large number of SNP markers that could be used in population-genetic studies of O. taurus and possibly other horned beetles.

Original languageEnglish (US)
Article number703
JournalBMC Genomics
Volume11
Issue number1
DOIs
StatePublished - Dec 14 2010

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Beetles
Genetic Association Studies
Expressed Sequence Tags
Genes
Single Nucleotide Polymorphism
Biochemical Phenomena
Tribolium
Molecular Sequence Annotation
Biological Phenomena
Gene Ontology
Gene Duplication
Alternative Splicing
Population Genetics
Sequence Analysis
Genome
Databases
RNA
Radiation

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Choi, J-H., Kijimoto, T., Snell-Rood, E., Tae, H., Yang, Y., Moczek, A. P., & Andrews, J. (2010). Gene discovery in the horned beetle Onthophagus taurus. BMC Genomics, 11(1), [703]. https://doi.org/10.1186/1471-2164-11-703

Gene discovery in the horned beetle Onthophagus taurus. / Choi, Jeong-Hyeon; Kijimoto, Teiya; Snell-Rood, Emilie; Tae, Hongseok; Yang, Youngik; Moczek, Armin P.; Andrews, Justen.

In: BMC Genomics, Vol. 11, No. 1, 703, 14.12.2010.

Research output: Contribution to journalArticle

Choi, J-H, Kijimoto, T, Snell-Rood, E, Tae, H, Yang, Y, Moczek, AP & Andrews, J 2010, 'Gene discovery in the horned beetle Onthophagus taurus', BMC Genomics, vol. 11, no. 1, 703. https://doi.org/10.1186/1471-2164-11-703
Choi J-H, Kijimoto T, Snell-Rood E, Tae H, Yang Y, Moczek AP et al. Gene discovery in the horned beetle Onthophagus taurus. BMC Genomics. 2010 Dec 14;11(1). 703. https://doi.org/10.1186/1471-2164-11-703
Choi, Jeong-Hyeon ; Kijimoto, Teiya ; Snell-Rood, Emilie ; Tae, Hongseok ; Yang, Youngik ; Moczek, Armin P. ; Andrews, Justen. / Gene discovery in the horned beetle Onthophagus taurus. In: BMC Genomics. 2010 ; Vol. 11, No. 1.
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