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  A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator).

Roeding, F., Borner, J., Kube, M., Klages, S., Reinhardt, R., & Burmester, T. (2009). A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator). Molecular Phylogenetics and Evolution, 53(3), 826-834. doi:10.1016/j.ympev.2009.08.014.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7D39-8 Version Permalink: http://hdl.handle.net/21.11116/0000-0004-42A1-B
Genre: Journal Article
Alternative Title : Mol. Phylogenet. Evol.

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 Creators:
Roeding, Falko, Author
Borner, Janus, Author
Kube, Michael1, Author              
Klages, Sven2, Author              
Reinhardt, Richard1, Author              
Burmester, Thorsten, Author
Affiliations:
1High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433552              
2Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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Free keywords: Arthropoda; Chelicerata; Expressed sequence tags; Next generation sequencing; Pyrosequencing
 Abstract: In recent years, phylogenetic tree reconstructions that rely on multiple gene alignments that had been deduced from expressed sequence tags (ESTs) have become a popular method in molecular systematics. Here, we present a 454 pyrosequencing approach to infer the transcriptome of the Emperor scorpion Pandinus imperator. We obtained 428,844 high-quality reads (mean length = 223 ± 50 b) from total cDNA, which were assembled into 8334 contigs (mean length 422 ± 313 bp) and 26,147 singletons. About 1200 contigs were successfully annotated by BLAST and orthology search. Specific analyses of eight distinct hemocyanin sequences provided further proof for the quality of the 454 reads and the assembly process. The P. imperator sequences were included in a concatenated alignment of 149 orthologous genes of 67 metazoan taxa that covers 39,842 amino acids. After removal of low-quality regions, 11,168 positions were employed for phylogenetic reconstructions. Using Bayesian and maximum likelihood methods, we obtained strongly supported monophyletic Ecdysozoa, Arthropoda (excluding Tardigrada), Euarthropoda, Pancrustacea and Hexapoda. We also recovered the Myriochelata (Chelicerata + Myriapoda). Within the chelicerates, Pycnogonida form the sister group of Euchelicerata. However, Arachnida were found paraphyletic because the Acari (mites and ticks) were recovered as sister group of a clade comprising Xiphosura, Scorpiones and Araneae. In summary, we have shown that 454 pyrosequencing is a cost-effective method that provides sufficient data and coverage depth for gene detection and multigene-based phylogenetic analyses.

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Language(s): eng - English
 Dates: 2009-08-19
 Publication Status: Published in print
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Title: Molecular Phylogenetics and Evolution
  Alternative Title : Mol. Phylogenet. Evol.
Source Genre: Journal
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Publ. Info: -
Pages: - Volume / Issue: 53 (3) Sequence Number: - Start / End Page: 826 - 834 Identifier: ISSN: 1055-7903