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  Exploiting Gene Families for Phylogenomic Analysis of Myzostomid Transcriptome Data

Hartmann, S., Helm, C., Nickel, B., Meyer, M., Struck, T. H., Tiedemann, R., et al. (2012). Exploiting Gene Families for Phylogenomic Analysis of Myzostomid Transcriptome Data. PLoS One, 7(1), e29843. doi:10.1371/journal.pone.0029843.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-1F97-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-1F98-D
Genre: Journal Article

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 Creators:
Hartmann, S.1, Author              
Helm, C.2, Author
Nickel, B.2, Author
Meyer, M.2, Author
Struck, T. H.2, Author
Tiedemann, R.2, Author
Selbig, J.1, Author              
Bleidorn, C.2, Author
Affiliations:
1BioinformaticsCRG, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753315              
2External Organizations, ou_persistent22              

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Free keywords: species trees sequence data parsimony genome life alignment program incongruence duplication supermatrix
 Abstract: Background: In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic ( or parasitic) protostomes that are either placed with annelids or flatworms. Methodology: Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. Conclusions: Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.

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Language(s): eng - English
 Dates: 2012
 Publication Status: Published in print
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 Identifiers: ISI: ISI:000301568100017
DOI: 10.1371/journal.pone.0029843
ISSN: 1932-6203
URI: ://000301568100017 http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0029843&representation=PDF
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Title: PLoS One
Source Genre: Journal
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Pages: - Volume / Issue: 7 (1) Sequence Number: - Start / End Page: e29843 Identifier: -