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Open Access Highly Accessed Research article

Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

Huan Qiu13, Falk Hildebrand14, Shigehiro Kuraku12* and Axel Meyer12

Author Affiliations

1 Laboratory for Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany

2 Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany

3 Bigelow Laboratory for Ocean Sciences, 180 McKown Point Road, West Boothbay Harbor, Maine 04575-0475, USA

4 Bioinformatics and (eco-) systems biology, VIB, Vrije Universiteit Brussel, 1050 Brussels, Belgium

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BMC Genomics 2011, 12:325  doi:10.1186/1471-2164-12-325

Published: 23 June 2011

Additional files

Additional file 1:

Figure S1-Sequence alignment of three human KCNA and 16 new KCNA proteins that were newly identified in this study. Only conserved regions are shown. Species names were abbreviated as in Figure 5.

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Additional file 2:

Figure S2-Maximum-likelihood tree of potassium voltage-gated channel, shaker-related (KCNA) genes rooted by other potassium channel protein families. 253 amino acid sites were used in the analysis. Statistical support values for crucial nodes regarding the monophyly of the KCNA family are shown in order, bootstrap values in the ML analysis and posterior probabilities. A hyphen indicates inconsistent phylogenetic tree topology between Maximum-likelihood tree and Bayesian tree.

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Additional file 3:

Figure S3-Molecular phylogenetic tree of KCNA genes inferred with the Bayesian method. Statistical support values for nodes with branches leading to sea lamprey or elephant shark genes are shown with ML bootstrap values left to the slash and posterior probabilities right to the slash. "-" indicates inconsistent topology between the ML tree and Bayesian tree.

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Additional file 4:

Table S1-All tree topologies within 1σ of log-likelihood from the ML trees for each sea lamprey KCNA gene.

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Additional file 5:

Table S2-Lamprey nucleotide sequences used in the present study.

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