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. 2013 Mar 27;4:62. doi: 10.3389/fpls.2013.00062

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Copyright © 2013 Tohge, Watanabe, Hoefgen and Fernie.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

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Phylogenetic tree analysis of shikimate and phenylalanine biosynthetic genes in 25 species. Amino acid sequence phylogenetic trees of (A) shikimate pathway: (a), DAHPS, (b) DHS, (c) DHQD/SD, (d) SK, (e) ESPS, and (f) CS, (B) phenylalanine related genes, (a) CM and (b) PAT. Amino acid sequences of shikimate biosynthetic genes are obtained from Plaza database (http://bioinformatics.psb.ugent.be/plaza/). Relationships among the species considered are presented on the Plaza website. The phylogenetic tree was constructed with the aligned protein sequences by MEGA (version 5.10; http://www.megasoftware.net/; Kumar et al., 2004) using the neighbor-joining method with the following parameters: Poisson correction, complete deletion, and bootstrap (1000 replicates, random seed). The protein sequences were aligned by Plaza. Values on the branches indicate bootstrap support in percentages.

Phylogenetic tree analysis of shikimate and phenylalanine biosynthetic genes in 25 species. Amino acid sequence phylogenetic trees of (A) shikimate pathway: (a), DAHPS, (b) DHS, (c) DHQD/SD, (d) SK, (e) ESPS, and (f) CS, (B) phenylalanine related genes, (a) CM and (b) PAT. Amino acid sequences of shikimate biosynthetic genes are obtained from Plaza database (http://bioinformatics.psb.ugent.be/plaza/). Relationships among the species considered are presented on the Plaza website. The phylogenetic tree was constructed with the aligned protein sequences by MEGA (version 5.10; http://www.megasoftware.net/; Kumar et al., 2004) using the neighbor-joining method with the following parameters: Poisson correction, complete deletion, and bootstrap (1000 replicates, random seed). The protein sequences were aligned by Plaza. Values on the branches indicate bootstrap support in percentages.