Supplement

Computational Analysis of the Evolution of the Structure and Function

of 1-Deoxy-D-xylulose-5-phosphate Synthase, a Key Regulator

of the Mevalonate-Independent Pathway in Plants

Julia Krushkal^a, Maxwell Pistilli^b, Kathryn M. Ferrell^b, Frederic F. Souret^b, and Pamela J. Weathers^b

^a Center of Genomics and Bioinformatics and Department of Preventive Medicine, University of Tennessee Health Science Center

^b Department of Biology and Biotechnology, Worcester Polytechnic Institute

Plant DXS Sequences Analyzed

Species	Common Name	Taxonomy Information^a	Genbank Accession	Gene
Arabidopsis thaliana	Thale cress	Eudicot, Rosidae, Brassicales, Brassicaceae	Y14333	DXS1 (CLA1)
Artemisia annua	Sweet wormwood	Eudicot, Asteridae, Asterales, Asteraceae	AF182286	DXS1
Capsicum annuum	Pepper	Eudicot, Asteridae, Solanales, Solanaceae	Y15782	DXS1
Catharanthus roseus	Rosy periwinkle	Eudicot, Asteridae, Geniantales, Apocynaceae	AJ011840	DXS2
Lycopersicon esculentum	Tomato	Eudicot, Asteridae, Solanales, Solanaceae	AF143812	DXS1
Mentha x piperita	Peppermint	Eudicot, Asteridae, Lamiales, Lamiaceae	AF019383	DXS2
Medicago truncatula	Barrel medic	Eudicot, Rosidae, Fabales, Fabaceae	AJ430047, AJ430048	DXS1, DXS2
Morinda citrifolia	Indian mulberry	Eudicot, Asteridae, Geniantales, Rubiaceae	AF443590	DXS1
Narcissus pseudonarcissus	Daffodil	Monocot, Asparagales, Amaryllidaceae	AJ279019	DXS2
Stevia rebaudiana	Sweetleaf	Eudicot, Asteridae, Asterales, Asteraceae	AJ429232	DXS2
Tagetes erecta	African marigold	Eudicot, Asteridae, Asterales, Asteraceae	AF251020	DXS2

^a Information from the National Center for Biotechnology Information Taxonomy Browser (available online at http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)

Sequence Alignment and Results of Phylogenetic Analysis

Alignment of DXS protein sequences from ten eudicot and one monocot species

Unrooted phylogenetic tree inferred by the neighbor-joining method using amino acid distances corrected for multiple hits and gamma distribution for substitution rates among sites

Unrooted phylogenetic tree inferred by the minimum evolution method using Poisson correction of amino acid distances

Consensus tree of 500 bootstrap replicate trees inferred from protein sequence data using parsimony

Rooted phylogenetic tree and Clustal X protein sequence alignment including bacterial outgroup sequences (Haemophilus influenzae, GenBank accession number U32822; Vibrio cholerae, AE004173, and Pseudomonas aeruginosa, AE004888). The tree was inferred by the neighbor-joining method using Poisson correction of amino acid distances.

Unrooted phylogenetic tree inferred by the neighbor-joining method from nucleotide distances corrected for multiple hits using Kimura’s 2-parameter model

Relative rate test results for Narcissus and Mentha DXS2 computed using Medicago DXS1 as an outgroup, with all substitutions combined

Relative rate test results for Narcissus and Mentha DXS2 computed using Medicago DXS1 as an outgroup, with transitions and transversions considered separately

Results of Fisher's exact test for selection, with distances computed by the Nei-Gojobori method

Disparity index test results

Secondary Structure Prediction of the C-terminal Functional Region

Secondary structure predicted by GOR IV

Secondary structure predicted by HNN