DOI: 10.5061/dryad.tj1p3
title: Data from: Phylogenomic mining of the mints reveals multiple mechanisms contributing to the evolution of chemical diversity in Lamiaceae

description: The evolution of chemical complexity has been a major driver of plant
 diversification, with novel compounds serving as key innovations. The
 species-rich mint family (Lamiaceae) produces an enormous variety of
 compounds that act as attractants and defense molecules in nature and are
 used widely by humans as flavor additives, fragrances, and anti-herbivory
 agents. To elucidate the mechanisms by which such diversity evolved, we
 combined leaf transcriptome data from 48 Lamiaceae species and four
 outgroups with a robust phylogeny and chemical analyses of three terpenoid
 classes (monoterpenes, sesquiterpenes, iridoids) that share and compete
 for precursors. Our integrated chemical-genomic-phylogenetic approach
 revealed that: 1) gene family expansion rather than increased enzyme
 promiscuity of terpene synthases is correlated with mono- and
 sesqui-terpene diversity; 2) differential expression of core genes within
 the iridoid biosynthetic pathway is associated with iridoid
 presence/absence; 3) generally, production of iridoids and canonical
 monoterpenes appeared to be inversely correlated; and 4) iridoid
 biosynthesis was significantly associated with expression of geraniol
 synthase, which diverts metabolic flux away from canonical monoterpenes,
 suggesting that competition for common precursors can be a central control
 point in specialized metabolism. These results suggest that multiple
 mechanisms contributed to the evolution of chemodiversity in this
 economically important family.
description: Consortium_MembersList of Mint Evolutionary Genomics Consortium members and institutional affiliations.dryad_files_master_readme_v3.rtfReadmeAncestral state reconstructions.zipAncestral state reconstructions of iridoids, monoterpenes, and sesquiterpenes across all 52 Lamiales species (Zipped folder).Expression abundances and functional annotataion of all 52 Lamiales species.zipThis folder contains expression abundance and functional annotation of all representative transcripts (the longest isoforms) of 52 Lamiales species (48 Lamiaceae species plus 4 outgroup species) (Zipped folder).GC-MS chromatograms of 52 Lamiales species.pdfGC-MS data from all 52 species (PDF file).LC-MS data of 52 Lamiales species.zipLC-MS data from all 52 species (Zipped folder).OrthoFinder derived orthologous and paralogous groups.zipAll orthogroups generated from all 52 Lamiales species and key reference proteomes using OrthoFinder/v0.7.1 usingTransDecoder-predicted peptide sequences (Zipped folder).Predicted CDS of all 52 Lamiales species.zipTransDecoder-predicted CDS sequences of all 52 species generated in this study (Zipped folder).Predicted peptides of all 52 Lamiales species.zipTransDecoder-predicted peptide sequences of all 52 species generated in this study (Zipped folder).Transcriptomes of all 52 Lamiales species.zipTranscriptomes of all 52 species generated in this study (Zipped folder).Photographs_of_Plants_Used_in_this_StudyAll 52 species, except Tectona and three outgroups (Aureolaria, Paulownia, Petrea), were kept in a common greenhouse room at the University of Florida with air-conditioning and sampled within a period of six months (July 2015-January 2016). Most plants were sampled between 10:00 AM and 1:00 PM. Mean temperature inside the greenhouse room was 76°F (67–81°F) and mean humidity was 62% (49–75%). All plants were at an adult stage and the majority were at the vegetative stage (i.e., not flowering) when sampled (see Dataset 1 for details). With the exception of four species with limited plant material, fully expanded young leaves were preferentially sampled from a single individual; however, older leaves had to be sampled, especially for species with smaller leaves, to fulfill the total amount of material needed to distribute to perform metabolite profiling and transcriptome sequencing. Photographs were taken on the day of sampling. (Zipped folder).520_genes_MAFFT_alignments.zipThis directory contains the original MAFFT alignments in relaxed Phylip multiple sequence alignment format. .phy (Zipped folder).520_genes_MAFFT_edited_alignments.zipThis directory contains all manually edited MAFFT alignments that were analyzed with RAxML. All files are in relaxed Phylip multiple sequence alignment format. _decoded_edited_alignment.phy (Zipped folder).520_genes_concatenated_alignments.zipThis directory contains 3 files: concatenated_matrix_520_genes.phy - matrix analyzed with RAxML /// concatenated_matrix_520_genes.nex - same matrix as above, but with gene partition info /// concatenated_matrix_table_520_genes.xlsx - matrix characteristics. (Zipped folder).520_genes_treefiles.zipThe gene_trees/ directory contains all gene tree files from RAxML as RAxML_bipartitions..tre /// The species_tree/ directory contains the species tree file with rotated nodes as shown in Figure 2. RAxML_bipartitions_concatenated_matrix_520_genes_rotated_nodes_Figure2.phy. (Zipped folder).