DOI: 10.5061/dryad.4mw6m90kp
title: Data from: A high-quality genome assembly of the tetraploid Teucrium chamaedrys unveils a recent whole genome duplication and a large biosynthetic gene cluster for diterpenoid metabolism

description: Teucrium chamaedrys, also called wall germander, is a small woody shrub
 native to the Mediterranean region. Its name is derived from the Greek
 words meaning ‘ground oak’, since its tiny leaves resemble those of an oak
 tree. Teucrium species are prolific producers of diterpene skeletons and
 compounds, which afford them valuable properties widely co-opted in
 traditional and Western medicines. Specifically, Teucrium is well known
 for making clerodane-type diterpenoids that are produced from the backbone
 kolavanyl diphosphate. In order to begin to elucidate some of the complex
 biosynthetic pathways of these medicinal compounds, we identified and
 functionally characterized several kolavanyl diphosphate synthases
 from T. chamaedrys. Along the way, we discovered the genome of
 this species to be one of the largest genomes published from the Lamiaceae
 family, to which it belongs. This tetraploid, 3 Gbp genome is especially
 rich in diterpene synthase genes, with 74 putative sequences identified.
 The vast majority of these diterpene synthase genes belong to four genomic
 loci, representative of the four copies of the genome. Comparative
 genomics show that this cluster is mirrored in the closely related
 species, T. marum. Along with the presence of several cytochrome p450
 sequences, this region is one of the largest biosynthetic gene clusters
 identified to date. Its remarkable chemistry and model tetraploidy make T.
 chamaedrys an interesting model for studying genomic evolution and
 adaptation in plants.
description: # Data from: A high-quality genome assembly of the tetraploid *Teucrium
 chamaedrys* unveils a recent whole genome duplication and a large
 biosynthetic gene cluster for diterpenoid metabolism ### Genome files:
 Finalized files for the genome assembly and annotation of *Teucrium
 chamaedrys*. Assembly is derived from Nanopore and Illumina reads,
 assembled with Flye and corrected with BWA. The annotation was created
 using Maker and Braker. * Teucrium_chamaedrys_final_assembly.fasta *
 Teucrium_chamaedrys_final_annotation.gff3 *
 Teucrium_chamaedrys_final_proteins.fasta *
 Teucrium_chamaedrys_final_transcripts.fasta ### Phylogeny files: FASTA
 file containing the amino acid sequence of each predicted diTPS in
 Teucrium chamaedrys, Teucrium marum, and Teucrium canadense. Sequences
 were predicted using BLAST from protein annotation files. This file
 represents figure 3A. * teucrium_sequences_for_tree.fasta ### GC-MS files:
 Date of file name indicates date run on instrument. All include DXS +
 GGPPS even if not explicitly stated. All samples were extracted in hexane
 and ran on an Agilent 7890 A. These files represent figure 4. *
 Teucrium_GC-MS.zip * 20240717_AEB282_DXS-GGPPS.CDF *
 20240717_AEB284_ArTPS2.CDF * 20240717_AEB288_ArTPS2-SsSS.CDF *
 20240717_AEB291_TchaTPS1.CDF * 20240717_AEB292_TchaTPS2.CDF *
 20240717_AEB293_TchaTPS3.CDF * 20240717_AEB294_TcanTPS1.CDF *
 20240717_AEB296_TchaTPS1-SsSS.CDF * 20240717_AEB297_TchaTPS2-SsSS.CDF *
 20240717_AEB298_TchaTPS3-SsSS.CDF * 20240717_AEB299_TcanTPS1-SsSS.CDF ###
 Code/Software: .CDF files can be viewed in the open source [OpenChrom
 software](https://www.openchrom.net/).