DOI: 10.5061/dryad.77b2422
title: Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

description: Background: Teak, a member of the Lamiaceae family, produces one of the
 most expensive hardwoods in the world. High demand coupled with
 deforestation have caused a decrease in natural teak forests, and future
 supplies will be reliant on teak plantations. Hence, selection of teak
 tree varieties for clonal propagation with superior growth performance is
 of great importance, and access to high-quality genetic and genomic
 resources can accelerate the selection process by identifying genes
 underlying desired traits. Findings: To facilitate teak research and
 variety improvement, we generated a highly contiguous, chromosomal-scale
 genome assembly using high-coverage PacBio long reads coupled with
 high-throughput chromatin conformation capture. Of the 18 teak
 chromosomes, we generated 17 near-complete pseudomolecules with one
 chromosome present as two chromosome arm scaffolds. Genome annotation
 yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and
 41,155 had Pfam domain and expression evidence, respectively. We
 identified 14 clusters of tandem-duplicated terpene synthases (TPSs),
 genes central to the biosynthesis of terpenes which are involved in plant
 defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs
 highly expressed in woody tissues, of which, 8 were in tandem, revealing
 the importance of resolving tandemly duplicated genes and the quality of
 the assembly and annotation. We also validated the enzymatic activity of
 four TPSs to demonstrate the function of key TPSs. Conclusions: In
 summary, this high-quality chromosomal-scale assembly and functional
 annotation of the teak genome will facilitate the discovery of candidate
 genes related to traits critical for sustainable production of teak and
 for anti-insecticidal natural products.
description: teak_tectona_grandis_26Jun2018_7GlFM_fmt_tp.fafasta sequences of the assemblyteak.working_models_HiC.cdna_con_sorted.facDNA sequences of all isoforms of the working gene setteak.working_models_HiC.cds_con_sorted.faCDS of all isoforms of the working gene setteak.working_models_HiC.pep_con_sorted.faPeptide sequence of all isoforms of the working gene setteak.working_models_HiC_fmtDes_con_sorted.gffGFF of all isoforms of the working gene setteak_hc_models_HiC_con_sorted_modiGeneID.gffGFF of all high-confidence gene modelsteak_hc_models_HiC.cdna_con_sorted_modiGeneID.facDNA sequences of all high-confidence gene modelsteak_hc_models_HiC.cds_con_sorted_modiGeneID.faCDS of all high-confidence gene modelsteak_hc_models_HiC.pep_con_sorted_modiGeneID.faPeptide sequences of all high-confidence gene modelsteak_repr_hc_models_HiC_con_sorted_modiGeneID.gffGFF of representative high-confidence gene modelsteak_repr_hc_models_HiC.cdna_con_sorted_modiGeneID.facDNA sequences of representative high-confidence gene modelsteak_repr_hc_models_HiC.cds_con_sorted_modiGeneID.faCDS of representative high-confidence gene modelsteak_repr_hc_models_HiC.pep_con_sorted_modiGeneID.faPeptide sequences of representative high-confidence gene modelsteak_working_gene_fpkm_matrix_con_sorted.txtExpression abundances of the working gene set were estimated using cufflinks RNAseq experiment atlas from NCBI SRA BioProject PRJNA2876042018.10.23-teak-data-readme.docxReadme