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

• Published in: Gigascience Vol. 8; no. 3
• Main Authors: Zhao, Dongyan, Hamilton, John P, Bhat, Wajid Waheed, Johnson, Sean R, Godden, Grant T, Kinser, Taliesin J, Boachon, Benoît, Dudareva, Natalia, Soltis, Douglas E, Soltis, Pamela S, Hamberger, Bjoern, Buell, C Robin
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.03.2019
• Subjects: Alkyl and Aryl Transferases - genetics; Annotations; Assembly; Biological Products - metabolism; Biosynthesis; Biosynthetic Pathways - genetics; Chromatin; Chromosomes; Chromosomes, Plant - genetics; Conformation; Cytochrome P-450 Enzyme System - metabolism; Data Note; Deforestation; Enzymatic activity; Gene Duplication; Gene Expression Regulation, Plant; Genes; Genes, Plant; Genome, Plant; Genomes; Hardwoods; Lamiaceae - genetics; Molecular Sequence Annotation; Natural products; Phylogeny; Propagation; Reproduction (copying); Tectona grandis; Terpenes; Transcriptome - genetics; Transcriptomes; tandem-duplicated genes; terpene synthases; teak; chromosomal-scale assembly
• ISSN: 2047-217X; 2047-217X
• DOI: 10.1093/gigascience/giz005

Abstract 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 Pacific Biosciences 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.