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Gigascience. 2019 Mar 1;8(3). pii: giz005. doi: 10.1093/gigascience/giz005.

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.

Author information

1
Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA.
2
Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA.
3
Department of Pharmacology and Toxicology, Michigan State University, 1355 Bogue Street, East Lansing, MI 48824, USA.
4
Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA.
5
Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL 32611, USA.
6
Department of Biochemistry, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
7
Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48872, USA.
8
MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48872, USA.

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.

KEYWORDS:

chromosomal-scale assembly; tandem-duplicated genes; teak; terpene synthases

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