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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

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 c...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394206/
https://www.ncbi.nlm.nih.gov/pubmed/30698701
http://dx.doi.org/10.1093/gigascience/giz005
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author 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
author_facet 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
author_sort Zhao, Dongyan
collection PubMed
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 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.
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spelling pubmed-63942062019-03-05 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 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 Gigascience Data Note 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. Oxford University Press 2019-01-30 /pmc/articles/PMC6394206/ /pubmed/30698701 http://dx.doi.org/10.1093/gigascience/giz005 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
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
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
title 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
title_full 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
title_fullStr 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
title_full_unstemmed 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
title_short 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
title_sort chromosomal-scale genome assembly of tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394206/
https://www.ncbi.nlm.nih.gov/pubmed/30698701
http://dx.doi.org/10.1093/gigascience/giz005
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