Academic Journal
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
| العنوان: | 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 |
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| المؤلفون: | 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 |
| المساهمون: | Michigan State University East Lansing, Michigan State University System, University of Florida Gainesville (UF), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System |
| المصدر: | EISSN: 2047-217X ; GigaScience ; https://hal.science/hal-04701224 ; GigaScience, 2024, 8 (3), pp.giz005. ⟨10.1093/gigascience/giz005⟩ |
| بيانات النشر: | HAL CCSD Oxford Univ Press |
| سنة النشر: | 2024 |
| المجموعة: | Université Jean Monnet – Saint-Etienne: HAL |
| مصطلحات موضوعية: | teak, chromosomal-scale assembly, terpene synthases, tandem-duplicated genes, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] |
| الوصف: | International audience ; 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. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| DOI: | 10.1093/gigascience/giz005 |
| الاتاحة: | https://hal.science/hal-04701224 https://hal.science/hal-04701224v1/document https://hal.science/hal-04701224v1/file/2019-Zhao%20et%20al-GigaScience-Tectona%20grandis%20genome.pdf https://doi.org/10.1093/gigascience/giz005 |
| Rights: | info:eu-repo/semantics/OpenAccess |
| رقم الانضمام: | edsbas.733C4CFC |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/gigascience/giz005 |
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