Taheri, Sima and Teo, Chee How and Heslop-Harrison, John S. and Schwarzacher, Trude and Tan, Yew Seong and Wee, Wei Yee and Norzulaani, Khalid and Biswas, Manosh Kumar and Mutha, Naresh V. R. and Yusmin, Mohd-Yusuf and Gan, Han Ming * and Harikrishna, Jennifer Ann (2022) Genome assembly and analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda). International Journal of Molecular Sciences, 23 (13). pp. 1-26. ISSN 1422-0067
Full text not available from this repository.Abstract
Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.
| Item Type: | Article |
|---|---|
| Additional Information: | This article belongs to the Special Issue 21st Anniversary of IJMS: Advances in Molecular Genetics and Genomics |
| Uncontrolled Keywords: | Boesenbergia rotunda; DNA methylation; SSR; TE; genome assembly; ginger; panduratin A. |
| Subjects: | Q Science > QH Natural history Q Science > QH Natural history > QH426 Genetics |
| Divisions: | Others > Non Sunway Academics Sunway University > School of Medical and Life Sciences [formerly School of Healthcare and Medical Sciences until 2020] > Dept. Biological Sciences |
| Depositing User: | Ms Yong Yee Chan |
| Related URLs: | |
| Date Deposited: | 14 Aug 2024 03:52 |
| Last Modified: | 14 Aug 2024 03:52 |
| URI: | http://eprints.sunway.edu.my/id/eprint/3136 |
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