Taheri, Sima and Teo, Chee How and Heslop-Harrison, John S. and Schwarzacher, Trude and Tan, Yew Seong and Wee, Wei Yee and Khalid, Norzulaani and Biswas, Manosh Kumar and Mutha, Naresh V. R. and Mohd Yusuf, Yusmin 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). ISSN 1661-6596, DOI https://doi.org/10.3390/ijms23137269.
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 similar to 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 |
|---|---|
| Funders: | Universiti Malaya [Grant No: UM.C/625/1/HIR/MOE/SC/15], UK Research & Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) [Grant No: BB/P02307X/1] |
| Uncontrolled Keywords: | Boesenbergia rotunda; DNA methylation; Genome assembly; ginger; panduratin A; SSR; TE |
| Subjects: | Q Science > Q Science (General) Q Science > QD Chemistry |
| Divisions: | Faculty of Science Faculty of Science > Institute of Biological Sciences Deputy Vice Chancellor (Research & Innovation) Office > Centre for Research in Biotechnology for Agriculture |
| Depositing User: | Ms. Juhaida Abd Rahim |
| Date Deposited: | 19 Oct 2023 04:04 |
| Last Modified: | 19 Oct 2023 04:04 |
| URI: | http://eprints.um.edu.my/id/eprint/41891 |
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