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Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda).
Taheri, Sima; Teo, Chee How; Heslop-Harrison, John S; Schwarzacher, Trude; Tan, Yew Seong; Wee, Wei Yee; Khalid, Norzulaani; Biswas, Manosh Kumar; Mutha, Naresh V R; Mohd-Yusuf, Yusmin; Gan, Han Ming; Harikrishna, Jennifer Ann.
  • Taheri S; Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia.
  • Teo CH; Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia.
  • Heslop-Harrison JS; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
  • Schwarzacher T; Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
  • Tan YS; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
  • Wee WY; Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
  • Khalid N; Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
  • Biswas MK; School of Science, Monash University Malaysia, Subang Jaya 47500, Malaysia.
  • Mutha NVR; Department of Biology, International University of Malaya-Wales, Kuala Lumpur 50603, Malaysia.
  • Mohd-Yusuf Y; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
  • Gan HM; Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
  • Harikrishna JA; Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia.
Int J Mol Sci ; 23(13)2022 Jun 30.
Article in English | MEDLINE | ID: covidwho-1934132
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Ginger / Zingiberaceae Topics: Traditional medicine Language: English Year: 2022 Document Type: Article Affiliation country: Ijms23137269

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Ginger / Zingiberaceae Topics: Traditional medicine Language: English Year: 2022 Document Type: Article Affiliation country: Ijms23137269