TY - JOUR T1 - Genome assembly and analysis of the flavonoid and phenylpropanoid biosynthetic pathways in Fingerroot ginger (<em>Boesenbergia rotunda</em>) JF - bioRxiv DO - 10.1101/2022.05.11.491478 SP - 2022.05.11.491478 AU - Sima Taheri AU - Teo Chee How AU - John S. Heslop-Harrison AU - Trude Schwarzacher AU - Tan Yew Seong AU - Wee Wei Yee AU - Norzulaani Khalid AU - Manosh Kumar Biswas AU - Naresh V R Mutha AU - Yusmin Mohd-Yusuf AU - Han Ming Gan AU - Jennifer Ann Harikrishna Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/05/11/2022.05.11.491478.abstract N2 - Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have high flavanone and chalcone content. Here we report 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 was assembled as 27,491 contigs with N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has 72% repeat content, with class I TEs occupying ∼67% of the assembled genome. Fluorescence In Situ Hybridization of the 18 chromosome pairs at metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. SSR analysis identified 238,441 gSSRs and 4,604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in leaf to 53% CpG, 18% CHG and 25% CHH in embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in watery callus. B rotunda has a relatively large genome with 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.Competing Interest StatementThe authors have declared no competing interest. ER -