Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda)

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.

Genome sequencing of Syzygium cumini (jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

“…The main classes of plant secondary metabolites are terpenoids, phenolic compounds, and alkaloids. The phenylpropanoid-flavonoid (PF) biosynthesis pathway is the key pathway for producing a wide range of phenolic compounds, such as flavonol, lignin, and anthocyanin ( Taheri et al., 2022 ). Flavonoids and phenylpropanoids were the most abundant bioactive compounds in the fruit extracts of S. cumini , showing a wide range of pharmacological activities and can be used as preventive measures in many diseases, including type-2 diabetes ( Correia et al., 2023 ).…”

“… Adaptive evolution of the phenylpropanoid-flavonoid (PF) biosynthesis pathway ( Yadav et al., 2020 ; Taheri et al., 2022 ). PAL , Phenylalanine ammonia lyase; C4H , Cinnamic acid 4-hydroxylase; 4CL , 4-hydroxycinnamoyl-CoA ligase; HCT , Shikimate O-hydroxycinnamoyltransferase; C3’H , p-coumaroyl shikimate 3′-hydroxylase; CCoAOMT , Caffeoyl-CoA O-methyltransferase; COMT , Caffeic acid 3-O-methyltransferase; CCR , Cinnamoyl-CoA reductase; F5H , Ferulate-5-hydroxylase; CAD , Cinnamyl-alcohol dehydrogenase; PER , Peroxidase; CHS , Chalcone synthase; CHI , Chalcone isomerase; F3H , Flavanone 3-hydroxylase; F3’H , Flavonoid 3′-monooxygenase; FLS , Flavonol synthase; DFR , Dihydroflavonol 4-reductase; ANS , Anthocyanidin synthase.…”

Genome sequencing of Syzygium cumini (Jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

“…The main classes of plant secondary metabolites are terpenoids, phenolic compounds, and alkaloids. The phenylpropanoid-flavonoid (PF) biosynthesis pathway is the key pathway for producing a wide range of phenolic compounds, such as flavonol, lignin, and anthocyanin [65]. Flavonoids and phenylpropanoids were the most abundant bioactive compounds in the fruit extracts of S. cumini, showing a wide range of pharmacological activities and can be used as preventive measures in many diseases, including type-2 diabetes [8].…”

“…Genes involved in the common phenylpropanoid pathway (conversion of phenylalanine to p-Coumaroyl CoA) showed gene family expansion, unique substitution with functional impact, and high gene expression (TPM > 1). p-Coumaroyl CoA, formed in the phenylpropanoid pathway, is also a precursor to flavonol, anthocyanin, and lignin biosynthesis [65,66]. In the downstream phenylpropanoid pathway, genes showed gene family expansion/contraction, signatures of adaptive evolution, and high gene expression (TPM > 1).…”

Relationship between Phenotypes and Chemical Profiling of Boesenbergia rotunda Collected from Different Habitats of Northern Thailand

“…However, the genetic similarity of the cultivated B. rotunda (Krachai Ban) and the wild type (Krachai Pah) with the identical morphological characteristics of having a small rhizome, green color on both sides of lamina and midrib, had been found [39]. The genome assembly of B. rotunda (2n = 36) of the vegetatively propagated species illustrated an unusually high heterozygosity of 3.01%, advising that the cultivated species may have undergone whole-genome duplication events or hybrid origin [40]. adapt to a variety of environmental stresses, thereby inducing the biosynthesis of the secondary metabolites.…”