Karyological, morphological and phytochemical characteristics of medicinal plants Sophora flavescens Aiton grown from seeds collected at different localities

Lin, Tzu Che; Sung, Jih Min; Yeh, Mau Shing

doi:10.1186/1999-3110-55-5

Cited by 4 publications

(4 citation statements)

References 22 publications

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“…The contact map of Hi-C interaction for our S. flavescens genome assembly revealed nine chromosomal level scaffolds, which is consistent with the reported S. flavescens karyotype (Fig. 1d) 30 , indicating the high contiguity of the genome assembly. With respect to the completeness of the genome assembly, the BUSCO analysis with lineage "fabales_odb10" showed that 93.3% of Fabales gene orthologs could be identified in this S. flavescens genome assembly, including complete and fragment percentages of 91.3% and 2.0%, respectively (Table 1).…”

Section: Technical Validationsupporting

confidence: 89%

Chromosomal level genome assembly of medicinal plant Sophora flavescens

Qu,

Wang,

Adelson

2023

Sci Data

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Sophora flavescens is a medicinal plant in the genus Sophora of the Fabaceae family. The root of S. flavescens is known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). In this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology to de novo assemble the S. flavescens genome. We obtained a chromosomal level high-quality S. flavescens draft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs), which have recently and rapidly proliferated. This genome size is ~5x larger than its closest sequenced relative Lupinus albus L. . We annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues, and also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids. The assembled genome highlights the very different evolutionary trajectories that have occurred in recently diverged Fabaceae, leading to smaller duplicated genomes.

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Section: Technical Validationsupporting

confidence: 89%

Chromosomal level genome assembly of medicinal plant Sophora flavescens

Qu,

Wang,

Adelson

2023

Sci Data

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“…These nine scaffolds most likely correspond to the nine chromosomes of S. flavescens (Fig. 1d) Lin et al (2014). The BUSCO assessment of the final draft genome indicated that 4,898 of the 5,366 (91.3%) Fabales BUSCO groups were complete, with 86.7% and 4.6% as single-copy and duplicated BUSCOs respectively (Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…These nine scaffolds most likely correspond to the nine chromosomes of S. flavescens (Fig. 1d) Lin et al (2014).…”

Section: Chromosomal Level Draft Genome Assembly Of S Flavescensmentioning

confidence: 99%

The genome of medicinal plantSophora flavescenshas undergone significant expansion of both transposons and genes

Wang

Adelson

2023

Preprint

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Purpose:Sophora flavescensis a medicinal plant in the genus Sophora of the Fabaceae family. The root ofS. flavescensis known in China as Kushen and has a long history of wide use in multiple formulations of Traditional Chinese Medicine (TCM). However, there is little genomic information available forS. flavescens.Methods:In this study, we used third-generation Nanopore long-read sequencing technology combined with Hi-C scaffolding technology tode novoassemble theS. flavescensgenome.Results:We obtained a chromosomal level high-qualityS. flavescensdraft genome. The draft genome size is approximately 2.08 Gb, with more than 80% annotated as Transposable Elements (TEs), which have recently and rapidly proliferated. This genome size is ~5x larger than its closest sequenced relativeLupinus albus l.. We annotated 60,485 genes and examined their expression profiles in leaf, stem and root tissues, and also characterised the genes and pathways involved in the biosynthesis of major bioactive compounds, including alkaloids, flavonoids and isoflavonoids.Conclusion:The assembled genome highlights the very different evolutionary trajectories that have occurred in recently diverged Fabaceae, leading to smaller duplicated genomes vs larger genomes resulting from TE expansion. Our assembly provides valuable resources for conservation, genetic research and breeding ofS. flavescens.

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“…Relatively little is known about the extent of genetic and phenotypic diversity in S. flavescens . In a study of plants from four locations (three in China and one in Taiwan), Lin et al (2014) established that the plants were diploid (2 n = 18) and observed statistically significant variation in biochemical composition (matrine, oxymatrine, flavonoids, and antioxidants) and 11 morphological traits among field-grown plants.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Genetic Diversity in the Traditional Chinese Medicine Plant ‘Kushen’ (Sophora flavescens Ait.)

et al. 2021

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Kushen root, from the woody legume Sophora flavescens, is a traditional Chinese medicine that is a key ingredient in several promising cancer treatments. This activity is attributed in part to two quinolizidine alkaloids (QAs), oxymatrine and matrine, that have a variety of therapeutic activities in vitro. Genetic selection is needed to adapt S. flavescens for cultivation and to improve productivity and product quality. Genetic diversity of S. flavescens was investigated using genotyping-by-sequencing (GBS) on 85 plants grown from seeds collected from 9 provinces of China. DArTSeq provided over 10,000 single nucleotide polymorphism (SNP) markers, 1636 of which were used in phylogenetic analysis to reveal clear regional differences for S. flavescens. One accession from each region was selected for PCR-sequencing to identify gene-specific SNPs in the first two QA pathway genes, lysine decarboxylase (LDC) and copper amine oxidase (CAO). To obtain SfCAO sequence for primer design we used a targeted transcript capture and assembly strategy using publicly available RNA sequencing data. Partial gene sequence analysis of SfCAO revealed two recently duplicated genes, SfCAO1 and SfCAO2, in contrast to the single gene found in the QA-producing legume Lupinus angustifolius. We demonstrate high efficiency converting SNPs to Kompetitive Allele Specific PCR (KASP) markers developing 27 new KASP markers, 17 from DArTSeq data, 7 for SfLDC, and 3 for SfCAO1. To complement this genetic diversity analysis a field trial site has been established in South Australia, providing access to diverse S. flavescens material for morphological, transcriptomic, and QA metabolite analysis. Analysis of dissected flower buds revealed that anthesis occurs before buds fully open suggesting a potential for S. flavescens to be an inbreeding species, however this is not supported by the relatively high level of heterozygosity observed. Two plants from the field trial site were analysed by quantitative real-time PCR and levels of matrine and oxymatrine were assessed in a variety of tissues. We are now in a strong position to select diverse plants for crosses to accelerate the process of genetic selection needed to adapt kushen to cultivation and improve productivity and product quality.

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Karyological, morphological and phytochemical characteristics of medicinal plants Sophora flavescens Aiton grown from seeds collected at different localities

Cited by 4 publications

References 22 publications

Chromosomal level genome assembly of medicinal plant Sophora flavescens

Chromosomal level genome assembly of medicinal plant Sophora flavescens

The genome of medicinal plantSophora flavescenshas undergone significant expansion of both transposons and genes

Analysis of Genetic Diversity in the Traditional Chinese Medicine Plant ‘Kushen’ (Sophora flavescens Ait.)

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