Abstract
Spatholobus suberectus Dunn (S. suberectus), has been widely used in traditional medicines plant source of the Leguminosae family. Its vine stem of which plays an important role in the prevention and treatment of various diseases because it contains various flavonoids. Comparative genome analysis suggested well-conserved genomic components and genetic collinearity between the genome of S. suberectus and other genera of Leguminosae such as Glycine max. We discovered two whole genome duplications (WGD) events in S. suberectus and G. max lineage underwent a WGD after speciation from S. suberectus. The determination of expansion and contractions of orthologous gene families revealed 1,001 expanded gene families and 3,649 contracted gene families in the S. suberectus lineage. Comparing to the model plants, many novel flavonoid biosynthesis-related genes were predicted in the genome of S. suberectus, and the expression patterns of these genes in the roots are similar to those in the stems [such as the isoflavone synthase (IFS) genes]. The expansion of IFS from a single copy in the Leguminosae ancestor to four copies in S. suberectus, will accelerate the biosynthesis of flavonoids. MYB genes are widely involved in plant flavonoid biosynthesis and the most abundant member of the TF family in S. suberectus. Activated retrotransponson positive regulates the accumulation of flavonoid in S. suberectus by introducing the cis-elements of tissue-specific expressed MYBs. Our study not only provides significant insight into the evolution of specific flavonoid biosynthetic pathways in S. suberectus, but also would facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding for alleviating resource shortage of S. suberectus.
Highlights
Spatholobus suberectus Dunn (S. suberectus) is an Leguminosae popularly used in Chinese Traditional Medicine
To investigate the evolution of S. suberectus genome, we compared it with the genome of seven other sequenced plant species (Figure 2A), namely, G. max, L. japonicus, G. uralensis, Cicer arietinum, M. truncatula, and Cajanus cajan, which are Leguminosae plants, and Arabidopsis thaliana as an outgroup
A total of 1,073 single-copy orthologs were obtained from eight species, indicating that the Leguminosae plants can be divided into galegoid (M. truncatula, five genes unique to G. uralensis and C. arietinum) and Millettioid (G. max, C. cajan, and S. suberectus) clades
Summary
Spatholobus suberectus Dunn (S. suberectus) is an Leguminosae popularly used in Chinese Traditional Medicine. Pharmacological and clinical studies have demonstrated that the dried stems of S. suberectus (Figure 1) exhibit various functions and flavonoids are the main bioactive components (Wang et al, 2011; Zhou et al, 2017). S. suberectus is widely used in patented Chinese medicines, and the market demand for the wild resource is increasing rapidly. The crud drug of S. suberectus must grow for more than 7 years before it can be used in medicine. Owing to its long growth cycle and increased use in medicines, the wild resources of S. suberectus in China are on the verge of extinction
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