Comparative Genomics of Spatholobus suberectus and Insight Into Flavonoid Biosynthesis

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.

A comparative study on photosynthetic characteristics and flavonoid metabolism between Camellia petelotii (Merr.) Sealy and Camellia impressinervis Chang &Liang

“…This finding suggests that an expansion in gene numbers explains why Camellia spp. is rich in flavonoids (Qin et al, 2020). Total leaf flavonoid concentration was significantly higher in C. impressinervis than that C. petelotii.…”

“…In C. impressinervis , the levels of these transcripts were lower in the recovery phase, associated with lower PSII efficiency (lower Fv/Fm), than the initial 300 µmol·m -2 ·s -1 treatment. The proteins encoded by these genes include PsbA (thylakoid located D1) and PsbB (chlorophyll A binding protein CP47), PsbC (CP43 protein), which are located in the PSII reaction center ( Vaistij et al., 2000 ; Raszewski and Renger, 2008 ; Chotewutmontri and Barkan, 2018 ); PsbO, Q, and R, which are the extrinsic subunits in PSII oxygen-evolving complex ( Allahverdiyeva et al., 2013 ); and PetE and F (cytochrome b559), which play important roles in the formation and stabilization of PSII structure by acting as electron carriers ( Pospisil, 2011 ; Ido et al., 2012 ).…”

Shade responses and resistant mechanisms in Spatholobus suberectus

“…In our former studies, we collected eight-year-old cultivated S. suberectus and quantified total flavonoids in all the five tissues, showing that the highest percentage of flavonoids were in the stem (Stem, ∼2.3%; flower, ∼1.3%; root, ∼1.2%; fruit, ∼0.7%; and leaf, ∼0.7%), and that catechins were the most abundant flavonoids (∼72.8%) in the stem (Catechins contents in other tissues were: Fruit, ∼22.1%; root, ∼7.4%; leaf, ∼3.9%; and flower, ∼0.5%). This result explained why stems were the traditionally used medicinal parts of S. suberectus [ 4 ]. We also detected eight forms of catechins in S. suberetus , including four non-gallated catechins (catechin, epicatechin, gallocatechin, and epigallocatechin) and their gallated forms (catechin gallate, epicatechin gallate, gallocatechin gallate, and epigallocatechin gallate).…”

Combining metabolomics and transcriptomics to reveal the potential medicinal value of rare species Glycyrrhiza squamulose

“…The isoflavone biosynthesis pathway, which is primarily distributed in leguminous plants, is unique among the eight major branches [ 17 ]. In this pathway, biosynthesis begins with flavanone production, which is catalyzed by isoflavone synthase (IFS) [ 18 ]. Hydroxyisoflavanone dehydratase (HID) converts the flavonones to isoflavones [ 19 ], genistein, and daidzein.…”