Discover how complete genome sequencing reveals the genetic secrets behind the medicinal properties of the "Chicken Blood Vine" and its conservation challenges.
Deep in the forests of Southern China grows a remarkable vine known as Spatholobus suberectus, a plant that has been used for centuries in traditional medicine. When its stem is cut, it bleeds a vivid, red sap, earning it the local name "Ji Xue Teng" or "Chicken Blood Vine." For generations, traditional healers have used this plant to treat blood disorders, rheumatism, and menstrual problems. However, its long growth cycle—requiring at least seven years to mature—coupled with increasing demand has pushed wild populations to the verge of extinction 1 2 .
Requires at least 7 years to mature, limiting supply and increasing pressure on wild populations.
In 2019, scientists sequenced the complete genome, opening new possibilities for research and conservation.
In 2019, a team of scientists tackled this challenge with a modern approach: they sequenced the complete genome of Spatholobus suberectus 1 . This groundbreaking work, published in Scientific Data, opened a new window into understanding what makes this plant medically valuable at the most fundamental level—its genetic code. The sequencing of its 798-million-letter genome provides science with a powerful tool to uncover the secrets of its medicinal properties and potentially solve its conservation crisis 1 5 .
The publication of the S. suberectus genome provided the first comprehensive look at the genetic makeup of this important medicinal plant. The draft genome revealed a diploid species (with two sets of chromosomes) with a total of nine chromosomes 1 . Through advanced sequencing technologies, researchers assembled a genome approximately 798 megabases (Mb) in size, with an impressive 93.73% of the sequence anchored to its nine chromosomes 1 3 .
Protein-coding genes
Genes functionally annotated
Almost half (47.82%) of the genome consists of repetitive elements, with 17.32% being long terminal repeat retrotransposons 1 .
The primary medicinal compounds in S. suberectus are flavonoids—a class of plant compounds with demonstrated antioxidant, anti-inflammatory, anti-viral, and anti-cancer properties 2 4 . Four key flavonoid compounds have been identified as particularly important:
The genomic research revealed how S. suberectus efficiently produces these valuable compounds. A key discovery was the expansion of the isoflavone synthase (IFS) gene family from a single copy in the Leguminosae ancestor to four copies in S. suberectus 2 7 . This gene duplication likely accelerates the biosynthesis of flavonoids, explaining why this plant is particularly rich in these medicinal compounds.
Beyond the genes that directly build flavonoids, researchers discovered an intricate regulatory network that controls flavonoid production. Two key transcription factor families—MYB and bHLH—emerged as master regulators of this process 4 .
Remarkably, over 70% of the promoters of genes involved in flavonoid biosynthesis contain MYB binding sites, confirming the crucial role of these transcription factors in regulating the production of medicinal compounds 6 .
The sequencing of the S. suberectus genome represented a sophisticated scientific achievement that utilized multiple cutting-edge technologies. The research team employed an innovative multi-platform approach to overcome the challenges of assembling a complex plant genome 1 .
Researchers collected fresh young leaves from 8-year-old S. suberectus plants at the Guangxi Botanical Garden of Medicinal Plants in China. The use of mature plants ensured the DNA represented the complete genetic code 1 .
Total genomic DNA was isolated using specialized plant DNA kits, carefully following manufacturer instructions to preserve the quality and integrity of the genetic material 1 .
The team employed three advanced sequencing technologies to generate complementary data: Illumina HiSeq X Ten, PacBio SMRT Sequencing, and 10X Genomics GemCode Platform 1 .
The team employed chromatin interaction mapping (Hi-C) technology, generating 233.19 Gb of data to map how different parts of the genome are organized in three-dimensional space 1 .
The long reads from PacBio sequencing were assembled using the FALCON assembler, specifically designed for long-read data. The assembly was then polished with Illumina short reads using the Pilon tool for error correction 1 .
Protein-coding genes were predicted using a combination of homology-based predictions, de novo predictions, and transcriptome-based predictions 1 .
The final assembly resulted in a high-quality draft genome with a scaffold N50 of 86.99 Mb and the longest scaffold being 103.57 Mb 1 . These metrics indicate a highly continuous assembly, which is remarkable for a plant genome of this size.
The success of this project marked S. suberectus as the first reported genome from the Subtribe Erythrininae Benth, which contains nine genera of Leguminosae 1 . This filled an important gap in our genomic knowledge of legume plants and provided a valuable resource for comparative genomic studies.
Genomic research relies on specialized reagents and technologies. The S. suberectus genome project utilized several crucial tools that represent the state-of-the-art in genomic science.
The sequencing of the S. suberectus genome has opened numerous avenues for future research and practical applications. Subsequent studies have built upon this genomic foundation to deepen our understanding of this medicinal plant.
In 2024, researchers used PacBio single-molecule real-time (SMRT) sequencing to generate a full-length transcriptome, identifying 61,548 transcripts including 12,311 novel gene loci and 6,781 transcription factors 6 . This more complete picture of the transcriptome provides deeper insights into the functional elements of the genome.
Scientists have begun to validate the function of specific genes identified in the genome. For instance, researchers demonstrated that SsbHLH112, a gene identified through genome analysis, significantly increased flavonoid and catechin accumulation when overexpressed in tobacco plants 4 . Similarly, SsMYB158 was shown to regulate flavonoid biosynthesis 6 . These functional studies confirm the practical value of the genomic information.
The genomic resources now available for S. suberectus offer promising tools for addressing its conservation crisis 1 2 . Researchers can use this genetic information to:
For selective breeding of high-yielding varieties
To produce valuable flavonoids without harvesting wild plants
Through genetic selection
Of medicinal material to combat adulteration 9
The draft genome of Spatholobus suberectus represents far more than just an technical achievement in genomics—it embodies the powerful convergence of traditional medicine and modern biotechnology. This genetic blueprint unlocks the secrets of what makes the "Chicken Blood Vine" medically valuable, revealing the genetic machinery behind its flavonoid production and evolutionary history.
As research continues to build upon this foundation, we move closer to solving the conservation challenges facing this valuable medicinal plant while potentially unlocking new therapeutic applications of its compounds. The S. suberectus genome story demonstrates how modern genomics can breathe new life into ancient medicinal wisdom, ensuring that these natural remedies remain available for future generations.
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