In a groundbreaking advancement in tropical plant genomics, researchers have unveiled the complete chromosomal reference genome of Merremia boisiana, a notoriously fast-growing climbing vine native to the tropical rainforests. Known for its aggressive growth rate exceeding 12 centimeters per day and its vibrant golden blossoms, M. boisiana has long been a subject of ecological concern due to its tendency to overwhelm native vegetation and disrupt delicate forest ecosystems. Until now, the genetic foundations that fuel its invasive vigor remained largely unexplored, limiting efforts to manage its spread and harness its unique biological traits. This latest study delivers unprecedented insights into the genomic architecture underlying the remarkable adaptability and rapid growth dynamics of this tropical powerhouse.
The research team, led by Fei Chen and Wenquan Wang from Hainan University, employed cutting-edge sequencing technologies to achieve a high-quality chromosome-level assembly of the M. boisiana genome. Initial genome size estimation was conducted through flow cytometry, calculating an approximate genome size of 523 megabases (Mb). Building on this estimate, the researchers generated a robust sequencing dataset, accumulating 68 gigabases (Gb) of high-accuracy Illumina paired-end reads alongside 59.5 Gb of long-read data from Oxford Nanopore sequencing platforms. This combined approach ensured an outstanding coverage of over 130% relative to the estimated genome size, laying a solid foundation for a comprehensive assembly.
Scaffolding the genome into chromosomal sequences necessitated the integration of high-throughput chromosome conformation capture (Hi-C) data, totaling 141 Gb, which unveiled the spatial organization and linkage information of the genome. The result was an assembly that elegantly resolved into 15 chromosomes, with a final genome size registration of 510 Mb—closely aligning with the preliminary estimates. Genome completeness was rigorously evaluated using Benchmarking Universal Single-Copy Orthologs (BUSCO), revealing a remarkable completeness score of 98.7%. Additional metrics, including an LTR Assembly Index (LAI) of 11.27 and a Merqury quality value of 33.2, further corroborated the assembly’s exceptional integrity, designating it as a reliable chromosomal reference genome.
Comprehensive gene annotation strategies combined de novo prediction methods, homology-based alignments, and transcriptomic data to identify genetic elements with high precision. This integrative approach led to the annotation of 37,389 protein-coding genes within the genome, supported by a BUSCO completeness of 99.2%, underscoring the exhaustiveness of gene representation. Intriguingly, repeat sequence analyses disclosed that repetitive elements constitute approximately 60.93% of the genome, with Long Terminal Repeat (LTR) retrotransposons alone accounting for 18.78%. These repetitive sequences have profound implications on genome structure and evolution, often influencing gene regulation and chromosomal dynamics.
Extending beyond M. boisiana itself, the study incorporated a comparative genomics framework involving 62 plant species to contextualize evolutionary relationships within the Convolvulaceae family. These analyses positioned M. boisiana in close phylogenetic proximity to the genus Ipomoea, which notably includes economically significant crops such as the sweet potato (Ipomoea batatas). Divergence between these lineages was estimated to have occurred roughly 20 million years ago. This evolutionary timeframe is critical for interpreting the genomic alterations that underpin species-specific traits and adaptability.
Gene family analyses illuminated a striking expansion in M. boisiana, featuring 1,377 gene families that have proliferated relative to its relatives. Many of these expanded genes are implicated in hormone biosynthesis pathways and stress response mechanisms, suggesting a genetic basis for the vine’s invasive growth and adaptability in dynamic tropical environments. The expansion of such gene clusters may enhance physiological responses to environmental stimuli, conferring resilience and competitive advantages over co-occurring plant species.
Adding another layer of complexity, ancestral genome reconstruction pointed to a historic whole-genome triplication event followed by extensive chromosomal rearrangements. This polyploidization, coupled with subsequent genomic reshaping, likely shaped the extant 15-chromosome karyotype, facilitating genetic diversification and innovation. These rearrangements are hypothesized to have preserved and diversified gene families particularly involved in hormone regulation, providing a mechanistic explanation for institutional traits observed in M. boisiana.
A hallmark of this genome is its rich repertoire of hormone biosynthesis genes, encompassing auxin, salicylic acid, abscisic acid (ABA), and jasmonic acid pathways. These phytohormonal circuits are central to plant growth, development, and stress adaptation. Gene expression profiling revealed many of these genes exhibit root-specific activity, which is consistent with enhanced root growth and nutrient acquisition supportive of the vine’s rapid vertical and lateral expansion. The interplay of these hormonal pathways conveys sophisticated regulatory networks enabling M. boisiana to thrive in competitive rainforest niches.
Further insights into functional genomics were gained through orthogroup and gene ontology analyses, which highlighted unique and expanded gene domains within the Convolvulaceae family. These functional enrichments inform potential molecular mechanisms of adaptability and invasiveness, furnishing a valuable resource for gene mining endeavors. Such knowledge paves the way for targeted comparative studies and molecular breeding efforts aimed at either mitigating invasive spread or harnessing beneficial traits for crop development.
The comprehensive genome assembly presented here serves as a benchmark for future research into tropical vine biology and evolution. By elucidating the genetic drivers of M. boisiana’s exceptional growth rates and environmental resilience, the study bridges fundamental plant genomics and applied ecological management. This chromosome-level reference provides an indispensable platform for advanced investigation into gene function, signaling pathways, and potential genetic interventions.
Beyond its immediate scientific impact, the insights gleaned from M. boisiana’s genome hold potential translational benefits for agriculture and conservation. Understanding the molecular underpinnings of rapid growth and robustness may inspire innovative strategies to improve crop yield, stress tolerance, and adaptability—traits of paramount importance under the looming challenges of climate change and biodiversity loss. Equally, such genomic knowledge equips ecologists and forest managers with the molecular tools to better monitor and control invasive species that threaten tropical ecosystems worldwide.
In summary, this landmark study delineates the genomic landscape of one of the world’s fastest-growing tropical vines, offering profound implications for plant science, ecology, and biotechnology. The integration of advanced sequencing technologies, meticulous annotation, and evolutionary analyses not only demystifies the biological secrets of Merremia boisiana but also enriches the broader narrative of plant adaptation and diversification in tropical rainforests. This work stands as a testament to the power of modern genomics in decoding complex biological phenomena and harnessing nature’s genetic bounty for sustainable futures.
Subject of Research: Not applicable
Article Title: Chromosomal reference genome of Merremia boisiana: unveiling the secrets of the tropical rainforest’s killer plant
News Publication Date: 24-Mar-2025
Web References:
http://dx.doi.org/10.48130/tp-0025-0007
References:
10.48130/tp-0025-0007
Image Credits: The authors
Keywords: Mathematics, Research methods
