Merremia boisiana, a captivating species endemic to tropical rainforest habitats, belongs to the esteemed Convolvulaceae family. Renowned for its dazzling golden flowers and exceptional growth rate. This plant stands as a vital component of the rainforest ecosystem, albeit endowed with potentially lethal attributes. Despite its ecological significance, the lack of a comprehensive genomic sequence has hindered our understanding of its formidable strangling capabilities and the genetic underpinnings of its tropical adaptability. Here, we report the first high-quality genome assembly for M. boisiana, achieved through advanced long-read sequencing technology. In this groundbreaking genomic endeavor, we have leveraged cutting-edge long-read sequencing technologies to assemble a high-quality (contig N50 reaching 21 Mb, with an assembly completeness of 98.7%) in 510 Mb genome of M. boisiana. This achievement encompasses the elucidation of 15 chromosomes and the annotation of an impressive 37,389 protein-coding genes, yielding an annotation rate of 99.2%. Our investigation delves into the realms of biodiversity, resistance traits, and environmental adaptability, offering profound insights into the unique biological traits of this ecologically significant rainforest species. This research not only sheds light on the intricacies of M. boisiana but also presents potential avenues for ecological studies. Our findings are poised to catalyze further research into this enigmatic rainforest killer plant, fostering its sustainable utilization while simultaneously broadening our horizons in the realm of tropical plant genomics. This endeavor represents a significant step forward in unraveling the mysteries of nature’s most intricate life forms and their contributions to the global ecosystem.

The dimensions of phylogenetic research have expanded to encompass the study of large-scale populations at the microevolutionary level and comparisons between different species or taxonomic units at the macroevolutionary level. Traditional phylogenetic tools often struggle to handle the diverse and complex data required for these different evolutionary scales. In response to this challenge, we introduce PhyloForge, a robust tool designed to seamlessly integrate the demands of both micro- and macro-evolution, comprehensively utilizing diverse phylogenomic signals, such as genes, SNPs, structural variations, as well as mitochondrial and chloroplast genomes. PhyloForge’s innovation lies in its capability to seamlessly integrate multiple phylogenomic signals, enabling unified analysis of multidimensional genomic data. This unique feature empowers researchers to gain a more comprehensive understanding of diverse aspects of biological evolution. PhyloForge not only provides highly customizable analysis tools for experienced researchers but also features an intuitively designed interface, facilitating effortless phylogenetic analysis for beginners. Extensive testing across various domains, including animals, plants, and fungi, attests to its broad applicability in the field of phylogenetics. In summary, PhyloForge has significant potential in the era of large-scale genomics, offering a new perspective and toolset for a deeper understanding of the evolution of life. PhyloForge codes could be found in GitHub (https://github.com/wangyayaya/PhyloForge/) and the program could be installed in Conda (https://anaconda.org/wangxiaobei/phyloforge).