Orchids constitute approximately 10% of flowering plant species. However, only about 10 orchid genomes have been published. Metabolites are the main way through which orchids respond to their environment. Dendrobium nobile, belonging to Dendrobium, the second largest genus in Orchidaceae, has high ornamental, medicinal, and ecological value. D. nobile is the source of many popular horticultural varieties. Among the Dendrobium species, D. nobile has the highest amount of dendrobine, which is regarded as one of the criteria for evaluating medicinal quality. Due to lack of data and analysis at the genomic level, the biosynthesis pathways of dendrobine and other related medicinal ingredients in D. nobile are unknown. In this paper, we report a chromosome-scale reference genome of D. nobile to facilitate the investigation of its genomic characteristics for comparison with other Dendrobium species. The assembled genome size of D. nobile was 1.19 Gb. Of the sequences, 99.45% were anchored to 19 chromosomes. Furthermore, we identified differences in gene number and gene expression patterns compared with two other Dendrobium species by integrating whole-genome sequencing and transcriptomic analysis [e.g., genes in the polysaccharide biosynthesis pathway and upstream of the alkaloid (dendrobine) biosynthesis pathway]. Differences in the TPS and CYP450 gene families were also found among orchid species. All the above differences might contribute to the species-specific medicinal ingredient biosynthesis pathways. The metabolic pathway-related analysis will provide further insight into orchid responses to the environment. Additionally, the reference genome will provide important insights for further molecular elucidation of the medicinal active ingredients of Dendrobium and enhance the understanding of orchid evolution.

The mechanisms of species formation and diversity within the Orchidaceae have always been a topic of great research interest, and molecular biology-based explanations for these phenomena are lacking. Here, we present a comparative genomic analysis comprising 24 chromosome-level genome assemblies and genome skimming data for 204 species from Dendrobium. We identify that the genetic conservation in Dendrobium is associated with its environmental adaptability. And the formation of species diversity in the genus Dendrobium is driven by the compression of the Indian plate and changes in sea level and precipitation. The CYP734A50 might play important role in Dendrobium self-incompatibility (SI) species and the type-1 SI system lost through deletion of the entire single polymorphic locus (S-locus). Our results reveal the genetics background of genomic variation, biosynthesis, and adaptive evolution in Dendrobium, providing fundamental insights into the relationships between the genome and trait evolution of orchids and into angiosperm diversification.

The process of migration and colonization is important in evolution; for example, modern humans experienced multiple waves of migrations out of Africa. However, no data cover the spatio-temporal patterns sufficiently to be truly informative. Metastatic cancer provides a unique in vivo model to study these processes through rapid somatic evolution. Here, we apply the high-resolution sampling technique (Dense 3D Crypt-scale Sampling) to analyze hundreds of spatially mapped micro-samples from the primary colorectal cancer and liver metastases in two representative cases. This would be analogous to recording the “out-of-Africa” events in two repeats. Our results support that liver metastases arise from polyphyletic and polyclonal seeding events where multiple, genetically distinct clones colonize a new site together. Following colonization, these multi-clonal populations can evolve into distinct spatial architectures: segregated territories formed by cells with low motility, or highly intermixed patterns driven by high motility. The colonization (or seeding) process begins within the first third of the primary tumor’s progression, creating a large number of widespread but clinically undetectable micrometastatic colonies. These findings support a model where metastatic competence is not an intrinsic trait of a single “winner” clone but an emergent property of multiple concurrent clones. Collectively, our work supports metastasis as a multi-stage process initiated early in tumor development, characterized by continuous polyclonal dissemination and the formation of spatially distinct clonal architectures. This general pattern may echo the ecology of migration and colonization in organismal evolution.