Asparagus is a morphologically and ecologically diverse genus with economic and medicinal importance, yet its chloroplast genome had received limited genus-wide attention compared with recent nuclear genomic efforts. The genus belongs to the family Asparagaceae and comprises well over two hundred species distributed across Europe, Africa, and Asia, ranging from the familiar cultivated vegetable with its tender young shoots to prickly desert shrubs, climbing plants, and ornamentals prized for their delicate feathery foliage. Several species are also staples of traditional medicine, most notably Asparagus racemosus, whose roots are used in Ayurvedic practice, and a number of Chinese species employed in herbal formulations. This combination of economic value, taxonomic difficulty, and ecological breadth makes the genus an attractive target for genomic characterization, and it also makes reliable species identification a genuine practical problem, since many Asparagus species look superficially similar and are easily confused in trade.

To close the genomic gap, the team de novo assembled 35 chloroplast genomes: one from newly generated sequencing data and 34 from publicly available sequencing reads downloaded from the National Center for Biotechnology Information. These were integrated with 40 previously published genomes, bringing the total dataset to 75 species. By combining freshly assembled material with existing resources, the study achieved a sampling breadth that no earlier chloroplast-focused work on the genus had reached. The strategy of mining archived sequencing reads is increasingly common in organelle genomics, because chloroplast genomes are present in many copies per cell and can often be recovered reliably even from nuclear-targeted sequencing projects, allowing researchers to extract organellar value from data originally generated for other purposes.

The most fundamental finding concerns genome structure. Every one of the 75 genomes retained the canonical quadripartite architecture typical of flowering plant chloroplasts, consisting of a pair of inverted repeats separated by a large and a small single-copy region. Genome size varied only narrowly, from 155,654 to 157,211 base pairs, and gene content was essentially invariant, with 131 genes representing 113 unique gene species. The boundaries of the inverted repeats were likewise conserved across the genus. This architecture, in which the inverted repeats act as a stabilizing element by buffering the single-copy regions against rearrangement, is broadly shared across angiosperms, but the degree of uniformity observed here is nonetheless notable given the genus’s diversity in habit, morphology, and ecology, from the succulent-cladode ornamentals to the cultivated vegetable. Chloroplast genomes are well known for their structural conservatism relative to nuclear genomes, and the Asparagus data provide a textbook illustration of that stasis.

While the architecture was static, the genes themselves were not all evolving under the same regime. Using codon-based selection analyses, the researchers identified episodic diversifying selection in four loci: ycf1, ccsA, rps8, and rbcL. The strongest signals came from ycf1 and rbcL, and both were independently corroborated by PAML site-model analysis, a complementary maximum-likelihood approach for detecting codon sites evolving under positive selection. The picture was more nuanced for the other two genes. The signal in ccsA, which is involved in cytochrome c biogenesis of the chloroplast respiratory chain, was restricted to just two codon sites but was recovered by PAML branch-site analysis. The gene-wide signal in rps8, a small ribosomal protein gene, was not recovered at individual sites and was also not supported by the branch-site approach, suggesting it should be interpreted with caution.

The functional implications of these selected genes are intriguing. rbcL encodes the large subunit of RuBisCO, the enzyme responsible for carbon fixation in photosynthesis and often cited as the most abundant protein on Earth, while ycf1 is a large, rapidly evolving gene of unknown but essential function whose product participates in the chloroplast protein translocation machinery. Because RuBisCO sits at the very entry point of carbon into the biosphere, even modest changes in its catalytic properties can matter for photosynthetic efficiency, and adaptive evolution at rbcL has been documented in a range of plant lineages, often in connection with shifts in climate, atmosphere, or photosynthetic strategy. That both rbcL and ycf1 show the clearest evidence of episodic diversifying selection across Asparagus species hints that adaptation, possibly related to photosynthetic performance in different environments, has left measurable footprints in the chloroplast genome even as its overall organization has remained frozen in place. The coexistence of a rigid genome scaffold with a few genes under shifting selective pressure is a recurring theme in organelle evolution, and the Asparagus dataset adds a well-sampled genus-level example.

Beyond selection, the study mapped the distribution of genetic variation across the chloroplast genome, a question of practical importance for DNA barcoding and species identification. Nucleotide diversity was substantially higher in non-coding regions than in coding regions, consistent with the general pattern in plant chloroplast genomes where intergenic spacers accumulate mutations more freely because they are not constrained by the need to preserve an amino acid sequence. Among coding loci, rps15 and ycf1 stood out as the most variable, while among intergenic spacers the psbC-trnS-UGA, ccsA-ndhD, and rps3-rpl22 regions showed the highest diversity. The authors highlight these six loci as candidate species-identification markers for Asparagus, offering a starting point for researchers seeking to distinguish closely related species, including those traded as medicinal herbs, using short chloroplast DNA segments. Chloroplast barcoding has long been pursued in plants, with mixed success, because many plant groups radiated too recently for standard barcode loci to accumulate diagnostic differences; identifying the most variable regions within a target genus is therefore a standard and sensible strategy for improving discrimination.

Phylogenetic reconstruction from the chloroplast data delivered a largely well-resolved species tree. Maximum-likelihood analysis based on complete chloroplast genomes recovered twelve previously recognized infrageneric clades, with strong support for relationships within each clade and a well-supported backbone. Notably, the tree built from coding sequences alone showed weaker backbone support than the whole-genome tree, an observation that underscores the phylogenetic value of non-coding spacers even though they are individually more variable. Collectively, the spacers contribute a large share of the informative sites in a complete chloroplast genome, and their combined signal can outweigh the noise introduced at any single locus. The recovery of all twelve recognized clades confirms that the chloroplast genome, sampled densely enough, can capture the genus’s internal diversification signal.

The most consequential result, however, is the comparison with nuclear data. The team quantitatively compared their chloroplast tree with a published nuclear species tree for the 59 species shared between the two datasets, using the Robinson–Foulds distance as a measure of topological disagreement. The unnormalized distance was 72, and the normalized Robinson–Foulds value was 0.64, indicating substantial discordance concentrated at the backbone nodes of the tree. In other words, while the chloroplast and nuclear genomes agree on many fine-scale relationships within clades, they tell partly conflicting stories about the deepest splits in the genus’s history.

Cytonuclear discordance of this kind is a well-recognized phenomenon in plant phylogenomics, and the Asparagus result illustrates why it matters. Chloroplast genomes are maternally inherited in most flowering plants and trace a single genealogical lineage, whereas nuclear genomes combine ancestry from both parents and are reshuffled by recombination. Processes such as incomplete lineage sorting, in which ancestral genetic polymorphisms persist through rapid speciation events, hybridization followed by chloroplast capture, or introgression between lineages can each drive the organellar and nuclear trees apart. Rapid ancient radiations, which are precisely the kind of event that tends to generate poorly resolved deep backbones, are especially prone to such discordance because there is little time for lineages to sort cleanly between speciation events. The authors do not adjudicate among these mechanisms in the abstract, but the magnitude of the normalized discordance they report makes clear that a chloroplast-only phylogeny of Asparagus cannot be treated as a complete account of the genus’s evolutionary history.

The study has limitations worth noting. Thirty-four of the 35 newly assembled genomes came from publicly archived reads rather than fresh sampling, so assembly quality depends on the underlying data, and the comparison with the nuclear tree was restricted to the 59 species common to both datasets. The selection signals in ccsA and especially rps8 rest on limited statistical support, with the ccsA signal confined to two codon sites and the rps8 signal not recovered at individual sites or by branch-site models. And while the identification of variable loci as barcoding candidates is a valuable practical output, validating their discriminatory power across the full breadth of the genus, and across populations within species, will require further testing.

Even so, the significance of the work is considerable. By establishing the first genus-wide chloroplast genome resource for Asparagus, the authors have created a reference framework that others can extend as new species are sequenced. The demonstration that structural conservation and gene-specific selection coexist within the same compact genome adds to a growing body of evidence that organelle evolution is not uniformly neutral. And the quantified chloroplast–nuclear discordance provides a concrete empirical baseline for future phylogenomic studies that integrate organellar and nuclear data, an approach the authors explicitly frame as the way forward.

For applied research, the implications reach into conservation genetics and the authentication of medicinal plant materials. Asparagus species are used in traditional medicine systems, and the study was supported by a Chinese government program dedicated to the sustainable use of valuable Chinese medicine resources. Reliable species-level identification is a prerequisite for both conserving wild genetic diversity and ensuring that herbal products contain the correct species, a concern that has grown alongside the expansion of the global herbal trade and the documented problems of adulteration and substitution in commercial plant materials. The variable loci identified here, particularly the high-diversity intergenic spacers, offer practical molecular tools toward those ends, while the genus-wide genome dataset provides the comparative context needed to interpret any single species’s chloroplast sequence in its proper evolutionary setting.

Börner was born in Leipzig on July 11, 1946, and studied biology at Martin Luther University Halle-Wittenberg between 1965 and 1969. There, in the laboratory of plant geneticist Rudolf Hagemann, he became fascinated by a question that was still largely unexplored: how is genetic information organized and expressed inside cellular structures other than the nucleus? Plant cells contain two genetic systems outside the nucleus, in chloroplasts and mitochondria. These organelles are descendants of ancient bacteria and retain their own DNA, but they depend heavily on proteins encoded by nuclear genes. Understanding how these genetic systems cooperate became the central theme of Börner’s scientific life.

In 1974, Börner completed his doctoral research on mutations in the chloroplast genome of higher plants. His habilitation, awarded in 1979, examined how plastid genes interact with nuclear genes during chloroplast development. His studies helped establish an idea now known as plastid-to-nucleus retrograde signaling. In simple terms, chloroplasts do not merely receive instructions from the nucleus; they also send molecular signals back, informing the nucleus about their developmental and physiological state. These signals can influence nuclear genes whose products are required for photosynthesis and chloroplast construction. At the time, this concept challenged the idea that genetic control flowed mainly in one direction.

Börner’s early research was conducted in East Germany, where access to equipment, chemicals and international travel was severely restricted. Yet in 1977 he received unusual permission to visit laboratories in the United Kingdom. The scientific exchange produced research that was published in Nature in 1979. The paper suggested that plastid-synthesized RNA could control the production of plastid proteins in the cell’s cytoplasm, providing evidence for communication between the organelle and the rest of the cell. For a scientist working behind the Iron Curtain, publication in one of the world’s most prestigious scientific journals was a remarkable achievement and a sign that his research had international importance.

In 1982, Börner moved to Humboldt University of Berlin, where he became a full-time lecturer in genetics and head of a newly established Genetics Division. He was appointed professor of genetics in 1984 and built a major center for molecular genetics in East Berlin. Even before the Berlin Wall fell, he maintained active scientific contacts with researchers in West Germany and West Berlin, including scientists at the Institute for Gene-Biology Research. When the Wall came down on November 9, 1989, those connections suddenly acquired historic significance. German reunification, however, brought major upheaval. The contracts of Humboldt University professors were terminated, and Börner had to compete again for his own position. He ultimately retained a professorship through a competitive selection process, becoming one of the scientists who helped reshape Berlin’s biological research landscape after reunification.

His institutional influence expanded dramatically in 1999, when he persuaded the German Research Foundation to fund Collaborative Research Centre 429. The large-scale program, focused on molecular physiology, energetics and the regulation of primary plant metabolism, united researchers from Humboldt University, Free University Berlin, Technical University Berlin, the University of Potsdam and the Max Planck Institute of Molecular Plant Physiology in Potsdam-Golm. These institutions had previously been divided by the political geography of the Cold War. Börner served as spokesperson from 1999 to 2010, transforming a scientific collaboration into a lasting network for plant molecular biology across the Berlin region.

The scientific problems pursued by Börner’s group were fundamental to modern cell biology. His research examined the structure, expression and inheritance of plastid DNA, including how chloroplast genomes behave in variegated plants and mutants lacking functional plastid ribosomes. His team also investigated chloroplast transcription, RNA processing, intron splicing and RNA editing. These mechanisms are essential because chloroplast genes are not simply copied into proteins in a single step. Their transcripts must be accurately initiated, processed and sometimes edited before they can support photosynthesis or organelle development. Work from Börner’s laboratory helped clarify how nuclear and plastid-encoded systems coordinate these processes.

A major achievement involved the discovery and characterization of nucleus-encoded, phage-like RNA polymerases that operate in plant chloroplasts and mitochondria. Unlike the multisubunit bacterial-type polymerases encoded partly by organelle genomes, these enzymes are produced from nuclear genes and imported into organelles. Börner and his collaborators showed that related polymerases can direct transcription in different genetic compartments, and in some cases that one enzyme can serve two genomes. This revealed an unexpected layer of genetic integration: plant organelles retain bacterial-style genomes, but their gene expression is increasingly controlled by proteins that evolved in, and are encoded by, the nucleus.

One of Börner’s most persistent scientific mysteries began with the barley mutant albostrians, a plant that develops white and green leaf sectors because some plastids fail to mature into photosynthetically competent chloroplasts. The mutant lacks plastid ribosomes, leaving its chloroplasts unable to produce essential proteins. Börner began studying the system in 1972, and the underlying nuclear mutation remained unidentified for decades. In 2019, seven years after his official retirement, researchers finally traced the defect to a truncated CCT-domain gene related to the chloroplast import apparatus gene CHLOROPLAST IMPORT APPARATUS2. The discovery connected a classic genetic mutant with the machinery that transports nuclear-encoded proteins into chloroplasts, closing a mystery that had lasted nearly half a century.

Börner’s scientific interests extended well beyond plant organelles. His group investigated cyanobacteria, helping characterize phytochrome-like photoreceptors that detect light in prokaryotic cells. They also contributed to the molecular study of non-ribosomal peptide synthesis in cyanobacteria, including the genes responsible for producing microcystins, toxins associated with blooms of Microcystis aeruginosa. These studies linked gene regulation, environmental conditions and toxin production, providing tools for understanding how cyanobacterial organisms adapt and become hazardous in aquatic ecosystems. In microbiology and mycology, his laboratory helped pioneer DNA fingerprinting and PCR-based methods for differentiating filamentous fungi and yeasts. Such techniques improved the identification, classification and tracking of fungal strains, including industrial and pathogenic organisms.

The article portrays Börner’s legacy as extending far beyond his publication record. He led Humboldt University’s Interdisciplinary Center for Biotechnology, served as dean of biology during the politically transformative years around reunification, and held senior positions in German genetics and research organizations. His honors included the Carl Correns Medal, the Goethe Prize and the Miescher-Ishida Prize, as well as election to the Berlin-Brandenburg Academy of Sciences and the German National Academy of Sciences Leopoldina. Yet former students and colleagues emphasize mentorship as one of his greatest contributions. They describe a scientist who encouraged independence, skepticism and curiosity while offering calm, practical support. His laboratory trained researchers who later became professors, group leaders and specialists across Europe and beyond. Even after retiring in 2012, Börner remained active in the scientific community, demonstrating how a research legacy can persist not only in data and discoveries but also through the people who carry scientific questions into the future.

Subject of Research: Molecular plant genetics, chloroplast and mitochondrial genetics, organelle–nucleus communication, cyanobacterial molecular biology, and fungal DNA fingerprinting.

Article Title: Professor Thomas Börner: the pioneer of molecular plant genetics in East Germany turns 80!

Article References: Schmitz-Linneweber, C., & Zoschke, R. “Professor Thomas Börner: the pioneer of molecular plant genetics in East Germany turns 80!” Molecular Genetics and Genomics, volume 301, article 176 (2026). https://doi.org/10.1007/s00438-026-02498-w

Image Credits: AI Generated

DOI: 10.1007/s00438-026-02498-w

Keywords: Thomas Börner, molecular plant genetics, chloroplast genetics, mitochondrial genetics, plastid-to-nucleus retrograde signaling, organelle biology, plant molecular biology, cyanobacteria, fungal DNA fingerprinting, German science history