@article{devasahayam2026nanopore,

title = {Nanopore sequencing reveals coordinated host and microbiome responses across barley genotypes},

author = {Bennet Rohan Fernando Devasahayam and Thomas McNeil and Tesfaye Wubet and Thomas Schmutzer},

doi = {10.1186/s12915-026-02688-3},

year  = {2026},

date = {2026-07-29},

urldate = {2026-07-29},

journal = {BMC Biology},

volume = {24},

number = {1},

pages = {177},

abstract = {BackgroundBarley (Hordeum vulgare L.) provides a suitable model for studying domestication-driven plant-microbiome interactions. Although wild, landrace, and modern genotypes host distinct rhizosphere communities, the extent to which roots and microbes reciprocally influence each other remains unclear. Here, we applied an integrated multi-omics approach combining long-read metagenomics, root transcriptomics, and plant genomics to understand genotype-specific host-microbiome coordination.ResultsOxford Nanopore whole metagenome sequencing (WMS) revealed genotype-associated shifts in rhizosphere communities across seasons. Functional profiling showed a conserved metabolic backbone including amino acid metabolism, energy production, and secondary metabolite biosynthesis, alongside genotype-dependent variation in carbohydrate metabolism and transport-associated pathways. Genome-resolved analysis through metagenome-assembled genomes (MAGs) further detailed the taxonomic and functional architecture of key rhizosphere lineages. Root transcriptome profiling identified extensive differential expression associated with microbial perception, signaling, defense, and metabolic processes. Integration of host and microbiome data revealed coordinated molecular patterns, indicating that barley genotypes are associated with distinct microbial assemblages and corresponding transcriptional responses.ConclusionsThese findings indicate that domestication has shaped coordinated associations between barley genotypes and their rhizosphere microbiomes, reflected in both microbial community composition and host transcriptional regulation. This work provides new insights into the evolutionary tuning of plant-microbiome relationships and highlights opportunities for microbiome-informed strategies in barley improvement.},

keywords = {DiP-DIAMANT, Host-microbiome interactions, Long-read nanopore sequencing, Metagenomics, Rhizosphere microbiome, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{vonmaydell2026population,

title = {Population structure, genetic diversity and core set construction of an international collection of 256 Melissa officinalis genotypes},

author = {Daniel Maydell and Johannes Schwerdt and Heike Lehnert and Yvonne P\"{o}schl-Grau and Thomas Schmutzer and Frank Marthe},

doi = {10.1186/s12870-026-08853-8},

issn = {1471-2229},

year  = {2026},

date = {2026-05-01},

urldate = {2026-05-01},

journal = {BMC Plant Biology},

volume = {26},

number = {1},

pages = {794},

abstract = {BackgroundMelissa officinalis (balm) is a perennial medicinal. Climate change and high cultivation costs necessitate the breeding of new cultivars with improved stress tolerance and high metabolite content. However, the high costs of phenotyping large collections limit breeding progress. This study characterized the genetic diversity and population structure of 256 genotypes from 215 international accessions using flow cytometry and genotyping by sequencing (GBS). The primary objective was to identify untapped genetic resources and establish core sets to streamline future breeding and research efforts.ResultsMorphological characterization and flow cytometry revealed a clear division by ploidy and subspecies. The collection comprised 209 diploid and three polyploid genotypes of ssp. officinalis (2C = 1.79 pg) and 44 tetraploid genotypes of ssp. altissima (4C = 3.57 pg). GBS generated 29,307 and 9,909 SNPs for the entire collection and a subset of ssp. officinalis genotypes, respectively. We identified significant genetic differentiation between the subspecies, as confirmed by PCA (PC1 = 69.9%), STRUCTURE, and hierarchical clustering. With 21,770 private alleles and HE = 0.38 subspecies altissima exhibited greater genetic divergence than ssp. officinalis (2,953 private alleles},

keywords = {DiP-DIAMANT, DiP-OptiLamia, Domestication, Gene flow, Gene pool, Genetic diversity, Identification (biology), Melissa officinalis, Officinalis, Population, Subspecies},

pubstate = {published},

tppubtype = {article}

}