A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm

Factors influencing metabolite profiles in global Arabica green coffee beans: Impact of continent, altitude, post-harvest processing, and variety

The metabolites of green coffee beans can be influenced by various factors, including species, variety, geographical origin, and post-harvest processing methods. However, previous studies often focused on limited factors separately and were not comprehensive in scope, utilizing only green coffee beans from a restricted area. To fill the gap, we simultaneously analyzed 176 global green coffee beans (C. arabica) from various continents, altitudes, post-harvest processing methods, and varieties to comprehensively investigate the primary factors influencing coffee quality, using metabolomics approach with GC-MS, and machine learning analysis. Partial least squares-discriminant analysis (PLS-DA) revealed that coffee bean characteristics were differently affected by each factor, highlighting 56 key metabolites that varied by each factor, while simultaneously identifying metabolites associated with sub-level variables within each factor. According to the F1 score of the Random Forest model (continent: 91.5 %, altitude: 74.2 %, processing method: 81.4 %, variety: 64.7 %), the continent had the greatest effect on coffee metabolite profiles, followed by the post-harvest processing, altitude, and variety. Additionally, comprehensive heatmap visualizations, incorporating the four factors, are presented, which can be utilized as valuable information for manufacturing customized coffee beans aligned with consumer preferences. These findings provide comprehensive insights into the association between various factors affecting coffee quality and coffee metabolites.

Prospects for functional genomics of genes involved in coffee-specialized metabolism through cross-species integrative omics

Coffee (Coffea spp.) is one of the most economically important crop species and serves as a rich source of bioactive specialized (secondary) metabolites with various health-promoting properties. Advances in analytical food chemistry and phytochemistry have elucidated an extensive and structurally diverse specialized metabolism in coffee beans, much of which contributes to both organoleptic attributes and adaptive physiological responses in coffee plants. Recent developments in omics-driven methodologies have provided new insights into both coffee metabolism and breeding strategies, particularly those aimed at enhancing both quality traits and environmental resilience. Comparative genomic analyses across Coffea species and cultivars have facilitated the detection of metabolic polymorphisms, enabling inter- and intra-species assessments of biosynthetic pathway variation and the refinement of biosynthetic frameworks for further functional genomics approaches. Such approaches yield critical information regarding the genetic and biochemical determinants underlying specialized metabolite accumulations, which can be directly applied for targeted metabolic engineering and crop improvement. Moreover, cross-species comparative omics and multi-omics integrative analyses, particularly in relation to phylogenetically relevant taxa such as Solanaceae species, exemplified by the model crop tomato (Solanum lycopersicum), provide valuable translational insights into conserved and divergent metabolic architectures.

Chromosome-scale genome assembly of Phyllanthus emblica L. 'Yingyu'

Phyllanthus emblica L. is an edible plant with medicinal properties native to the dry-hot valley of Yunnan, China. Here, we report a de novo chromosome-scale genome of P. emblica wild type 'Yingyu'. 'Yingyu' is an octopoid plant with a total of 104 chromosomes. In total, we assembled and clustered 480 Mb of the genome and constructed 26 pseudochromosomes (haplotypes) of P. emblica wild type 'Yingyu' that encompass 97.9% of the genome and demonstrate to have relatively high integrity. We annotated 31,111 genes found in the genome of P. emblica. We screened 5 different tissues for searching the tissue-specific expression candidate genes. Four unknown function candidate genes were expressed at high levels in the flowers while genes relating to the biosynthesis of gibberellins and cellulose were specifically expressed in the fruits. The ascorbate biosynthesis-related genes were screened on P. emblica 'Yingyu' genome. The high expression level of 2 GDP-mannose epimerases and one L-galactono-1,4- lactone dehydrogenases in the fruit may be related to the activity of absorbate biosynthesis in the fruit. The chromosome-level genomic data for P. emblica we report will be important for the development of molecular markers to facilitate the selection of superior cultivars for processing and pharmaceuticals.

De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee

Geisha coffee is recognized for its unique aromas and flavors and, accordingly, has achieved the highest prices in the specialty coffee markets. We report the development of a chromosome-level, well-annotated, genome assembly of Coffea arabica var. Geisha. Geisha is considered an Ethiopian landrace that represents germplasm from the Ethiopian center of origin of coffee. We used a hybrid de novo assembly approach combining 2 long-read single molecule sequencing technologies, Oxford Nanopore and Pacific Biosciences, together with scaffolding with Hi-C libraries. The final assembly is 1.03 Gb in size with BUSCO assessment of the assembly completeness of 97.7% of single-copy orthologs clusters. RNA-Seq and Iso-Seq data were used as transcriptional experimental evidence for annotation and gene prediction revealing the presence of 47,062 gene loci encompassing 53,273 protein-coding transcripts. Comparison of the assembly to the progenitor subgenomes separated the set of chromosome sequences inherited from Coffea canephora from those of Coffea eugenioides. Corresponding orthologs between the 2 Arabica varieties, Geisha and Red Bourbon, had a 99.67% median identity, higher than what we observe with the progenitor assemblies (median 97.28%). Both Geisha and Red Bourbon contain a recombination event on chromosome 10 relative to the 2 progenitors that must have happened before the geographical separation of the 2 varieties, consistent with a single allopolyploidization event giving rise to C. arabica. Broadening the availability of high-quality genome assemblies of C. arabica varieties paves the way for understanding the evolution and domestication of coffee, as well as the genetic basis and environmental interactions of why a variety like Geisha is capable of producing beans with such exceptional and unique high quality.

Unveiling the Genetic Diversity and Demographic History of Coffea stenophylla in Sierra Leone Using Genotyping-By-Sequencing

Coffea stenophylla is a rare Coffea species boasting a flavor profile comparable to Arabica coffee (Coffea arabica) and has a good adaptability to lowland tropical climates. This species faces increasing threats from climate change, deforestation, and habitat fragmentation in its West African homeland. Using 1037 novel SNP markers derived from Genotyping-by-Sequencing (GBS), we revealed the presence of three distinct natural populations (mean Fst = 0.176) in Sierra Leone. Evidence of recent bottlenecks and small effective population size (118-140) was found across all three populations, reflecting the impact of recent anthropogenic disturbances on this species. Using a model-flexible inference approach, we unveiled a strong ancient bottleneck approximately 23,000 years ago, coinciding with the last glacial maximum (LGM), followed by post-glacial expansion and divergence into distinct genetic clusters. A comparative analysis between ex situ genebanks and natural populations detected a significant gap in genetic diversity, with two out of three natural populations missing from the ex situ genebank collection. These findings highlight the urgent need to improve conservation practices for C. stenophylla in Sierra Leone. The novel SNP markers developed in this study provided valuable tools to support future efforts in conservation and utilization of C. stenophylla genetic resources in West Africa.