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In the past, the Silk Road was a vital trade route that spanned Eurasia, connecting East Asia to the Mediterranean Sea. The genus Prunus, belonging to the Rosaceae family and encompassing plums, peaches, apricots, cherries, and almonds, thrived as human travel along the Silk Road increased. The majority of fruits within this genus, whether wild or cultivated, are naturally sweet and easily preserved by drying for storage and transport. The interaction along the Silk Road between wild populations and diverse varieties of Prunus fruits led to the development of various hybrids. This article provides a summary of archaeological findings related to prominent Prunus fruits such as peaches, apricots, plums, cherries, and almonds, shedding light on their evolutionary history, genetic diversity, population structure, and historical dynamics crucial for species conservation. The origins of biodiversity may involve factors like migration of pre-adapted lineages, in situ variation, or the persistence of ancestral lineages. Furthermore, climate change is affecting spatial genetic patterns and potentially further threatening rare Prunus species. Evaluating the scope and composition of genetic diversity within germplasm collections is essential for enhancing plant breeding initiatives and preserving genetic resources in this changing context. From a molecular point of view, techniques such as genome-wide association studies (GWASs) and the identification of quantitative trait loci (QTLs) and genes responsible for phenotypic changes in cultivars and germplasm collections should be of great interest in these breeding programs, while genomic estimated breeding values (GEBVs) derived from genome-wide DNA polymorphism information can facilitate the selection of superior genotypes. 

Although microorganisms are known to dominate Earth’s biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome—tripartite and monopartite—with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture. 

Abstract Legumes, comprising one of the largest, most diverse, and most economically important plant families, are the subject of vibrant research and development worldwide. Continued improvement of legume crops will benefit from the recent proliferation of genetic (including genomic) resources; but the diversity, scale, and complexity of these resources presents challenges to those managing and using them. A workshop held in March of 2019 addressed questions of data resources and priorities for the legumes. The workshop identified various needs and recommendations: (a) Develop strategies to effectively store, integrate, and relate genetic resources collected in different projects. (b) Leverage information collected across many legume species by standardizing data formats and ontologies, improving the state of metadata about datasets, and increasing use of the FAIR data principles. (c) Advocate for the critical role that curators exercise in integrating complex datasets into databases and adding high value metadata that enable downstream analytics and facilitate practical applications. (d) Implement standardized software and database development practices to best leverage limited developer time and expertise gained from the various legume (and other) species. (e) Develop tools and databases that can manage genetic information for the world's plant genetic resources, enabling efficient incorporation of important traits into breeding programs. (f) Centralize information on databases, tools, and training materials and establish funding streams to support training and outreach.