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Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F ST, and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F ST value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.

Mesoamerican food agriculture is defined by the milpa cropping system, consisting of maize (Zea mays L.), common bean (Phaseolus vulgaris L.), and squash (Cucurbita spp.). In recent years, a domestication center for maize has been proposed in the Balsas River basin in west-central Mexico, raising the question whether the Balsas basin was also the center of origin for Mesoamerican food agriculture in general. We conducted a survey of genetic diversity for 26 microsatellite markers in a representative sample of 155 wild and domesticated common bean from its Mesoamerican gene pool. Microsatellite diversity was analyzed with STRUCTURE, neighbor-joining tree construction, and principal coordinate analysis. Most Mesoamerican domesticated accessions clustered in a single group, suggesting a single domestication. Furthermore, the most closely related wild beans to the domesticated clade originated from a restricted region in the Rio Lerma-Rio Grande de Santiago basin in west-central Mexico, distinct from the Balsas basin. Although wild maize and Phaseolus beans grow together in the wild, they appear to have been domesticated in different regions to be reunited later on in a single cropping system. Crop domestications in Mesoamerica may therefore have a diffuse rather than a single geographic origin. Archaeological and ecological investigations into the origins of agriculture should be refocused from the arid eastern half of Mexico to the west-central part of the country.

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single‐copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian‐western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets. [ABSTRACT FROM AUTHOR]

Cymbidium goeringii, commonly known as the spring orchid, has long been favoured for horticultural purposes in Asian countries. It is a popular orchid with much demand for improvement and development for its valuable varieties. Until now, its reference genome has not been published despite its popularity and conservation efforts. Here, we report the de novo assembly of the C. goeringii genome, which is the largest among the orchids published to date, using a strategy that combines short‐ and long‐read sequencing and chromosome conformation capture (Hi‐C) information. The total length of all scaffolds is 3.99 Gb, with an N50 scaffold size of 178.2 Mb. A total of 29,556 protein‐coding genes were annotated and 3.55 Gb (88.87% of genome) repetitive sequences were identified. We constructed pseudomolecular chromosomes using Hi‐C, incorporating 89.4% of the scaffolds in 20 chromosomes. We identified 220 expanded and 106 contracted genes families in C. goeringii after divergence from its close relative. We also identified new gene families, resistance gene analogues and changes within the MADS‐box genes, which control a diverse set of developmental processes during orchid evolution. Our high quality chromosomal‐level assembly of C. goeringii can provide a platform for elucidating the genomic evolution of orchids, mining functional genes for agronomic traits and for developing molecular markers for accelerated breeding as well as accelerating conservation efforts. [ABSTRACT FROM AUTHOR]