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The repetitive part of the genome (the repeatome) contains a wealth of often overlooked information that can be used to resolve phylogenetic relationships and test evolutionary hypotheses for clades of related plant species such as Pelargonium. We have generated genome skimming data for 18 accessions of Pelargonium section Ciconium and one outgroup. We analyzed repeat abundancy and repeat similarity in order to construct repeat profiles and then used these for phylogenetic analyses. We found that phylogenetic trees based on read similarity were largely congruent with previous work based on morphological and chloroplast sequence data. For example, results agreed in identifying a "Core Ciconium " group which evolved after the split with P. elongatum. We found that this group was characterized by a unique set of repeats, which confirmed currently accepted phylogenetic hypotheses. We also found four species groups within P. sect. Ciconium that reinforce previous plastome-based reconstructions. A second repeat expansion was identified in a subclade which contained species that are considered to have dispersed from Southern Africa into Eastern Africa and the Arabian Peninsula. We speculate that the Core Ciconium repeat set correlates with a possible WGD event leading to this branch. [ABSTRACT FROM AUTHOR]

The improvement and promotion of leafy vegetables, used for both food and medicine, benefits greatly from detailed knowledge of their health-promoting specialised metabolites. In the present study, we investigated the global metabolite variation in the leaves of 48 accessions of the leafy vegetable Gynandropsis gynandra using two complementary analytical platforms: liquid-chromatography mass spectrometry (LC-MS) for an untargeted comparison of non-volatile semi-polar metabolites and gas-chromatography mass spectrometry (GC-MS) for an untargeted comparison of volatile metabolites. Our results revealed large variation in 936 semi-polar compounds including flavonoids, terpene glycosides, glucosinolates and various phenolic compounds. Unsupervised multivariate analysis indicated the variation in levels of the semi-polar metabolites was mainly driven by geography, with accessions from both West Africa and Asia forming a group clearly separated from East African accessions. Detected volatile metabolites included various sesquiterpenes, aldehydes, ketones, and sulphur-containing isothiocyanates. Variation in these compounds was however not geographically specific, but most likely linked to the taste and aroma of the leaves. The relative abundance in glucosinolates and isothiocyanates in the leaves allowed the clustering of accessions into two main groups that could be used for further plant-herbivore interaction studies. This study revealed both the broad spectrum of phytochemicals present in Gynandropsis gynandra leaves and the substantial variation in metabolite profiles among accessions from different regions of the world. Our results provide a basis for the development of breeding programs aiming at improving the levels of specialised metabolites in this tropical leafy vegetable for increased resistance against pests and diseases and improved human health., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Rice is a staple food for the majority of the world's population. Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice-either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest-suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view., Competing Interests: The authors have declared that no competing interests exist.

Engineering C 4 photosynthesis into C 3 crops could substantially increase their yield by alleviating photorespiratory losses. This objective is challenging because the C 4 pathway involves complex modifications to the biochemistry, cell biology, and anatomy of leaves. Forward genetics has provided limited insight into the mechanistic basis of these properties, and there have been no reports of significant quantitative intraspecific variation of C 4 attributes that would allow trait mapping. Here, we show that accessions of the C 4 species Gynandropsis gynandra collected from locations across Africa and Asia exhibit natural variation in key characteristics of C 4 photosynthesis. Variable traits include bundle sheath size and vein density, gas-exchange parameters, and carbon isotope discrimination associated with the C 4 state. The abundance of transcripts encoding core enzymes of the C 4 cycle also showed significant variation. Traits relating to water use showed more quantitative variation than those associated with carbon assimilation. We propose that variation in these traits likely adapted the hydraulic system for increased water use efficiency rather than improving carbon fixation, indicating that selection pressure may drive C 4 diversity in G. gynandra by modifying water use rather than photosynthesis. The accessions analyzed can be easily crossed and produce fertile offspring. Our findings, therefore, indicate that natural variation within this C 4 species is sufficiently large to allow genetic mapping of key C 4 traits and regulators., (© 2018 American Society of Plant Biologists. All rights reserved.)