Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding historyDilan Sarange Rajapaksha Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, Karl Schmid, Sandra Schmöckel, Mark Tester & Christian Jung
Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and fast LD decay of 6.5 and 49.8 Kb, respectively....
Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume colorMichael Abrouk, Naveenkumar Athiyannan, Thomas Müller & Simon Krattinger
The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference-grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe...
A droplet reactor on a super-hydrophobic surface allows control and characterization of amyloid fibril growthPeng Zhang, Enzo Di Fabrizio, Manola Moretti, Marco Allione, Yuansi Tian, Javier Ordonez-Loza, Davide Altamura, Cinzia Giannini, Bruno Torre, Gobind Das, Erqiang Li, Sigurdur T. Thoroddsen, Mani Sarathy, Ida Autiero, Andrea Giugni, Francesco Gentile, Natalia Malara & Monica Marini
Methods to produce protein amyloid fibrils, in vitro, and in situ structure characterization, are of primary importance in biology, medicine, and pharmacology. We first demonstrated the droplet on a super-hydrophobic substrate as the reactor to produce protein amyloid fibrils with real-time monitoring of the growth process by using combined light-sheet microscopy and thermal imaging. The molecular structures were characterized by Raman spectroscopy, X-ray diffraction and X-ray scattering. We demonstrated that the convective flow induced by...
Cloning agronomically important genes from large, complex crop genomes remains challenging. Here, we generate a 14.7-gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping, and chromosome conformation capture. The resulting assembly is an order of magnitude more contiguous than previous wheat assemblies. Kariega shows durable resistance against the devastating fungal stripe rust disease. We identified the race-specific disease resistance gene Yr27, encoding an intracellular...
Data for: Are feeding modes concealing morphofunctional diversity? The case of the New World ParrotfishesLucía Pombo-Ayora & Jose Tavera
In functional ecology, morphology is expected to reflect function, however, occasional decoupling of these two can be found. We did not find a relationship between feeding functional morphology and feeding modes of the American parrotfishes of the genera Scarus and Sparisoma. We explore some possible morpho-functional reasons for this phenomenon and reconsider the functional diversity within the scrapers. A phylogenetic tree including 50 species of parrotfishes, based on 12 genes, was reconstructed over which all...
Understanding larval connectivity patterns in exploited fishes is a fundamental prerequisite for developing effective management strategies and assessing the vulnerability of a fishery to recruitment overfishing and localised extinction. To date however, researchers have not considered how regional variations in fishing pressure also influence recruitment. We used genetic parentage analyses and modelling to infer the dispersal patterns of bumphead parrotfish (Bolbometopon muricatum) larvae in the Kia fishing grounds, Isabel Province, Solomon Islands. We then extrapolated...
Raw Illumina short reads (~40x) for TA299 Triticum monococcum subsp. aegilopoides.
In situ monitoring reveals cellular environmental instabilities in human pluripotent stem cell cultureShannon Klein, Samhan Alsolami, Silvia Arossa, Gerardo Ramos Mandujano, Anieka Parry, Alexandra Steckbauer, Carlos Duarte & Mo Li
Mammalian cell cultures are a keystone resource in biomedical research, but the results of published experiments often suffer from reproducibility challenges. This has led to a focus on the influence of cell culture conditions on cellular responses and reproducibility of experimental findings. Here, we perform frequent in situ monitoring of dissolved O2 and CO2 with optical sensor spots and contemporaneous evaluation of cell proliferation and medium pH in standard batch cultures of three widely used...
Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation datasetsBenjamin Hume, Susann Rossbach, Anny Cardenas, Gabriela Perna, Christian Voolstra & Carlos Duarte
Giant clams (Tridacninae) are important members of Indo-Pacific coral reefs and among the few bivalve groups that live in a symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remains relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We...
Animal-attached devices have transformed our understanding of vertebrate ecology. To minimize any associated harm, researchers have long advocated that tag masses should not exceed 3% of carrier body mass. However, this ignores tag forces resulting from animal movement. Using data from collar-attached accelerometers on 10 diverse free-ranging terrestrial species from koalas to cheetahs, we detail a tag-based acceleration method to clarify acceptable tag mass limits. We quantify animal athleticism in terms of fractions of animal...
Environmental DNA (eDNA) is increasingly being used to assess community composition in marine ecosystems. Applying eDNA approaches across broad spatial scales now provide the potential to inform biogeographic analyses. However, to date, few studies have employed this technique to assess broad biogeographic patterns across multiple taxonomic groups. Here, we compare eDNA-derived communities of bony fishes and invertebrates, including corals and sponges, from 15 locations spanning the entire length of the Omani coast. This survey includes...
King Abdullah University of Science and Technology11
University of Konstanz2
National Research Institute for Agriculture, Food and Environment1
University of the Free State1
University of Hohenheim1
University of Pretoria1
The Nature Conservancy1
Queen's University Belfast1
University of Queensland1
Max Planck Institute of Animal Behavior1