Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencingHollis Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa Komoroske, Tanya Lama, Andrew Crawford, Robert Murphy, Samara Brown, Alan Scott, Phillip Morin, Erich Jarvis & Olivier Fedrigo
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different...
Data from: A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architectureHernán Morales-Navarrete, Fabián Segovia-Miranda, Piotr Klukowski, Kirstin Meyer, Hidenori Nonaka, Giovanni Marsico, Mikhail Chernykh, Alexander Kalaidzidis, Marino Zerial & Yannis Kalaidzidis
A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to...
Data from: Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyonAnne C. Roulin, Christoph Stritt, Michele Wyler, Elena L. Gimmi & Martin Pippel
Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272...
Here we provide measurements of cell morphology in the proliferating Drosophila larval wing disc, specifically the wing disc pouch, as it grows in ex vivo culture. The tables provided here include measurements of cell morphology (area and elongation) at each timepoint in each of 5 wing disc samples. For cell elongation, we report the elongation values for each of its component triangles (formed by connecting the cell to the center of its neighbors). We also...
Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where the factors promoting increased species numbers and phenotypic divergence in two closely related lineages is notably different. We investigated one such natural experiment using two de novo assembled and 40 re-sequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the...
data for publication: Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocellsN/A Alan Ianeselli & N/A Dora Tang
Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in miceJoão P. L. Castro, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, Ronald Naumann, Isabella Skuplik, John Cobb, Nick H. Barton, Campbell Rolian & Yingguang Frank Chan
Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory,...
Genome assembly and annotation of the Iberian ribbed newt, Pleurodeles waltl
Data from: A tunable refractive index matching medium for live imaging cells, tissues and model organismsTobias Boothe, Lennart Hilbert, Michael Heide, Lea Berninger, Wieland B. Huttner, Vasily Zaburdaev, Nadine L. Vastenhouw, Eugene W. Myers, David N. Drechsel & Jochen C. Rink
In light microscopy, refractive index mismatches between media and sample cause spherical aberrations that often limit penetration depth and resolution. Optical clearing techniques can alleviate these mismatches, but they are so far limited to fixed samples. We present Iodixanol as a non-toxic medium supplement that allows refractive index matching in live specimens and thus a substantial improvement of the live-imaging of primary cell cultures, planarians, zebrafish and human cerebral organoids.
Raw data files from EM rotary shadowing experiments of Early Endosome Antigen 1 (EEA1) under various conditions. The datasets have been obtained for the study of Murray & Jahnel et al., "An endosomal tether undergoes an entropic collapse to bring vesicles together", Nature, 2016. Different datasets correspond to different mutants of EEA1 and different conditions, for example, the presence of the binding partner, the small GTPase Rab5. Each data directory corresponds to a different condition....
This directory contains code needed for denoising the images, producing the max projections and normalisation of the signal.
The transition from “well-marked varieties” into “well-defined species” has puzzled evolutionary biologists ever since Darwin — especially when extensive gene flow between incipient species is possible due to the lack of physical barriers (sympatric speciation). Gene flow counteracts the build-up of genome-wide differentiation, which is both a hallmark of speciation and forms the underlying basis of irreversible reproductive barriers (incompatibilities) that ultimately complete the speciation process. Theory predicts that the genetic architecture of divergently selected...
Data from: Outstanding intraindividual genetic diversity in fissiparous planarians (Dugesia, Platyhelminthes) with facultative sexLaia Leria, Miquel Vila-Farré, Eduard Solà & Marta Riutort
Background: Predicted genetic consequences of asexuality include high intraindividual genetic diversity (i.e., the Meselson effect) and accumulation of deleterious mutations (i.e., Muller’s Ratchet), among others. These consequences have been largely studied in parthenogenetic organisms, but studies on fissiparous species are scarce. Differing from parthenogens, fissiparous organisms inherit part of the soma of the progenitor, including somatic mutations. Thus, in the long term, fissiparous reproduction may also result in genetic mosaicism, besides the presence of the...
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large...
Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode Pristionchus pacificus as a case study to investigate thermal adaptation on the Indian...
Max Planck Institute of Molecular Cell Biology and Genetics20
Max Planck Institute for the Physics of Complex Systems2
University of Konstanz2
Max Planck Institute for Psycholinguistics1
University of Massachusetts Amherst1
Centre for Ecology and Conservation Sciences1
Johns Hopkins University1
Arima Genomics (United States)1
Max Planck Society1
John Jay College of Criminal Justice1