8 Works

Data from: Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting

Mary Gehring, Daniela Pignatta, Robert M. Erdmann, George W. Bell, Elias Scheer & Colette L Picard
Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However,...

Data from: Evolutionary history and biogeographical patterns of barnacles endemic to deep-sea hydrothermal vents

Santiago Herrera & Timothy M. Shank
The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep-sea hydrothermal vent barnacles represent an excellent model for testing biogeographic hypotheses regarding the origin, dispersal, and diversity of modern vent fauna. Here we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal, and diversification. Our approach was to target a...

Data from: Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

Steven J. Biller, Paul M. Berube, Jessie W. Berta-Thompson, Libusha Kelly, Sara E. Roggensack, Lana Awad, Kathryn H. Roache-Johnson, Huiming Ding, Stephen J. Giovannoni, Lisa R. Moore & Sallie W. Chisholm
The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To...

Data from: Reading the leaves: a comparison of leaf rank and automated areole measurement for quantifying aspects of leaf venation

Walton A. Green, Stefan A. Little, Charles A. Price, Scott L. Wing, Selena Y. Smith, Benjamin Kotrc & Gabriela Doria
The reticulate venation that is characteristic of a dicot leaf has excited interest from systematists for more than a century, and from physiological and developmental botanists for decades. The tools of digital image acquisition and computer image analysis, however, are only now approaching the sophistication needed to quantify aspects of the venation network found in real leaves quickly, easily, accurately, and reliably enough to produce biologically meaningful data. In this paper, we examine 120 leaves...

Data from: Evidence for a time-invariant phase variable in human ankle control

Robert D. Gregg, Elliott J. Rouse, Levi J. Hargrove & Jonathon W. Sensinger
Human locomotion is a rhythmic task in which patterns of muscle activity are modulated by state-dependent feedback to accommodate perturbations. Two popular theories have been proposed for the underlying embodiment of phase in the human pattern generator: a time-dependent internal representation or a time-invariant feedback representation (i.e., reflex mechanisms). In either case the neuromuscular system must update or represent the phase of locomotor patterns based on the system state, which can include measurements of hundreds...

Data from: Extensive introgression in a malaria vector species complex revealed by phylogenomics

Michael C. Fontaine, James B. Pease, Aaron Steele, Robert M. Waterhouse, Daniel E. Neafsey, Igor V. Sharakhov, Xiofang Jiang, Andrew B. Hall, Flaminia Catteruccia, Evdoxia Kakani, Sarah N. Mitchell, Yi-Chieh Wu, Hilary A. Smith, R. Rebecca Love, Mara K. Lawniczak, Michel A. Slotman, Scott J. Emrich, Matthew W. Hahn & Nora J. Besansky
Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny, and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between...

Data from: Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

Eduardo M. Torres, Noah Dephoure, Sunyoung Hwang, Ciara O’Sullivan, Stacie E. Dodgson, Steve P. Gygi, Angelika Amon & Ciara O'Sullivan
Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our...

Data from: Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus

Nadav Kashtan, Sara E. Roggensack, Sébastien Rodrigue, Jessie W. Thompson, Steven J. Biller, Allison Coe, Huiming Ding, Pekka Marttinen, Rex R. Malmstrom, Roman Stocker, Michael J. Follows, Ramunas Stepanauskas & Sallie W. Chisholm
Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct “genomic backbones,” each backbone consisting of a different set of...

Registration Year

  • 2014
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Resource Types

  • Dataset
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Affiliations

  • Massachusetts Institute of Technology
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  • Northwestern University
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  • Howard Hughes Medical Institute
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  • University of Michigan-Ann Arbor
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  • University of Notre Dame
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  • Oregon State University
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  • Texas A&M University
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  • Smithsonian Institution
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  • Rehabilitation Institute of Chicago
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  • Indiana University Bloomington
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