4 Works

Data from: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

Maggie R. Wagner, Derek S. Lundberg, Devin Coleman-Derr, Susannah G. Tringe, Jeffery L. Dangl & Thomas Mitchell-Olds
Plant phenology is known to depend on many different environmental variables, but soil microbial communities have rarely been acknowledged as possible drivers of flowering time. Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. Flowering time was sensitive to both microbes and the abiotic properties of different soils; varying soil microbiota also altered...

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...

Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Kevin L. Childs, Aruna Nandety, Candice N. Hirsch, Elsa Góngora-Castillo, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum) is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing reads derived from crown, young shoot and leaf tissues, we generated sequence data from seven switchgrass cultivars,...

Data from: Insights into the maize pan-genome and pan-transcriptome

Candice N. Hirsch, Jillian M. Foerster, James M. Johnson, Rajandeep S. Sekhon, German Muttoni, Brieanne Vaillancourt, Francisco Peñagaricano, Erika Lindquist, Mary Ann Pedraza, Kerrie Barry, Natalia De Leon, Shawn M. Kaeppler & C. Robin Buell
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs...

Registration Year

  • 2014
    4

Resource Types

  • Dataset
    4

Affiliations

  • Joint Genome Institute
    4
  • University of Wisconsin-Madison
    2
  • Michigan State University
    2
  • Duke University
    1
  • University of North Carolina
    1
  • Great Lakes Bioenergy Research Center
    1
  • Bigelow Laboratory for Ocean Sciences
    1
  • Massachusetts Institute of Technology
    1
  • HudsonAlpha Institute for Biotechnology
    1
  • Helsinki Institute for Information Technology
    1