17 Works

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 6 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 6: Supplemental Table S5. Genomic abundance of MEROPS proteae gene per MAG. Columns indicate MEROPS protease families. APE = atom percent excess.

Additional file 7 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 7: Supplemental Table S6. CAZymes for the Myxococcota MAGs. Fen-1088 MAGs are highlighted in yellow. MAGs are sorted by increasing atom percent excess (APE) 13C.

Additional file 8 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 8: Supplemental Table S7. Number of CAZy gene homologs that can potentially target a particular substrate. Substrate assignments based off of the Glycoside Hydrolase categories from Berlemonte and Martiny 2015.

Additional file 3 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 3: Supplemental Table S2. Assembly metrics using single fraction assembly (metaspades) verses co-assembly of all fractions (MetaHipMer2).

Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

Rubén Sancho, Luis Ángel Inda, Antonio Díaz-Pérez, David L Des Marais, Sean Gordon, John Vogel, Joanna Lusinska, Robert Hasterok, Bruno Contreras-Moreira & Pilar Catalán
Unraveling the evolution of plant polyploids is a challenge when their diploid progenitor species are extinct or unknown or when genome sequences of known progenitors are unavailable. Existing subgenome identification methods cannot adequately infer the homeologous genomes that are present in the allopolyploids if they do not take into account the potential existence of unknown progenitors. We addressed this challenge in the widely distributed dysploid grass genus Brachypodium, which is a model genus for temperate...

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures

Jørn Henrik Sønstebø, Emiliano Trucchi, Jenni Nordén, Inger Skrede, Otto Miettinen, Sajeet Haridas, Jasmyn Pangilinan, Igor V. Grigoriev, Francis Martin, Håvard Kauserud & Sundy Maurice
Genome sequencing of spatially distributed individuals sheds light on how evolution structures genetic variation. Populations of Phellopilus nigrolimitatus, a red-listed wood-inhabiting fungus associated with old-growth coniferous forests, have decreased in size over the last century due to a loss of suitable habitats. We assessed the population genetic structure and investigated local adaptation in P. nigrolimitatus, by establishing a reference genome and genotyping 327 individuals sampled from 24 locations in Northern Europe by RAD sequencing. We...

Additional file 6 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 6: Supplemental Table S5. Genomic abundance of MEROPS proteae gene per MAG. Columns indicate MEROPS protease families. APE = atom percent excess.

Additional file 7 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 7: Supplemental Table S6. CAZymes for the Myxococcota MAGs. Fen-1088 MAGs are highlighted in yellow. MAGs are sorted by increasing atom percent excess (APE) 13C.

Census and phenotype data supporting Drosophila adaptive tracking

Seth Rudman, Paul Schmidt, Subhash Rajpurohit, Sharon Greenblum & Dmitri Petrov
Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked evolution of fitness-associated phenotypes and allele frequencies genome-wide in ten replicate field populations of Drosophila melanogaster over ten generations from summer to late fall. Adaptation was evident over each sampling interval (1-4 generations) with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent...

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Additional file 8 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 8: Supplemental Table S7. Number of CAZy gene homologs that can potentially target a particular substrate. Substrate assignments based off of the Glycoside Hydrolase categories from Berlemonte and Martiny 2015.

Additional file 3 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 3: Supplemental Table S2. Assembly metrics using single fraction assembly (metaspades) verses co-assembly of all fractions (MetaHipMer2).

Registration Year

  • 2022
    17

Resource Types

  • Dataset
    17

Affiliations

  • Joint Genome Institute
    17
  • University of Massachusetts Amherst
    14
  • University of California, Merced
    14
  • University of California, Berkeley
    14
  • Lawrence Berkeley National Laboratory
    14
  • Lawrence Livermore National Laboratory
    14
  • University of Pennsylvania
    1
  • Stanford University
    1
  • Marche Polytechnic University
    1
  • University of Silesia
    1