Nature Search

Recruitment, rewiring and deep conservation in flowering plant gene regulation

A highly scalable approach is used to generate 3,000 genome-wide maps of transcription factor binding in ten flowering plants, along with multi-species single-nucleus RNA-seq atlases. Together, the results reveal both ancient regulation and key regulatory adaptations.

Leo A. Baumgart
Sharon I. Greenblum
Ronan C. O’Malley
Research15 Jul 2025
Nature Plants

Volume: 11, P: 1514-1527
Erratum: Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae

Chew Yee Ngan
Chee-Hong Wong
Chia-Lin Wei
Amendments and Corrections29 Sept 2015
Nature Plants

Volume: 1, P: 1
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients.

Kara Martin
Katrin Schmidt
Thomas Mock
ResearchOpen Access16 Sept 2021
Nature Communications

Volume: 12, P: 1-15
Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Genome assemblies of four filamentous Zygnematophyceae and co-expression network analyses shed light on the evolutionary roots of the mechanism for balancing environmental responses and multicellular growth.

Xuehuan Feng
Jinfang Zheng
Yanbin Yin
ResearchOpen Access01 May 2024
Nature Genetics

Volume: 56, P: 1018-1031
Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass

Paspalum vaginatum is a stress tolerant wild relative of maize and sorghum. Here, the authors assemble its genome at pseudomolecule level and reveal the role of trehalose mediated autophagy in increasing maize biomass productivity under nutrient-deficit conditions.

Guangchao Sun
Nishikant Wase
James C. Schnable
ResearchOpen Access13 Dec 2022
Nature Communications

Volume: 13, P: 1-20
A comparative genomics study of 23 Aspergillus species from section Flavi

Aspergillus fungi classified within the section Flavi include harmful and beneficial species. Here, Kjærbølling et al. analyse the genomes of 23 Flavi species, showing high genetic diversity and potential for synthesis of over 13,700 CAZymes and 1600 secondary metabolites.

Inge Kjærbølling
Tammi Vesth
Mikael R. Andersen
ResearchOpen Access27 Feb 2020
Nature Communications

Volume: 11, P: 1-12
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

John T. Lovell
Alice H. MacQueen
Jeremy Schmutz
ResearchOpen Access27 Jan 2021
Nature

Volume: 590, P: 438-444
Persistence and plasticity in bacterial gene regulation

This work presents biotin-DNA affinity purification (DAP) sequencing, that is, an in vitro, clone-free workflow to profile transcription factor (TF) DNA binding, as well as multiDAP to simultaneously characterize TF DNA binding in multiple bacterial genomes.

Leo A. Baumgart
Ji Eun Lee
Ronan C. O’Malley
Research25 Nov 2021
Nature Methods

Volume: 18, P: 1499-1505
The genomic landscape of molecular responses to natural drought stress in Panicum hallii

Drought is a major factor limiting crop productivity. Here, via eQTL analysis and comparative genomics, the authors show compensatory evolution between trans-regulatory loci and transcription factor binding sites that shape the drought response networks in the model C4 grass Panicum hallii.

John T. Lovell
Jerry Jenkins
Thomas E. Juenger
ResearchOpen Access06 Dec 2018
Nature Communications

Volume: 9, P: 1-10
Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae

The production of alga-derived lipids, a valuable source of biofuels, is restricted by the growth arrest of algae. Now a regulator of algal lipid accumulation is identified using an integrative chromatin signature and transcriptomic analysis.

Chew Yee Ngan
Chee-Hong Wong
Chia-Lin Wei
Research27 Jul 2015
Nature Plants

Volume: 1, P: 1-12
The role of zinc in the adaptive evolution of polar phytoplankton

Polar microalgae have high zinc demand. Here, the authors use quantitative proteomics and transcriptomics of polar and non-polar model algae combined with cellular physiology to show that zinc plays an important role in supporting photosynthetic growth in eukaryotic polar phytoplankton.

Naihao Ye
Wentao Han
Thomas Mock
Research02 Jun 2022
Nature Ecology & Evolution

Volume: 6, P: 965-978
Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

Tiffany Oliver
Neha Varghese
Emiley A. Eloe-Fadrosh
ResearchOpen Access04 Sept 2024
Scientific Data

Volume: 11, P: 1-7
Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

Eva Högfors-Rönnholm
Margarita Lopez-Fernandez
Mark Dopson
ResearchOpen Access16 Oct 2019
Scientific Data

Volume: 6, P: 1-6
Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi

Probing the evolution of bacterial endosymbionts in Mucoromycota - Mollicutes-related endobacteria (MRE) - reveals that the genera Linnemannia and Benniella acquired MRE after host divergence from a common ancestor.

Reid Longley
Aaron Robinson
Gregory Bonito
ResearchOpen Access18 Sept 2023
Communications Biology

Volume: 6, P: 1-13
Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Marc Van Goethem et al. combine short- and long-read sequencing from biocrust samples to report nearly 3,000 biosynthetic gene clusters (BGCs) encoding microbial secondary metabolites. Their results demonstrate the advantage of integrated metatranscriptomic and long-read metagenomic sequencing in analyzing BGCs and provides insight into the role of secondary metabolites in maintaining phylogenetic niches in biocrusts.

Marc W. Van Goethem
Andrew R. Osborn
Trent R. Northen
ResearchOpen Access18 Nov 2021
Communications Biology

Volume: 4, P: 1-10
Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days

Brook L. Nunn
Emma Timmins-Schiffman
Emiley A. Eloe-Fadrosh
ResearchOpen Access22 Nov 2024
Scientific Data

Volume: 11, P: 1-8
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot

Antonio Pedro Camargo
Rafael Soares Correa de Souza
Rafael Silva Oliveira
ResearchOpen Access31 Jul 2019
Scientific Data

Volume: 6, P: 1-11
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

Brent Nowinski
Christa B. Smith
Mary Ann Moran
ResearchOpen Access22 Jul 2019
Scientific Data

Volume: 6, P: 1-7

Search

Recruitment, rewiring and deep conservation in flowering plant gene regulation

Erratum: Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass

A comparative genomics study of 23 Aspergillus species from section Flavi

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

Persistence and plasticity in bacterial gene regulation

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae

The role of zinc in the adaptive evolution of polar phytoplankton

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials

Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot

Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

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