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Supplementary data on the four genomes of Zygnema
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January 2024 |
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Genome Annotation and Curation Using MAKER and MAKER‐P
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BUSCO: Assessing Genome Assembly and Annotation Completeness
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Ultrastructure of mitosis and cytokinesis inZygnema sp. (Zygnematales, Chlorophyta)
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An ELIP-like gene in the freshwater green alga, Spirogyra varians (Zygnematales), is regulated by cold stress and CO2 influx
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MYB transcription factor genes as regulators for plant responses: an overview
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The SCARECROW Gene Regulates an Asymmetric Cell Division That Is Essential for Generating the Radial Organization of the Arabidopsis Root
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KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
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Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
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October 2017 |
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The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization
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July 2018 |
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Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution
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November 2019 |
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The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants
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May 2020 |
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The Evolutionary Origin of a Terrestrial Flora
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October 2015 |
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The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte
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March 2018 |
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An Evolutionarily Conserved Abscisic Acid Signaling Pathway Regulates Dormancy in the Liverwort Marchantia polymorpha
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November 2018 |
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The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty
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February 2020 |
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Plant immunity: Crosstalk between plant immune receptors
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June 2021 |
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A phylogenomically informed five-order system for the closest relatives of land plants
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October 2022 |
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Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land
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February 2024 |
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Phylogenomic insights into the first multicellular streptophyte
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February 2024 |
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A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants
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February 2022 |
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The vegetative arctic freshwater green alga Zygnema is insensitive to experimental UV exposure
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December 2009 |
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An alternative, zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants
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January 2022 |
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Major episodes of horizontal gene transfer drove the evolution of land plants
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May 2022 |
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Something ancient and something neofunctionalized—evolution of land plant hormone signaling pathways
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February 2019 |
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MYB transcription factors in Arabidopsis
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October 2010 |
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Cellulose Synthesis – Central Components and Their Evolutionary Relationships
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May 2019 |
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The plant perceptron connects environment to development
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March 2017 |
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Widespread impact of horizontal gene transfer on plant colonization of land
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January 2012 |
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Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation
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May 2014 |
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Phytochrome diversity in green plants and the origin of canonical plant phytochromes
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July 2015 |
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Fast gapped-read alignment with Bowtie 2
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March 2012 |
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ModelFinder: fast model selection for accurate phylogenetic estimates
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May 2017 |
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Conservation of ethylene as a plant hormone over 450 million years of evolution
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January 2015 |
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Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions
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April 2019 |
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Role of Raf-like kinases in SnRK2 activation and osmotic stress response in plants
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December 2020 |
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Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants
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February 2022 |
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Genomes of early-diverging streptophyte algae shed light on plant terrestrialization
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December 2019 |
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Environmental gradients reveal stress hubs pre-dating plant terrestrialization
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August 2023 |
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Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants
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September 2022 |
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One thousand plant transcriptomes and the phylogenomics of green plants
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October 2019 |
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Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
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August 2019 |
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Efficient hybrid de novo assembly of human genomes with WENGAN
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December 2020 |
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Fast and accurate long-read assembly with wtdbg2
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December 2019 |
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Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs)
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August 2019 |
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From The Cover: A chimeric photoreceptor gene, NEOCHROME, has arisen twice during plant evolution
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September 2005 |
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Early light-induced proteins protect Arabidopsis from photooxidative stress
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April 2003 |
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Phylotranscriptomic analysis of the origin and early diversification of land plants
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October 2014 |
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Embryophyte stress signaling evolved in the algal progenitors of land plants
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March 2018 |
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The timescale of early land plant evolution
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February 2018 |
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A ligand-independent origin of abscisic acid perception
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November 2019 |
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RepeatModeler2 for automated genomic discovery of transposable element families
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April 2020 |
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Biochemical Characterization and Molecular Cloning of an α-1,2-Fucosyltransferase That Catalyzes the Last Step of Cell Wall Xyloglucan Biosynthesis in Pea
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March 2000 |
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CAFE 5 models variation in evolutionary rates among gene families
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December 2020 |
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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
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April 2012 |
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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January 2014 |
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hybridSPAdes: an algorithm for hybrid assembly of short and long reads
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November 2015 |
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Minimap2: pairwise alignment for nucleotide sequences
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May 2018 |
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Evo-physio: on stress responses and the earliest land plants
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January 2020 |
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Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution
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March 2020 |
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The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates
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February 2009 |
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
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February 2020 |
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The Origin of Floral Quartet Formation—Ancient Exon Duplications Shaped the Evolution of MIKC-type MADS-domain Transcription Factor Interactions
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April 2023 |
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
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UFBoot2: Improving the Ultrafast Bootstrap Approximation
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October 2017 |
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Database resources of the National Center for Biotechnology Information
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October 2020 |
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PhycoCosm, a comparative algal genomics resource
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October 2020 |
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The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
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December 2011 |
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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
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GeSeq – versatile and accurate annotation of organelle genomes
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May 2017 |
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CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses
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May 2018 |
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dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
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May 2018 |
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OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes
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April 2019 |
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ACTIN-RELATED PROTEIN8 Encodes an F-Box Protein Localized to the Nucleolus in Arabidopsis
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May 2008 |
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Two Endosomal NHX-Type Na+/H+ Antiporters are Involved in Auxin-Mediated Development in Arabidopsis thaliana
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May 2018 |
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
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March 2010 |
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Fast and accurate de novo genome assembly from long uncorrected reads
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January 2017 |
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Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
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March 2017 |
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Environmental and Developmental Regulation of the Wound-Induced Cell Wall Protein WI12 in the Halophyte Ice Plant
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October 2001 |
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Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm
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November 2009 |
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SHORT-ROOT and SCARECROW Regulate Leaf Growth in Arabidopsis by Stimulating S-Phase Progression of the Cell Cycle
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August 2010 |
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Insights into the Origin and Evolution of the Plant Hormone Signaling Machinery
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January 2015 |
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Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells
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February 2019 |
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The Arabidopsis Intracellular Na + /H + Antiporters NHX5 and NHX6 Are Endosome Associated and Necessary for Plant Growth and Development
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January 2011 |
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Coping with Stresses: Roles of Calcium- and Calcium/Calmodulin-Regulated Gene Expression
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June 2011 |
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Structural Basis for the Oligomerization of the MADS Domain Transcription Factor SEPALLATA3 in Arabidopsis
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September 2014 |
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TheArabidopsisEDR1 Protein Kinase Negatively Regulates the ATL1 E3 Ubiquitin Ligase to Suppress Cell Death
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November 2014 |
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Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a Zygnema green algal mat from Svalbard (High Arctic)
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September 2019 |
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The TUMOROUS SHOOT DEVELOPMENT2 gene of Arabidopsis encoding a putative methyltransferase is required for cell adhesion and co-ordinated plant development: The Arabidopsis TSD2 gene
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April 2007 |
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A HECT E3 ubiquitin ligase negatively regulates Arabidopsis leaf senescence through degradation of the transcription factor WRKY53: E3 ubiquitin ligase regulates senescence
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April 2010 |
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Evolutionary and comparative analysis of MYB and bHLH plant transcription factors: Plant MYB and bHLH factors
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March 2011 |
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Origin of strigolactones in the green lineage
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June 2012 |
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Mitogen‐activated protein kinase cascades in plant signaling
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February 2022 |
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Phylogenetic position of Zygogonium ericetorum (Zygnematophyceae, Charophyta) from a high alpine habitat and ultrastructural characterization of unusual aplanospores
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September 2014 |
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A divergent RWP‐RK transcription factor determines mating type in heterothallic Closterium
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January 2023 |
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WI12Rhg1 interacts with DELLAs and mediates soybean cyst nematode resistance through hormone pathways
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journal
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October 2021 |
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The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
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January 2018 |
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Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms
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January 2018 |
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The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families
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July 2021 |
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The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
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October 2007 |
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Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri
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July 2010 |
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Chromatin plasticity: A versatile landscape that underlies cell fate and identity
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September 2018 |
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Lipid exchanges drove the evolution of mutualism during plant terrestrialization
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May 2021 |
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Plant “helper” immune receptors are Ca 2+ -permeable nonselective cation channels
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June 2021 |
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Green Algal Models for Multicellularity
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November 2021 |
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The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales
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October 2005 |
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Evolutionary history and functional implications of protein domains and their combinations in eukaryotes
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January 2007 |
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MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
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October 2018 |
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OrthoFinder: phylogenetic orthology inference for comparative genomics
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November 2019 |
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MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution
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September 2016 |
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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
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November 2014 |
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Nitrogen Limitation and Slow Drying Induce Desiccation Tolerance in Conjugating Green Algae (Zygnematophyceae, Streptophyta) from Polar Habitats
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journal
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November 2014 |
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Improved Methods for Acetocarmine and Haematoxylin Staining to Visualize Chromosomes in the Filamentous Green Alga Zygnema (Charophyta)
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journal
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January 2023 |
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Messages From the Past: New Insights in Plant Lectin Evolution
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journal
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January 2019 |
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Homogalacturonan Accumulation in Cell Walls of the Green Alga Zygnema sp. (Charophyta) Increases Desiccation Resistance
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journal
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April 2019 |
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Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion
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June 2019 |
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Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface
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journal
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December 2020 |
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Characterization of Two Zygnema Strains (Zygnema circumcarinatum SAG 698-1a and SAG 698-1b) and a Rapid Method to Estimate Nuclear Genome Size of Zygnematophycean Green Algae
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journal
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February 2021 |
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Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity
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July 2021 |
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Patterns of cell division in the filamentous Desmidiaceae, close green algal relatives of land plants
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journal
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June 2008 |
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Supplementary data on the four genomes of Zygnema
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dataset
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January 2024 |
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MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
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collection
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January 2018 |
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Plant Trans-Golgi Network/Early Endosome pH regulation requires Cation Chloride Cotransporter (CCC1)
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January 2022 |