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

Journal Article · · Nature Genetics
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  1. Univ. of Nebraska, Lincoln, NE (United States); et al.

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
2407022
Journal Information:
Nature Genetics, Journal Name: Nature Genetics Journal Issue: 5 Vol. 56; ISSN 1061-4036
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

References (125)

Supplementary data on the four genomes of Zygnema dataset January 2024
Genome Annotation and Curation Using MAKER and MAKER‐P journal December 2014
BUSCO: Assessing Genome Assembly and Annotation Completeness book January 2019
Ultrastructure of mitosis and cytokinesis inZygnema sp. (Zygnematales, Chlorophyta) journal June 1987
An ELIP-like gene in the freshwater green alga, Spirogyra varians (Zygnematales), is regulated by cold stress and CO2 influx journal January 2013
MYB transcription factor genes as regulators for plant responses: an overview journal April 2013
The SCARECROW Gene Regulates an Asymmetric Cell Division That Is Essential for Generating the Radial Organization of the Arabidopsis Root journal August 1996
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies journal March 2010
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome journal October 2017
The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization journal July 2018
Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution journal November 2019
The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants journal May 2020
The Evolutionary Origin of a Terrestrial Flora journal October 2015
The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte journal March 2018
An Evolutionarily Conserved Abscisic Acid Signaling Pathway Regulates Dormancy in the Liverwort Marchantia polymorpha journal November 2018
The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty journal February 2020
Plant immunity: Crosstalk between plant immune receptors journal June 2021
A phylogenomically informed five-order system for the closest relatives of land plants journal October 2022
Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land journal February 2024
Phylogenomic insights into the first multicellular streptophyte journal February 2024
A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants journal February 2022
The vegetative arctic freshwater green alga Zygnema is insensitive to experimental UV exposure journal December 2009
An alternative, zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants journal January 2022
Major episodes of horizontal gene transfer drove the evolution of land plants journal May 2022
Something ancient and something neofunctionalized—evolution of land plant hormone signaling pathways journal February 2019
MYB transcription factors in Arabidopsis journal October 2010
Cellulose Synthesis – Central Components and Their Evolutionary Relationships journal May 2019
The plant perceptron connects environment to development journal March 2017
Widespread impact of horizontal gene transfer on plant colonization of land journal January 2012
Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation journal May 2014
Phytochrome diversity in green plants and the origin of canonical plant phytochromes journal July 2015
Fast gapped-read alignment with Bowtie 2 journal March 2012
ModelFinder: fast model selection for accurate phylogenetic estimates journal May 2017
Conservation of ethylene as a plant hormone over 450 million years of evolution journal January 2015
Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions journal April 2019
Role of Raf-like kinases in SnRK2 activation and osmotic stress response in plants journal December 2020
Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants journal February 2022
Genomes of early-diverging streptophyte algae shed light on plant terrestrialization journal December 2019
Environmental gradients reveal stress hubs pre-dating plant terrestrialization journal August 2023
Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants journal September 2022
One thousand plant transcriptomes and the phylogenomics of green plants journal October 2019
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype journal August 2019
Efficient hybrid de novo assembly of human genomes with WENGAN journal December 2020
Fast and accurate long-read assembly with wtdbg2 journal December 2019
Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs) journal August 2019
From The Cover: A chimeric photoreceptor gene, NEOCHROME, has arisen twice during plant evolution journal September 2005
Early light-induced proteins protect Arabidopsis from photooxidative stress journal April 2003
Phylotranscriptomic analysis of the origin and early diversification of land plants journal October 2014
Embryophyte stress signaling evolved in the algal progenitors of land plants journal March 2018
The timescale of early land plant evolution journal February 2018
A ligand-independent origin of abscisic acid perception journal November 2019
RepeatModeler2 for automated genomic discovery of transposable element families journal April 2020
Biochemical Characterization and Molecular Cloning of an α-1,2-Fucosyltransferase That Catalyzes the Last Step of Cell Wall Xyloglucan Biosynthesis in Pea journal March 2000
CAFE 5 models variation in evolutionary rates among gene families journal December 2020
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data journal April 2012
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies journal January 2014
hybridSPAdes: an algorithm for hybrid assembly of short and long reads journal November 2015
Minimap2: pairwise alignment for nucleotide sequences journal May 2018
Evo-physio: on stress responses and the earliest land plants journal January 2020
Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution journal March 2020
The diversity of plant U-box E3 ubiquitin ligases: from upstream activators to downstream target substrates journal February 2009
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era journal February 2020
The Origin of Floral Quartet Formation—Ancient Exon Duplications Shaped the Evolution of MIKC-type MADS-domain Transcription Factor Interactions journal April 2023
PAML 4: Phylogenetic Analysis by Maximum Likelihood journal April 2007
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability journal January 2013
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies journal November 2014
UFBoot2: Improving the Ultrafast Bootstrap Approximation journal October 2017
Database resources of the National Center for Biotechnology Information journal October 2020
PhycoCosm, a comparative algal genomics resource journal October 2020
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools journal December 2011
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity journal January 2012
GeSeq – versatile and accurate annotation of organelle genomes journal May 2017
CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses journal May 2018
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation journal May 2018
OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes journal April 2019
ACTIN-RELATED PROTEIN8 Encodes an F-Box Protein Localized to the Nucleolus in Arabidopsis journal May 2008
Two Endosomal NHX-Type Na+/H+ Antiporters are Involved in Auxin-Mediated Development in Arabidopsis thaliana journal May 2018
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 journal March 2010
Fast and accurate de novo genome assembly from long uncorrected reads journal January 2017
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation journal March 2017
Environmental and Developmental Regulation of the Wound-Induced Cell Wall Protein WI12 in the Halophyte Ice Plant journal October 2001
Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm journal November 2009
SHORT-ROOT and SCARECROW Regulate Leaf Growth in Arabidopsis by Stimulating S-Phase Progression of the Cell Cycle journal August 2010
Insights into the Origin and Evolution of the Plant Hormone Signaling Machinery journal January 2015
Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells journal February 2019
The Arabidopsis Intracellular Na + /H + Antiporters NHX5 and NHX6 Are Endosome Associated and Necessary for Plant Growth and Development journal January 2011
Coping with Stresses: Roles of Calcium- and Calcium/Calmodulin-Regulated Gene Expression journal June 2011
Structural Basis for the Oligomerization of the MADS Domain Transcription Factor SEPALLATA3 in Arabidopsis journal September 2014
TheArabidopsisEDR1 Protein Kinase Negatively Regulates the ATL1 E3 Ubiquitin Ligase to Suppress Cell Death journal November 2014
Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a Zygnema green algal mat from Svalbard (High Arctic) journal September 2019
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 journal April 2007
A HECT E3 ubiquitin ligase negatively regulates Arabidopsis leaf senescence through degradation of the transcription factor WRKY53: E3 ubiquitin ligase regulates senescence journal April 2010
Evolutionary and comparative analysis of MYB and bHLH plant transcription factors: Plant MYB and bHLH factors journal March 2011
Origin of strigolactones in the green lineage journal June 2012
Mitogen‐activated protein kinase cascades in plant signaling journal February 2022
Phylogenetic position of Zygogonium ericetorum (Zygnematophyceae, Charophyta) from a high alpine habitat and ultrastructural characterization of unusual aplanospores journal September 2014
A divergent RWP‐RK transcription factor determines mating type in heterothallic Closterium journal January 2023
WI12Rhg1 interacts with DELLAs and mediates soybean cyst nematode resistance through hormone pathways journal October 2021
The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution journal January 2018
Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms journal January 2018
The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families journal July 2021
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions journal October 2007
Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri journal July 2010
Chromatin plasticity: A versatile landscape that underlies cell fate and identity journal September 2018
Lipid exchanges drove the evolution of mutualism during plant terrestrialization journal May 2021
Plant “helper” immune receptors are Ca 2+ -permeable nonselective cation channels journal June 2021
Green Algal Models for Multicellularity journal November 2021
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 journal October 2005
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes journal January 2007
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes journal October 2018
OrthoFinder: phylogenetic orthology inference for comparative genomics journal November 2019
MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution journal September 2016
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement journal November 2014
Nitrogen Limitation and Slow Drying Induce Desiccation Tolerance in Conjugating Green Algae (Zygnematophyceae, Streptophyta) from Polar Habitats journal November 2014
Improved Methods for Acetocarmine and Haematoxylin Staining to Visualize Chromosomes in the Filamentous Green Alga Zygnema (Charophyta) journal January 2023
Messages From the Past: New Insights in Plant Lectin Evolution journal January 2019
Homogalacturonan Accumulation in Cell Walls of the Green Alga Zygnema sp. (Charophyta) Increases Desiccation Resistance journal April 2019
Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion journal June 2019
Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface journal December 2020
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 journal February 2021
Signatures of Transcription Factor Evolution and the Secondary Gain of Red Algae Complexity journal July 2021
Patterns of cell division in the filamentous Desmidiaceae, close green algal relatives of land plants journal June 2008
Supplementary data on the four genomes of Zygnema dataset January 2024
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes collection January 2018
Plant Trans-Golgi Network/Early Endosome pH regulation requires Cation Chloride Cotransporter (CCC1) journal January 2022


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