Reticulate evolution in eukaryotes: Origin and evolution of the nitrate assimilation pathway

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

(2018) Matthew W Brown et al.   Genome Biology and Evolution

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

“Prokaryotic Pathway” Is Not Prokaryotic: Noncyanobacterial Origin of the Chloroplast Lipid Biosynthetic Pathway Revealed by Comprehensive Phylogenomic Analysis

(2017) Naoki Sato et al.   Genome Biology and Evolution

CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection

(2017) Jananan Sylvestre Pathmanathan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Between a Pod and a Hard Test: The Deep Evolution of Amoebae

(2017) Seungho Kang et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria

(2017) Judit Ámon et al.   Open Biology

Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome

(2017) Richard G Dorrell et al.   eLife

Dynamics of genomic innovation in the unicellular ancestry of animals

(2017) Xavier Grau-Bové et al.   eLife

A Eukaryote without a Mitochondrial Organelle

(2016) Anna Karnkowska et al.   CURRENT BIOLOGY

The evolution of Earth's biogeochemical nitrogen cycle

(2016) Eva E. Stüeken et al.   EARTH-SCIENCE REVIEWS

A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts)

(2016) Romain Derelle et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria

(2016) Ding He et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

(2016) Fabien Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

(2016) Eduardo Corel et al.   TRENDS IN MICROBIOLOGY

Nitrate reductase, nitrite reductase, glutamine synthetase, and glutamate synthase expression and activity in response to different nitrogen sources in nitrogen-starved wheat seedlings

(2015) Sadegh Balotf et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi

(2015) Guifré Torruella et al.   CURRENT BIOLOGY

Phylogenomic analysis of Emiliania huxleyi provides evidence for haptophyte–stramenopile association and a chimeric haptophyte nuclear genome

(2015) John J. Miller et al.   Marine Genomics

Evolutionary Origins of Rhizarian Parasites

(2015) Roberto Sierra et al.   MOLECULAR BIOLOGY AND EVOLUTION

Endosymbiotic origin and differential loss of eukaryotic genes

(2015) Chuan Ku et al.   NATURE

Bacterial proteins pinpoint a single eukaryotic root

(2015) Romain Derelle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens

(2015) Emile Gluck-Thaler et al.   PLoS Pathogens

The Role of Horizontal Gene Transfer in the Evolution of the Oomycetes

(2015) Fiona Savory et al.   PLoS Pathogens

Fungal metabolic gene clusters—caravans traveling across genomes and environments

(2015) Jennifer H. Wisecaver et al.   Frontiers in Microbiology

Understanding nitrate assimilation and its regulation in microalgae

(2015) Emanuel Sanz-Luque et al.   Frontiers in Plant Science

Horizontal Gene Transfer in Eukaryotic Plant Pathogens

(2014) Darren Soanes et al.   Annual Review of Phytopathology

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins

(2014) Blaise Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

(2014) Natalie Ward et al.   PLoS One

The evolution of photosynthesis in chromist algae through serial endosymbioses

(2014) John W. Stiller et al.   Nature Communications

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

The Number, Speed, and Impact of Plastid Endosymbioses in Eukaryotic Evolution

(2013) Patrick J. Keeling   Annual Review of Plant Biology

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

(2013) Christopher Sibthorp et al.   BMC GENOMICS

Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea)

(2013) Sally L. Glockling et al.   Fungal Ecology

Pseudo-constitutivity of nitrate-responsive genes in nitrate reductase mutants

(2013) Thorsten Schinko et al.   FUNGAL GENETICS AND BIOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis NIN-like transcription factors have a central role in nitrate signalling

(2013) Mineko Konishi et al.   Nature Communications

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

(2013) Michael Clarke et al.   GENOME BIOLOGY

Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen

(2012) Kiyotaka Takishita et al.   Biology Direct

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

(2012) Bruce A. Curtis et al.   NATURE

Marine Fungi: Their Ecology and Molecular Diversity

(2011) Thomas A. Richards et al.   Annual Review of Marine Science

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution

(2011) RLM Guedes et al.   BMC GENOMICS

Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria

(2011) Alexis Criscuolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Gene transfer into the fungi

(2011) Thomas A. Richards et al.   Fungal Biology Reviews

Nitrate Assimilatory Genes and Their Transcriptional Regulation in a Unicellular Red Alga Cyanidioschyzon merolae: Genetic Evidence for Nitrite Reduction by a Sulfite Reductase-Like Enzyme

(2010) Sousuke Imamura et al.   PLANT AND CELL PHYSIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Evolution and Future of Earth’s Nitrogen Cycle

(2010) Donald E. Canfield et al.   SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Reticulate Evolution and Marine Organisms: The Final Frontier?

(2009) Michael Arnold et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

R2R3-type MYB transcription factor, CmMYB1, is a central nitrogen assimilation regulator in Cyanidioschyzon merolae

(2009) S. Imamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS