Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium

Symbiodiniaceae‐bacteria interactions: rethinking metabolite exchange in reef‐building corals as multi‐partner metabolic networks

(2020) Jennifer L. Matthews et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)

(2020) Kshitij Tandon et al.   ISME Journal

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

(2020) Andrea Del Cortona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

(2020) Sonja I. Repetti et al.   PeerJ

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Functional diversity of microboring Ostreobium algae isolated from corals

(2020) Anaïs Massé et al.   ENVIRONMENTAL MICROBIOLOGY

Carbonate dissolution by reef microbial borers: a biogeological process producing alkalinity under different pCO2 conditions

(2019) A. Tribollet et al.   FACIES

A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes

(2019) Waldan K. Kwong et al.   NATURE

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

(2019) Steven J. Robbins et al.   Nature Microbiology

Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes

(2019) Yibi Chen et al.   JOURNAL OF PHYCOLOGY

Phytochrome evolution in 3D: deletion, duplication, and diversification

(2019) Nathan C. Rockwell et al.   NEW PHYTOLOGIST

Beneath the surface: community assembly and functions of the coral skeleton microbiome

(2019) Francesco Ricci et al.   Microbiome

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Reactive oxygen species, oxidative signaling and the regulation of photosynthesis

(2018) Christine H. Foyer   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

(2018) Ma Chiela M Cremen et al.   Genome Biology and Evolution

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

(2018) Alexandre Lomsadze et al.   GENOME RESEARCH

Rapid and precise alignment of raw reads against redundant databases with KMA

(2018) Philip T. L. C. Clausen et al.   BMC BIOINFORMATICS

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Identification and characterization of a solute carrier, CIA8, involved in inorganic carbon acclimation in Chlamydomonas reinhardtii

(2017) Marylou C Machingura et al.   JOURNAL OF EXPERIMENTAL BOTANY

Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data

(2017) Heroen Verbruggen et al.   JOURNAL OF PHYCOLOGY

Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions

(2017) Tilman Kottke et al.   JOURNAL OF PLANT PHYSIOLOGY

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversity and stability of coral endolithic microbial communities at a naturally high p CO2 reef

(2017) Vanessa Rossetto Marcelino et al.   MOLECULAR ECOLOGY

Photoprotection in a monophyletic branch of chlorophyte algae is independent of energy-dependent quenching (qE)

(2017) Gregor Christa et al.   NEW PHYTOLOGIST

Algal light sensing and photoacclimation in aquatic environments

(2017) Deqiang Duanmu et al.   PLANT CELL AND ENVIRONMENT

Taxonomic revision of Halimeda (Bryopsidales, Chlorophyta) in south-western Australia

(2016) Ma. Chiela M. Cremen et al.   AUSTRALIAN SYSTEMATIC BOTANY

Empty Niches after Extinctions Increase Population Sizes of Modern Corals

(2016) Carlos Prada et al.   CURRENT BIOLOGY

Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green AlgaOstreobium quekettii

(2016) Vanessa R. Marcelino et al.   Genome Biology and Evolution

Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the GenusSymbiodinium

(2016) John E. Parkinson et al.   Genome Biology and Evolution

The ‘other’ coral symbiont: Ostreobium diversity and distribution

(2016) Javier del Campo et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae

(2016) Vanessa Rossetto Marcelino et al.   Scientific Reports

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

(2016) M. Aranda et al.   Scientific Reports

Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

(2015) Heather M Hunsperger et al.   BMC EVOLUTIONARY BIOLOGY

The genome ofAiptasia, a sea anemone model for coral symbiosis

(2015) Sebastian Baumgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis

(2015) S. Lin et al.   SCIENCE

Nitrogen cycling in corals: the key to understanding holobiont functioning?

(2015) Nils Rädecker et al.   TRENDS IN MICROBIOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

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

Marine algae and land plants share conserved phytochrome signaling systems

(2014) D. Duanmu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Phylogeny and Molecular Evolution of the Green Algae

(2012) Frederik Leliaert et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Evidence that glucose is the major transferred metabolite in dinoflagellate-cnidarian symbiosis

(2012) M. S. Burriesci et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

PredAlgo: A New Subcellular Localization Prediction Tool Dedicated to Green Algae

(2012) Marianne Tardif et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Flavin Binding Cryptochrome Photoreceptor Responds to Both Blue and Red Light in Chlamydomonas reinhardtii

(2012) B. Beel et al.   PLANT CELL

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Genotypic diversity and distribution of Ostreobium quekettii within scleractinian corals

(2011) Eldad Gutner-Hoch et al.   CORAL REEFS

Boring algae

(2011) Heroen Verbruggen et al.   CURRENT BIOLOGY

Insights into the Evolution of Vitamin B12 Auxotrophy from Sequenced Algal Genomes

(2011) K. E. Helliwell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Evolutionary distribution of light-harvesting complex-like proteins in photosynthetic eukaryotes

(2010) Jonathan A.D. Neilson et al.   GENOME

Structural and functional diversification of the light-harvesting complexes in photosynthetic eukaryotes

(2010) Jonathan A. D. Neilson et al.   PHOTOSYNTHESIS RESEARCH

Microbial excavation of solid carbonates powered by P-type ATPase-mediated transcellular Ca2+ transport

(2010) F. Garcia-Pichel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A short overview of chlorophyll biosynthesis in algae

(2008) Eliška Gálová et al.   BIOLOGIA

IMAGING OF OXYGEN DYNAMICS WITHIN THE ENDOLITHIC ALGAL COMMUNITY OF THE MASSIVE CORALPORITES LOBATA

(2008) Michael Kühl et al.   JOURNAL OF PHYCOLOGY

A multi-locus time-calibrated phylogeny of the siphonous green algae

(2008) Heroen Verbruggen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY