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

A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants

(2019) Asuka Arimoto et al.   DNA RESEARCH

The mitochondrial and chloroplast genomes of the green alga Haematococcus are made up of nearly identical repetitive sequences

(2019) Xi Zhang et al.   CURRENT BIOLOGY

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

(2019) Francesco Ricci et al.   Microbiome

Protein evolution depends on multiple distinct population size parameters

(2018) Alexander Platt et al.   BMC EVOLUTIONARY BIOLOGY

The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration

(2018) Fengrong Zheng et al.   GENE

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

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria

(2018) Markéta Petrů et al.   BMC BIOLOGY

The GIY-YIG endonuclease domain of Arabidopsis MutS homolog 1 specifically binds to branched DNA structures

(2018) Kenji Fukui et al.   FEBS LETTERS

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

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

(2017) Heroen Verbruggen et al.   JOURNAL OF PHYCOLOGY

Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes

(2017) Marc Krasovec et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of the Chlorophyta: Insights from chloroplast phylogenomic analyses

(2017) Ling Fang et al.   Journal of Systematics and Evolution

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

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

Mitochondrial genome structure of photosynthetic eukaryotes

(2016) N. P. Yurina et al.   BIOCHEMISTRY-MOSCOW

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

Plant mitochondria contain the protein translocase subunits TatB and TatC

(2016) Chris Carrie et al.   JOURNAL OF CELL SCIENCE

The mutational hazard hypothesis of organelle genome evolution: 10 years on

(2016) David Roy Smith   MOLECULAR ECOLOGY

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Massive and Widespread Organelle Genomic Expansion in the Green Algal Genus Dunaliella

(2015) Michael Del Vasto et al.   Genome Biology and Evolution

Direct Estimate of the Spontaneous Mutation Rate Uncovers the Effects of Drift and Recombination in theChlamydomonas reinhardtiiPlastid Genome

(2015) Rob W. Ness et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cell wall and cell growth characteristics of giant-celled algae

(2015) Ichiro Mine et al.   PHYCOLOGICAL RESEARCH

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

(2015) David Roy Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genes and Junk in Plant Mitochondria—Repair Mechanisms and Selection

(2014) Alan C. Christensen   Genome Biology and Evolution

The plant mitochondrial genome: Dynamics and maintenance

(2013) José M. Gualberto et al.   BIOCHIMIE

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Is ftsH the Key to Plastid Longevity in Sacoglossan Slugs?

(2013) Jan de Vries et al.   Genome Biology and Evolution

Organelle Genome Complexity Scales Positively with Organism Size in Volvocine Green Algae

(2013) David Roy Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Phylogeny and Molecular Evolution of the Green Algae

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Contributions of Wobbling and Superwobbling to the Reading of the Genetic Code

(2012) Sibah Alkatib et al.   PLoS Genetics

Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

(2011) Jaime I Davila et al.   BMC BIOLOGY

The intriguing evolutionary dynamics of plant mitochondrial DNA

(2011) Nicolas Galtier   BMC BIOLOGY

Boring algae

(2011) Heroen Verbruggen et al.   CURRENT BIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape

(2011) David Roy Smith et al.   PLoS One

The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

(2010) David Smith et al.   BMC PLANT BIOLOGY

Low Nucleotide Diversity for the Expanded Organelle and Nuclear Genomes of Volvox carteri Supports the Mutational-Hazard Hypothesis

(2010) D. R. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and Cytological Diversification of the Green Seaweeds (Ulvophyceae)

(2010) E. Cocquyt et al.   MOLECULAR BIOLOGY AND EVOLUTION

tRNADB-CE 2011: tRNA gene database curated manually by experts

(2010) T. Abe et al.   NUCLEIC ACIDS RESEARCH

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA

(2009) David Smith et al.   BMC GENOMICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Disruption of a mitochondrial MutS DNA repair enzyme homologue confers drug resistance in the parasiteToxoplasma gondii

(2009) Erin M. Garrison et al.   MOLECULAR MICROBIOLOGY

Suppression of Repeat-Mediated Gross Mitochondrial Genome Rearrangements by RecA in the Moss Physcomitrella patens

(2009) M. Odahara et al.   PLANT CELL

The causes of mutation accumulation in mitochondrial genomes

(2009) M. Neiman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mitochondrial Genome of the Colorless Green Alga Polytomella capuana: A Linear Molecule with an Unprecedented GC Content

(2008) D. R. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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