Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an insight into genome evolution and environmental adaptations in the Sphaeropleales

Cell reproductive patterns in the green alga Pseudokirchneriella subcapitata (=Selenastrum capricornutum) and their variations under exposure to the typical toxicants potassium dichromate and 3,5-DCP

(2017) Takahiro Yamagishi et al.   PLoS One

Chromosome-level genome assembly and transcriptome of the green algaChromochloris zofingiensisilluminates astaxanthin production

(2017) Melissa S. Roth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acidophilic green algal genome provides insights into adaptation to an acidic environment

(2017) Shunsuke Hirooka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous biological desalination and lipid production by Scenedesmus obliquus cultured with brackish water

(2016) Xinyu Gan et al.   DESALINATION

Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution

(2016) Karolina Fučíková et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Unique mitochondrial genome structure of the green algal strain YC001 (Sphaeropleales, Chlorophyta), with morphological observations

(2016) Hyung-Gwan Lee et al.   PHYCOLOGIA

The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity

(2016) Erik R. Hanschen et al.   Nature Communications

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)

(2015) Claude Lemieux et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic patterns of gene rearrangements in four mitochondrial genomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae)

(2015) Audrey A. Farwagi et al.   BMC GENOMICS

Comparative toxicity of 20 herbicides to 5 periphytic algae and the relationship with mode of action

(2015) Takashi Nagai et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Gene Arrangement Convergence, Diverse Intron Content, and Genetic Code Modifications in Mitochondrial Genomes of Sphaeropleales (Chlorophyta)

(2014) Karolina Fučíková et al.   Genome 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

Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits

(2014) Dongmei Wang et al.   PLoS Genetics

Identification of Monoraphidium contortum as a promising species for liquid biofuel production

(2013) Christian Bogen et al.   BIORESOURCE TECHNOLOGY

Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production

(2013) Christian Bogen et al.   BMC GENOMICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Screening Microalgae Strains for Biodiesel Production: Lipid Productivity and Estimation of Fuel Quality Based on Fatty Acids Profiles as Selective Criteria

(2012) Iracema Andrade Nascimento et al.   BioEnergy Research

Isolation of a novel strain of Monoraphidium sp. and characterization of its potential application as biodiesel feedstock

(2012) Xuya Yu et al.   BIORESOURCE TECHNOLOGY

Phylogeny and Molecular Evolution of the Green Algae

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

Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14

(2012) Daniel Wibberg et al.   JOURNAL OF BIOTECHNOLOGY

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

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

Lineage-specific fragmentation and nuclear relocation of the mitochondrial cox2 gene in chlorophycean green algae (Chlorophyta)

(2012) Elizabeth Rodríguez-Salinas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Salinity promotes growth of freshwaterNeochloris oleoabundansUTEX 1185 (Sphaeropleales, Chlorophyta): morphophysiological aspects

(2012) Costanza Baldisserotto et al.   PHYCOLOGIA

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana

(2012) Randor Radakovits et al.   Nature Communications

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Evolutionary view of acyl-CoA diacylglycerol acyltransferase (DGAT), a key enzyme in neutral lipid biosynthesis

(2011) Andreia C Turchetto-Zolet et al.   BMC EVOLUTIONARY BIOLOGY

Algal MIPs, high diversity and conserved motifs

(2011) Hanna I Anderberg et al.   BMC EVOLUTIONARY BIOLOGY

SSU rRNA GENE PHYLOGENY OF MORPHOSPECIES AFFILIATED TO THE BIOASSAY ALGA “SELENASTRUM CAPRICORNUTUM” RECOVERED THE POLYPHYLETIC ORIGIN OF CRESCENT-SHAPED CHLOROPHYTA1

(2011) Lothar Krienitz et al.   JOURNAL OF PHYCOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Differential lipid and fatty acid profiles of photoautotrophic and heterotrophic Chlorella zofingiensis: Assessment of algal oils for biodiesel production

(2010) Jin Liu et al.   BIORESOURCE TECHNOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Evolution of an Expanded Sex-Determining Locus in Volvox

(2010) P. Ferris et al.   SCIENCE

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

(2010) S. E. Prochnik et al.   SCIENCE

Microalga Scenedesmus obliquus as a potential source for biodiesel production

(2009) Shovon Mandal et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Both selective and neutral processes drive GC content evolution in the human genome

(2008) Uberto Pozzoli et al.   BMC EVOLUTIONARY BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Sugar-based growth, astaxanthin accumulation and carotenogenic transcription of heterotrophic Chlorella zofingiensis (Chlorophyta)

(2008) Ni Sun et al.   PROCESS BIOCHEMISTRY