Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance

(2018) Zhichao Xu et al.   Molecular Plant

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

HINGE: long-read assembly achieves optimal repeat resolution

(2017) Govinda M. Kamath et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion

(2017) ZhouXian Ni et al.   MOLECULES

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

(2017) Su-Juan Wei et al.   Frontiers in Plant Science

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants

(2017) Zheng Xiao-Ming et al.   Scientific Reports

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

(2017) Francesca Giordano et al.   Scientific Reports

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

The Complete Chloroplast Genome Sequence of the Medicinal Plant Swertia mussotii Using the PacBio RS II Platform

(2016) Beibei Xiang et al.   MOLECULES

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Complete chloroplast genome sequences of Eucommia ulmoides: genome structure and evolution

(2016) Lin Wang et al.   Tree Genetics & Genomes

The Complete Chloroplast Genome Sequences for Four Amaranthus Species (Amaranthaceae)

(2016) Lindsay Chaney et al.   Applications in Plant Sciences

Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species

(2016) Zhiwen Chen et al.   PLoS One

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

(2016) Spyros Oikonomopoulos et al.   Scientific Reports

A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification

(2016) Bo Li et al.   Scientific Reports

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data

(2015) Amin Allam et al.   BIOINFORMATICS

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

(2015) R. M. Redwan et al.   BMC PLANT BIOLOGY

The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication

(2015) Delene J. Oldenburg et al.   CURRENT GENETICS

Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

(2015) N. Scarcelli et al.   Molecular Ecology Resources

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Comparative Analysis of Asteraceae Chloroplast Genomes: Structural Organization, RNA Editing and Evolution

(2015) Mengxing Wang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Evidence for local climate adaptation in early-life traits of Tasmanian populations of Eucalyptus pauciflora

(2015) Archana Gauli et al.   Tree Genetics & Genomes

Diurnal and seasonal variation in light and dark respiration in field-grownEucalyptus pauciflora

(2015) Danielle A. Way et al.   TREE PHYSIOLOGY

Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus

(2015) Peng-Fei Ma et al.   Scientific Reports

Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

(2014) Hui Huang et al.   BMC EVOLUTIONARY BIOLOGY

A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots

(2014) Zhihua Wu et al.   BMC PLANT BIOLOGY

Plastid DNA insertions in plant nuclear genomes: the sites, abundance and ages, and a predicted promoter analysis

(2014) Hongyu Chen et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Combined Analysis of the Chloroplast Genome and Transcriptome of the Antarctic Vascular Plant Deschampsia antarctica Desv

(2014) Jungeun Lee et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

(2013) Jun-Bo Yang et al.   BMC EVOLUTIONARY BIOLOGY

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

(2013) Marco Ferrarini et al.   BMC GENOMICS

Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)

(2013) Michael J. Bayly et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rapid hydraulic recovery inEucalyptus paucifloraafter drought: linkages between stem hydraulics and leaf gas exchange

(2013) SEBASTIÀ MARTORELL et al.   PLANT CELL AND ENVIRONMENT

Chloroplast phylogeny ofCucurbita: Evolution of the domesticated and wild species

(2013) Yi-Hong ZHENG et al.   Journal of Systematics and Evolution

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

(2012) Nolan Kane et al.   AMERICAN JOURNAL OF BOTANY

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Complete Chloroplast Genome Sequence of a Major Invasive Species, Crofton Weed (Ageratina adenophora)

(2012) Xiaojun Nie et al.   PLoS One

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

(2011) Dorothy A. Steane et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Nocturnal water loss in mature subalpineEucalyptus delegatensistall open forests and adjacentE. pauciflorawoodlands

(2011) Thomas N. Buckley et al.   Ecology and Evolution

Phylogeny and classification ofEucalyptussubgenusEudesmia(Myrtaceae) based on nuclear ribosomal DNA, chloroplast DNA and morphology

(2009) Adele K. Gibbs et al.   AUSTRALIAN SYSTEMATIC BOTANY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Uptake of inorganic and amino acid nitrogen from soil by Eucalyptus regnans and Eucalyptus pauciflora seedlings

(2009) C. R. Warren   TREE PHYSIOLOGY

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

(2008) Tomonori Hirao et al.   BMC PLANT BIOLOGY

Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)

(2008) Robert K. Jansen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection

(2008) Kerstin Diekmann et al.   PLoS One