Optimized Method of Extracting Rice Chloroplast DNA for High-Quality Plastome Resequencing and de Novo Assembly

An analytical workflow for accurate variant discovery in highly divergent regions

(2016) Shulan Tian et al.   BMC GENOMICS

N-Glycomic and Microscopic Subcellular Localization Analyses of NPP1, 2 and 6 Strongly Indicate thattrans-Golgi Compartments Participate in the Golgi to Plastid Traffic of Nucleotide Pyrophosphatase/Phosphodiesterases in Rice

(2016) Kentaro Kaneko et al.   PLANT AND CELL PHYSIOLOGY

Chloroplasts: state of research and practical applications of plastome sequencing

(2016) Szymon Adam Olejniczak et al.   PLANTA

Cytonuclear interactions affect adaptive traits of the annual plantArabidopsis thalianain the field

(2016) Fabrice Roux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing

(2016) Wei Tong et al.   Rice

Impact of three Illumina library construction methods on GC bias and HLA genotype calling

(2015) James H. Lan et al.   HUMAN IMMUNOLOGY

The complete chloroplast genome ofCinnamomum kanehiraeHayata (Lauraceae)

(2015) Chia-Chen Wu et al.   Mitochondrial DNA

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

(2015) Kyunghee Kim et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Using plants to elucidate the mechanisms of cytonuclear co-evolution

(2014) Daniel B. Sloan   NEW PHYTOLOGIST

Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data

(2014) Ming Yi et al.   NUCLEIC ACIDS RESEARCH

Tuning a ménage à trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants

(2013) Stephan Greiner et al.   BIOESSAYS

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

(2013) Marco Ferrarini et al.   BMC GENOMICS

De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers

(2013) Ken Naito et al.   BREEDING SCIENCE

Patterns of Genomic Integration of Nuclear Chloroplast DNA Fragments in Plant Species

(2013) T. Yoshida et al.   DNA RESEARCH

Variant Callers for Next-Generation Sequencing Data: A Comparison Study

(2013) Xiangtao Liu et al.   PLoS One

Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

(2013) Bindu Joseph et al.   eLife

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

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

Cytonuclear epistatic quantitative trait locus mapping for plant height and ear height in maize

(2012) Zaixiang Tang et al.   MOLECULAR BREEDING

An Improved Chloroplast DNA Extraction Procedure for Whole Plastid Genome Sequencing

(2012) Chao Shi et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape

(2011) GEOFFREY P. MORRIS et al.   MOLECULAR ECOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Chloroplast genome sequences from total DNA for plant identification

(2010) Catherine J. Nock et al.   PLANT BIOTECHNOLOGY JOURNAL

Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thaliana

(2010) Michaël Moison et al.   PLANT JOURNAL

A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly

(2010) Bjarne Knudsen et al.   Genes

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A multiple-method approach reveals a declining amount of chloroplast DNA during development in Arabidopsis

(2009) Beth A Rowan et al.   BMC PLANT BIOLOGY

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

(2009) R. Li et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

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

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato DDB1-interacting protein CUL4

(2008) Songhu Wang et al.   PLANT JOURNAL

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