High-accuracyde novoassembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy

Plant DNA barcoding: from gene to genome

(2014) Xiwen Li et al.   BIOLOGICAL REVIEWS

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

(2013) Marco Ferrarini et al.   BMC GENOMICS

Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae)

(2013) Hoang Dang Khoa Do et al.   GENE

Phylogenetic Analysis of 47 Chloroplast Genomes Clarifies the Contribution of Wild Species to the Domesticated Apple Maternal Line

(2013) Svetlana V. Nikiforova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-Gen phylogeography of rainforest trees: exploring landscape-level cpDNA variation from whole-genome sequencing

(2013) M. van der Merwe et al.   Molecular Ecology Resources

Biogenesis and homeostasis of chloroplasts and other plastids

(2013) Paul Jarvis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

(2013) Dan G. Bock et al.   NEW PHYTOLOGIST

Synthetic biology in plastids

(2013) Lars B. Scharff et al.   PLANT JOURNAL

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2013) Jun Qian et al.   PLoS One

Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants

(2013) Yue Liu et al.   PLoS One

Comparative Genome Analysis and Phylogenetic Relationship of Order Liliales Insight from the Complete Plastid Genome Sequences of Two Lilies (Lilium longiflorum and Alstroemeria aurea)

(2013) Jung Sung Kim et al.   PLoS One

Comparative Chloroplast Genomes of Camellia Species

(2013) Jun-Bo Yang et al.   PLoS One

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree

(2013) Hannah McPherson et al.   BMC ECOLOGY

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

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

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire

(2012) Peter A Larsen et al.   BMC IMMUNOLOGY

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

(2012) E. E. Schadt et al.   GENOME RESEARCH

Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia

(2012) Catherine C. Smith et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

The Complete Chloroplast and Mitochondrial Genome Sequences of Boea hygrometrica: Insights into the Evolution of Plant Organellar Genomes

(2012) Tongwu Zhang et al.   PLoS One

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

(2012) Xiaojun Nie et al.   PLoS One

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

(2012) Y. H. Grad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

(2011) L. Doorduin et al.   DNA RESEARCH

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

(2011) Tyson A. Clark et al.   NUCLEIC ACIDS RESEARCH

High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA

(2011) Wenqin Wang et al.   PLoS One

Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies

(2010) Ching-Ping Lin et al.   Genome Biology and Evolution

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)

(2010) A. J. Alverson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

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

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE