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

The evolution of phylogeographic data sets

(2015) Ryan C. Garrick et al.   MOLECULAR ECOLOGY

Why are most organelle genomes transmitted maternally?

(2014) Stephan Greiner et al.   BIOESSAYS

History of Plastid DNA Insertions Reveals Weak Deletion and AT Mutation Biases in Angiosperm Mitochondrial Genomes

(2014) Daniel B. Sloan et al.   Genome Biology and Evolution

Changes in DNA damage, molecular integrity, and copy number for plastid DNA and mitochondrial DNA during maize development

(2014) Rachana A. Kumar et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

(2014) Cédric Mariac et al.   Molecular Ecology Resources

Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars

(2014) Jamal S. M. Sabir et al.   PLoS One

Detailed comparison of two popular variant calling packages for exome and targeted exon studies

(2014) Charles D. Warden et al.   PeerJ

Mitochondrial genetics

(2013) P. F. Chinnery et al.   BRITISH MEDICAL BULLETIN

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

(2013) T. Yoshida et al.   DNA RESEARCH

Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization

(2013) M Michalovova et al.   HEREDITY

Updating benchtop sequencing performance comparison

(2013) Sebastian Jünemann et al.   NATURE BIOTECHNOLOGY

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

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

(2013) Xiangtao Liu et al.   PLoS One

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

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

Plastid Sequences Contribute to Some Plant Mitochondrial Genes

(2012) D. Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

A Set of 100 Chloroplast DNA Primer Pairs to Study Population Genetics and Phylogeny in Monocotyledons

(2011) Nora Scarcelli et al.   PLoS One

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

(2011) André E Minoche et al.   GENOME BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Heteroplasmic mitochondrial DNA mutations in normal and tumour cells

(2010) Yiping He et al.   NATURE

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

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

Heteroplasmy and stoichiometric complexity of plant mitochondrial genomes--though this be madness, yet there's method in't

(2009) M. Woloszynska   JOURNAL OF EXPERIMENTAL BOTANY

Reconstructing evolution: Gene transfer from plastids to the nucleus

(2008) Ralph Bock et al.   BIOESSAYS