Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

The Complete Plastid Genome Sequence of Madagascar Periwinkle Catharanthus roseus (L.) G. Don: Plastid Genome Evolution, Molecular Marker Identification, and Phylogenetic Implications in Asterids

(2013) Chuan Ku et al.   PLoS One

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

(2012) Massimo Iorizzo et al.   BMC PLANT BIOLOGY

BamView: visualizing and interpretation of next-generation sequencing read alignments

(2012) T. Carver et al.   BRIEFINGS IN BIOINFORMATICS

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase

(2012) P. Zhelyazkova et al.   PLANT CELL

Plastid non-coding RNAs: emerging candidates for gene regulation

(2012) Amber M. Hotto et al.   TRENDS IN PLANT SCIENCE

A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins

(2012) Alice Barkan et al.   PLoS Genetics

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

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

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

Extending the Limited Transfer Window Hypothesis to Inter-organelle DNA Migration

(2011) David Roy Smith   Genome Biology and Evolution

A PORR domain protein required for rpl2 and ccmFC intron splicing and for the biogenesis of c-type cytochromes in Arabidopsis mitochondria

(2011) Catherine Colas des Francs-Small et al.   PLANT JOURNAL

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

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

Recombination and the maintenance of plant organelle genome stability

(2010) Alexandre Maréchal et al.   NEW PHYTOLOGIST

Microhomology-mediated and nonhomologous repair of a double-strand break in the chloroplast genome of Arabidopsis

(2010) T. Kwon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion

(2010) W. Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-long terminal repeat (non-LTR) retrotransposons: mechanisms, recent developments, and unanswered questions

(2010) Jeffrey S Han   Mobile DNA

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

Site-specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts

(2009) Jeannette Pfalz et al.   EMBO JOURNAL

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes

(2009) W. Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The give-and-take of DNA: horizontal gene transfer in plants

(2009) Ralph Bock   TRENDS IN PLANT SCIENCE

Recent developments in the MAFFT multiple sequence alignment program

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

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer

(2008) V. V. Goremykin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

Chlamydomonas chloroplasts can use short dispersed repeats and multiple pathways to repair a double-strand break in the genome

(2008) Obed W. Odom et al.   PLANT JOURNAL

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY