Reference-Free Comparative Genomics of 174 Chloroplasts

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

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

Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

(2011) Chung-Shien Wu et al.   Genome Biology and Evolution

Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes

(2011) E. Delannoy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)

(2011) J. Chris Blazier et al.   PLANT MOLECULAR BIOLOGY

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

(2010) Thomas J. Givnish et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Calling SNPs without a reference sequence

(2010) Aakrosh Ratan et al.   BMC BIOINFORMATICS

Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes

(2010) Melvin J Oliver et al.   BMC GENOMICS

Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage

(2010) M. M. Guisinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assembly free comparative genomics of short-read sequence data discovers the needles in the haystack

(2010) CHARLES H. CANNON et al.   MOLECULAR ECOLOGY

Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects

(2010) Lei GAO et al.   Journal of Systematics and Evolution

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

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

Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: Selection toward a lower-cost strategy

(2009) Chung-Shien Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

The new paradigm of flow cell sequencing

(2008) R. A. Holt et al.   GENOME RESEARCH

Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes

(2008) Rosemarie C. Haberle et al.   JOURNAL OF MOLECULAR EVOLUTION

Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions

(2008) Zhengqiu Cai et al.   JOURNAL OF MOLECULAR EVOLUTION

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

The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera , subsection Oenothera : I. Sequence evaluation and plastome evolution †

(2008) Stephan Greiner et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS