Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion

Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids

(2017) Choun-Sea Lin et al.   PLANT JOURNAL

Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny

(2017) Yiheng Hu et al.   Frontiers in Plant Science

The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species

(2017) Sajjad Asaf et al.   Frontiers in Plant Science

The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales

(2017) Luiz A. Cauz-Santos et al.   Frontiers in Plant Science

Chloroplast genome structures in Gentiana (Gentianaceae), based on three medicinal alpine plants used in Tibetan herbal medicine

(2016) Lianghong Ni et al.   CURRENT GENETICS

Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes

(2016) Sonali Sachin Ranade et al.   MOLECULAR GENETICS AND GENOMICS

Colonization and diversification in the African ‘sky islands’: insights from fossil-calibrated molecular dating ofLychnis(Caryophyllaceae)

(2016) Abel Gizaw et al.   NEW PHYTOLOGIST

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae

(2016) Jia Li et al.   Scientific Reports

Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae

(2015) R. M. Redwan et al.   BMC PLANT BIOLOGY

The complete chloroplast genome of Armand pinePinus armandii, an endemic conifer tree species to China

(2015) Zhong-Hu Li et al.   Mitochondrial DNA

The complete chloroplast genome of the Taiwan red pinePinus taiwanensis(Pinaceae)

(2015) Min-Feng Fang et al.   Mitochondrial DNA

The complete plastid genome of Bunge’s pinePinus bungeana(Pinaceae)

(2015) Zhong-Hu Li et al.   Mitochondrial DNA

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

(2015) Andan Zhu et al.   NEW PHYTOLOGIST

Comparative analysis of complete chloroplast genome sequences of two tropical trees Machilus yunnanensis and Machilus balansae in the family Lauraceae

(2015) Yu Song et al.   Frontiers in Plant Science

The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes

(2014) E. M. Goss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms

(2013) Xuan Yi et al.   Genome Biology and Evolution

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers

(2013) Chung-Shien Wu et al.   PLANT BIOTECHNOLOGY JOURNAL

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

(2012) Matthew Parks et al.   BMC EVOLUTIONARY BIOLOGY

The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction

(2012) Ching-Ping Lin et al.   Genome Biology and Evolution

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

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

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

Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies

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

Plastid ndh genes in plant evolution

(2010) Mercedes Martín et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny

(2009) Thomas Werner Anthony Braukmann et al.   CURRENT GENETICS

A DNA barcode for land plants

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

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

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

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

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH