The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng

Evolutionary dynamics of emblematic Araucariaspecies (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species

(2014) Myriam Gaudeul et al.   BMC EVOLUTIONARY BIOLOGY

Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution

(2014) Wenhu Guo et al.   Genome Biology and Evolution

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

Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers

(2013) Barbara Turner et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Marker-free genetic engineering of the chloroplast in the green microalgaChlamydomonas reinhardtii

(2013) Hsu-Ching Chen et al.   PLANT BIOTECHNOLOGY JOURNAL

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

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2013) Jun Qian et al.   PLoS One

Development of chloroplast microsatellite markers for phylogenetic analysis in Brassicaceae

(2012) Praveen Awasthi et al.   ACTA BIOLOGICA HUNGARICA

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

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

The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

(2012) Cheng-Fong Jheng et al.   PLANT SCIENCE

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

(2012) Xiaojun Nie et al.   PLoS One

Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding

(2012) Wenpan Dong et al.   PLoS One

Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics

(2011) Dai-Yong Kuang et al.   GENOME

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

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

Phylogenetic relationships among subgenera, species, and varieties of Japanese Salvia L. (Lamiaceae)

(2010) Atsuko Takano et al.   JOURNAL OF PLANT RESEARCH

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships

(2009) S. Tangphatsornruang et al.   DNA 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

Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms

(2009) Jin-Hua Ran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

(2008) Rui-Jiang Wang et al.   BMC EVOLUTIONARY BIOLOGY

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

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

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

Saturation and base composition bias explain phylogenomic conflict in Plasmodium

(2008) Liliana M. Dávalos et al.   GENOMICS