Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae)

Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae)

(2017) Xiao-Jian Qu et al.   Genome Biology and Evolution

A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

(2017) Yunsoo Kim et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae)

(2017) Armel S.L. Donkpegan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

(2017) Shu-Dong Zhang et al.   NEW PHYTOLOGIST

The distinct plastid genome structure of Maackia fauriei (Fabaceae: Papilionoideae) and its systematic implications for genistoids and tribe Sophoreae

(2017) In-Su Choi et al.   PLoS One

A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG)

(2017) Nasim Azani et al.   TAXON

Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication

(2017) Yin-Huan Wang et al.   Tree Genetics & Genomes

Complete plastid genomes of the genus Ammopiptanthus and identification of a novel 23-kb rearrangement

(2017) Lei Feng et al.   Conservation Genetics Resources

The complete chloroplast genomes of Adenolobus garipensis and Cercis glabra (Cercidoideae, Fabaceae)

(2017) Yin-Huan Wang et al.   Conservation Genetics Resources

Cheniella gen. nov. (Leguminosae: Cercidoideae) from southern China, Indochina and Malesia

(2017) Ruth P. Clark et al.   European Journal of Taxonomy

Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)

(2017) Xiao-Jian Qu et al.   Scientific Reports

Variable presence of the inverted repeat and plastome stability inErodium

(2016) John C. Blazier et al.   ANNALS OF BOTANY

Birth of Four Chimeric Plastid Gene Clusters in Japanese Umbrella Pine

(2016) Chih-Yao Hsu et al.   Genome Biology and Evolution

Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs

(2016) Ting Zhang et al.   Journal of Systematics and Evolution

Comparative analysis of the complete chloroplast genome sequences in psammophyticHaloxylonspecies (Amaranthaceae)

(2016) Wenpan Dong et al.   PeerJ

The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae)

(2016) Cuihua Gu et al.   PLoS One

Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus

(2016) Wanjun Lei et al.   Scientific Reports

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

(2015) Anna V. Williams et al.   PLoS One

Orchid phylogenomics and multiple drivers of their extraordinary diversification

(2015) Thomas J. Givnish et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions

(2015) Stephen R. Downie et al.   SYSTEMATIC BOTANY

Plastid genome sequences of legumes reveal parallel inversions and multiple losses ofrps16in papilionoids

(2015) Erika N. Schwarz et al.   Journal of Systematics and Evolution

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

(2015) Diana V. Dugas et al.   Scientific Reports

The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family

(2014) Guillaume E. Martin et al.   ANNALS OF BOTANY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium)

(2014) Saemundur Sveinsson et al.   BMC EVOLUTIONARY BIOLOGY

Two Distinct Plastid Genome Configurations and Unprecedented Intraspecies Length Variation in the accD Coding Region in Medicago truncatula

(2014) C. Gurdon et al.   DNA RESEARCH

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

Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs

(2014) Jun-Bo Yang et al.   Molecular Ecology Resources

Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes

(2014) Jamal Sabir et al.   PLANT BIOTECHNOLOGY JOURNAL

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

(2014) Peng-Fei Ma et al.   SYSTEMATIC BIOLOGY

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

Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates

(2013) Mao-Lun Weng et al.   MOLECULAR 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

Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family

(2013) S. Wicke et al.   PLANT CELL

Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades

(2013)   TAXON

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia pinnata

(2012) Stephen H. Kazakoff et al.   PLoS One

Comparative Chloroplast Genomes of Pinaceae: Insights into the Mechanism of Diversified Genomic Organizations

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

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Localized hypermutation and associated gene losses in legume chloroplast genomes

(2010) A. M. Magee et al.   GENOME 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

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

An organellar maturase associates with multiple group II introns

(2010) R. Zoschke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genus Bauhinia s.l. (Leguminosae): a phylogeny based on the plastid trnL–trnF region

(2009) Carole Sinou et al.   Botany

Phylogenetic patterns and diversification in the caesalpinioid legumesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

(2008) Anne Bruneau et al.   Botany

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