Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae)

Total duplication of the small single copy region in the angiosperm plastome: Rearrangement and inverted repeat instability in Asarum

(2018) Brandon T. Sinn et al.   AMERICAN JOURNAL OF BOTANY

IRscope: an online program to visualize the junction sites of chloroplast genomes

(2018) Ali Amiryousefi et al.   BIOINFORMATICS

Phylogeny, biogeography and character evolution in the tribe Desmodieae (Fabaceae: Papilionoideae), with special emphasis on the New Caledonian endemic genera

(2018) Florian Jabbour et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2018) Yin-Huan Wang et al.   Frontiers in Plant Science

The complete chloroplast genome sequence of Asarum sieboldii Miq. (Aristolochiaceae), a medicinal plant in Korea

(2018) Chae Eun Lim et al.   Mitochondrial DNA Part B-Resources

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

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

Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies

(2017) Erika N. Schwarz et al.   JOURNAL OF MOLECULAR EVOLUTION

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

Parsing polyphyletic Pueraria: Delimiting distinct evolutionary lineages through phylogeny

(2016) Ashley N. Egan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

(2015) M. J. Sanderson et al.   AMERICAN JOURNAL OF BOTANY

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

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

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Phylogenetic Relationships and Species Delimitation in Pinus Section Trifoliae Inferrred from Plastid DNA

(2013) Sergio Hernández-León et al.   PLoS One

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

(2013)   TAXON

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

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

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

Analysis of DNA sequences of six chloroplast and nuclear genes suggests incongruence, introgression, and incomplete lineage sorting in the evolution of Lespedeza (Fabaceae)

(2011) Bo Xu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic analysis of eastern Asian and eastern North American disjunct Lespedeza (Fabaceae) inferred from nuclear ribosomal ITS and plastid region sequences

(2010) JEONG EUN HAN et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The evolution of chloroplast genome structure in ferns

(2010) Paul G. Wolf et al.   GENOME

Localized hypermutation and associated gene losses in legume chloroplast genomes

(2010) A. M. Magee et al.   GENOME RESEARCH

Relationships Among Phaseoloid Legumes Based on Sequences from Eight Chloroplast Regions

(2010) Saša Stefanović et al.   SYSTEMATIC BOTANY

Phylogeny of Camassia (Agavaceae) Inferred from Plastid rpl16 Intron and trnD–trnY–trnE–trnT Intergenic Spacer DNA Sequences: Implications for Species Delimitation

(2010) Mark Fishbein et al.   SYSTEMATIC BOTANY

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

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

Substitution of the Gene for Chloroplast RPS16 Was Assisted by Generation of a Dual Targeting Signal

(2008) M. Ueda et al.   MOLECULAR BIOLOGY AND 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