Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes

Phylogenetic relationships and chloroplast capture in the Amelanchier-Malacomeles-Peraphyllum clade (Maleae, Rosaceae): evidence from chloroplast genome and nuclear ribosomal DNA data using genome skimming

(2020) Bin-Bin Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Natural Products, Traditional Uses and Pharmacological Activities of the Genus Biebersteinia (Biebersteiniaceae)

(2020) Benyin Zhang et al.   Plants-Basel

NtCIPK9: A Calcineurin B-Like Protein-Interacting Protein Kinase From the Halophyte Nitraria tangutorum, Enhances Arabidopsis Salt Tolerance

(2020) Lu Lu et al.   Frontiers in Plant Science

Phylogenetic and Comparative Analyses of Complete Chloroplast Genomes of Chinese Viburnum and Sambucus (Adoxaceae)

(2020) Hang Ran et al.   Plants-Basel

Comparative Genomics and Phylogenetic Analyses of Christia vespertilionis and Urariopsis brevissima in the Tribe Desmodieae (Fabaceae: Papilionoideae) Based on Complete Chloroplast Genomes

(2020) Xue-Li Zhao et al.   Plants-Basel

CPGAVAS2, an integrated plastome sequence annotator and analyzer

(2019) Linchun Shi et al.   NUCLEIC ACIDS RESEARCH

Analysis of synonymous codon usage of chloroplast genome in Porphyra umbilicalis

(2019) Guoling Li et al.   Genes & Genomics

PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

(2019) Dong Zhang et al.   Molecular Ecology Resources

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

(2018) Ali Amiryousefi et al.   BIOINFORMATICS

The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis

(2018) Xiaofeng Chi et al.   MOLECULES

Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium

(2017) Seongjun Park et al.   Genome Biology and Evolution

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

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

Molecular phylogenetics and molecular clock dating of Sapindales based on plastid rbcL, atpB and trnL-trnF DNA sequences

(2016) Alexandra N. Muellner-Riehl et al.   TAXON

Tree of life for the genera of Chinese vascular plants

(2016) Zhi-Duan Chen et al.   Journal of Systematics and Evolution

Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement

(2016) J. Chris Blazier et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Plant DNA barcoding: from gene to genome

(2014) Xiwen Li et al.   BIOLOGICAL REVIEWS

Embryology of Biebersteinia (Biebersteiniaceae, Sapindales): characteristics and comparisons with related families

(2014) Takenori Yamamoto et al.   JOURNAL OF PLANT RESEARCH

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen 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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae)

(2012) Mao-Lun Weng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus

(2011) Meng Wang et al.   BIOSYSTEMS

Chloroplast genomes of photosynthetic eukaryotes

(2011) Beverley R. Green   PLANT JOURNAL

Testing for Selection on Synonymous Sites in Plant Mitochondrial DNA: The Role of Codon Bias and RNA Editing

(2010) Daniel B. Sloan et al.   JOURNAL OF MOLECULAR EVOLUTION

Forces that influence the evolution of codon bias

(2010) P. M. Sharp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes

(2008) S. Subramanian   GENETICS

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

(2008) M. M. Guisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA