4.7 Article

Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships

Related references

Note: Only part of the references are listed.
Article Plant Sciences

Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes

Gurusamy Raman et al.

Summary: This study conducted extensive comparative analysis of Corydalis plastomes, revealing independent evolution events such as genome rearrangement and IR expansion. The loss of the ndh gene in Corydalis species coincides with the distribution of sub-clade species in the Qinghai-Tibetan plateau region.

FRONTIERS IN PLANT SCIENCE (2022)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Plant Sciences

Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation

Myong-Suk Cho et al.

Summary: This study revealed the origin and evolution of Prunus takesimensis using multiple molecular markers, demonstrating the monophyly of the species, clear genetic differentiation between P. takesimensis and its continental progenitor P. sargentii, and a likely single colonization event from the source population of P. sargentii in the Korean Peninsula. Additionally, it found no significant reduction in genetic diversity in the insular derivative species compared to its continental progenitor, and suggested the MIG-seq method as an effective tool for elucidating the complex evolutionary history of plant groups.

FRONTIERS IN PLANT SCIENCE (2021)

Article Biochemistry & Molecular Biology

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

Stephan Greiner et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Remco Bouckaert et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

Chao-Nan Fu et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)

Article Plant Sciences

Origin of angiosperms and the puzzle of the Jurassic gap

Hong-Tao Li et al.

NATURE PLANTS (2019)

Article Biochemistry & Molecular Biology

Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia

Pablo Munoz-Rodriguez et al.

CURRENT BIOLOGY (2018)

Article Biochemistry & Molecular Biology

The Complete Chloroplast Genome Sequence of Tree of Heaven (Ailanthus altissima (Mill.) (Sapindales: Simaroubaceae), an Important Pantropical Tree

Josphat K. Saina et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)

Article Evolutionary Biology

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Andrew Rambaut et al.

SYSTEMATIC BIOLOGY (2018)

Article Biochemistry & Molecular Biology

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

Julio Rozas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

GeSeq - versatile and accurate annotation of organelle genomes

Michael Tillich et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Heatmapper: web-enabled heat mapping for all

Sasha Babicki et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

Yan Yu et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2015)

Article Multidisciplinary Sciences

Three keys to the radiation of angiosperms into freezing environments

Amy E. Zanne et al.

NATURE (2014)

Article Geography, Physical

Time-spatial distribution of Pinus in the Korean Peninsula

Woo-seok Kong et al.

QUATERNARY INTERNATIONAL (2014)

Article Biochemistry & Molecular Biology

Application of the phylogenetic informativeness method to chloroplast markers: A test case of closely related species in tribe Hydrangeeae (Hydrangeaceae)

Carolina Granados Mendoza et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2013)

Article Evolutionary Biology

Mutational Dynamics of Aroid Chloroplast Genomes

Ibrar Ahmed et al.

GENOME BIOLOGY AND EVOLUTION (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Evolutionary Biology

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

Fredrik Ronquist et al.

SYSTEMATIC BIOLOGY (2012)

Article Evolutionary Biology

PhyDesign: an online application for profiling phylogenetic informativeness

Francesc Lopez-Giraldez et al.

BMC EVOLUTIONARY BIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Chloroplast genome sequences from total DNA for plant identification

Catherine J. Nock et al.

PLANT BIOTECHNOLOGY JOURNAL (2011)

Article Biochemistry & Molecular Biology

Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

Michael J. McDonald et al.

PLOS BIOLOGY (2011)

Article Biochemical Research Methods

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Localized hypermutation and associated gene losses in legume chloroplast genomes

Alan M. Magee et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

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

Daniel R. Zerbino et al.

GENOME RESEARCH (2008)

Article Evolutionary Biology

A Rapid Bootstrap Algorithm for the RAxML Web Servers

Alexandros Stamatakis et al.

SYSTEMATIC BIOLOGY (2008)

Article Multidisciplinary Sciences

Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns

Robert K. Jansen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

Markus Wiederstein et al.

NUCLEIC ACIDS RESEARCH (2007)

Review Geography, Physical

Paleobiogeography of Africa: How distinct from Gondwana and Laurasia?

Emmanuel Gheerbrant et al.

PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY (2006)

Article Biochemical Research Methods

HyPhy: hypothesis testing using phylogenies

SLK Pond et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

APE: Analyses of Phylogenetics and Evolution in R language

E Paradis et al.

BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

VISTA: computational tools for comparative genomics

KA Frazer et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

Can correct protein models be identified?

B Wallner et al.

PROTEIN SCIENCE (2003)

Article Geography, Physical

A refined age for the earliest opening of Bering Strait

AY Gladenkov et al.

PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY (2002)

Article Biochemistry & Molecular Biology

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Multidisciplinary Sciences

Palaeovegetation - Diversity of temperate plants in east Asia

SP Harrison et al.

NATURE (2001)