4.7 Article

Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae)

Related references

Note: Only part of the references are listed.
Review Biochemistry & Molecular Biology

Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis

Rory F. Little et al.

Summary: This review discusses the diversity of enzymes and mechanisms involved in the release of polyketide and non-ribosomal peptide natural products, and how they impact the structure of the products. It also explores how these mechanisms can be utilized to introduce structural diversity in engineered biosynthetic pathways.

NATURAL PRODUCT REPORTS (2022)

Article Biochemistry & Molecular Biology

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Chao-Nan Fu et al.

Summary: Utilizing extensive plastid genome data can enhance the discriminatory power in identifying plant species, although many species remain unresolved. Accessing multiple unlinked nuclear loci is crucial for obtaining transformative gains in species discrimination in plants.

MOLECULAR ECOLOGY RESOURCES (2022)

Article Plant Sciences

Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera

Yunheng Ji et al.

Summary: The study used plastome data to analyze the phylogenetic relationships of Cephalotaxus and related genera, supporting the taxonomic proposal of recognizing Cephalotaxaceae as a monotypic family. The analysis also provided a well-supported resolution of interspecific relationships within Cephalotaxus, Taxus, Torreya, and Amentotaxus. Most extant species are relatively young, not evolutionary relics compared to ancient plant lineages.

ANNALS OF BOTANY (2021)

Article Biology

Plastid phylogenomic insights into relationships of all flowering plant families

Hong-Tao Li et al.

Summary: The study compiled the largest dataset of angiosperm plastomes to date, resulting in a phylogenetic tree that is largely congruent with previous plastid genomic analyses but with greater clade support. The research provided strong resolution for many interordinal and interfamilial relationships within core eudicots, but relationships among the five major clades of Mesangiospermae remain unresolved despite increased sampling.

BMC BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Repeated intercontinental migrations and recurring hybridizations characterise the evolutionary history of yew (Taxus L.)

Michael Moller et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2020)

Article Biotechnology & Applied Microbiology

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

Jian-Jun Jin et al.

GENOME BIOLOGY (2020)

Article Biochemical Research Methods

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

Xiao-Jian Qu et al.

PLANT METHODS (2019)

Article Biochemistry & Molecular Biology

Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae)

Yunheng Ji et al.

MOLECULAR ECOLOGY RESOURCES (2019)

Article Plant Sciences

A new species of Amentotaxus (Taxaceae) from China, Vietnam, and Laos

Lian-Ming Gao et al.

PHYTOKEYS (2019)

Article Plant Sciences

Origin of angiosperms and the puzzle of the Jurassic gap

Hong-Tao Li et al.

NATURE PLANTS (2019)

Article Plant Sciences

Plastid phylogenomic analysis of green plants: A billion years of evolutionary history

Matthew A. Gitzendanner et al.

AMERICAN JOURNAL OF BOTANY (2018)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Plant Sciences

DNA barcoding of East Asian Amentotaxus (Taxaceae): Potential new species and implications for conservation

Lian-Ming Gao et al.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2017)

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

Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques

J. C. Zimmers et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2017)

Article Plant Sciences

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

Shu-Dong Zhang et al.

NEW PHYTOLOGIST (2017)

Article Plant Sciences

What can we do with 1000 plastid genomes?

Julian Tonti-Filippini et al.

PLANT JOURNAL (2017)

Article Biochemistry & Molecular Biology

Development of chloroplast genomic resources for Cynara

Pasquale L. Curci et al.

MOLECULAR ECOLOGY RESOURCES (2016)

Article Biochemistry & Molecular Biology

From barcodes to genomes: extending the concept of DNA barcoding

Eric Coissac et al.

MOLECULAR ECOLOGY (2016)

Article Biochemistry & Molecular Biology

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

Todd M. Lowe et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biology

Telling plant species apart with DNA: from barcodes to genomes

Peter M. Hollingsworth et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2016)

Article Biochemistry & Molecular Biology

Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria?

Markus Ruhsam et al.

MOLECULAR ECOLOGY RESOURCES (2015)

Letter Multidisciplinary Sciences

Plant identification is key to conservation

Anna Trias-Blasi et al.

NATURE (2015)

Review Ecology

DNA barcodes for ecology, evolution, and conservation

W. John Kress et al.

TRENDS IN ECOLOGY & EVOLUTION (2015)

Article Biology

Plant DNA barcoding: from gene to genome

Xiwen Li et al.

BIOLOGICAL REVIEWS (2015)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead

Simon Joly et al.

MOLECULAR ECOLOGY RESOURCES (2014)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Plant Sciences

A taxonomic revision of the genus Cephalotaxus (Taxaceae)

Xue-Dong Lang et al.

PHYTOTAXA (2013)

Article Plant Sciences

NAVIGATING THE TIP OF THE GENOMIC ICEBERG: NEXT-GENERATION SEQUENCING FOR PLANT SYSTEMATICS

Shannon C. K. Straub et al.

AMERICAN JOURNAL OF BOTANY (2012)

Article Biochemistry & Molecular Biology

Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus

Jie Liu et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2012)

Article Multidisciplinary Sciences

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

Ravi K. Patel et al.

PLOS ONE (2012)

Article Biochemistry & Molecular Biology

DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species

Jie Liu et al.

MOLECULAR ECOLOGY RESOURCES (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

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

Susann Wicke et al.

PLANT MOLECULAR BIOLOGY (2011)

Editorial Material Multidisciplinary Sciences

Refining the DNA barcode for land plants

Peter M. Hollingsworth

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

De-Zhu Li et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Michael J. Moore et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants

Michelle L. Hollingsworth et al.

MOLECULAR ECOLOGY RESOURCES (2009)

Article Plant Sciences

Plant species delimitation: A comparison of morphological and molecular markers

J. Duminil et al.

PLANT BIOSYSTEMS (2009)

Article Plant Sciences

A proposal for a standardised protocol to barcode all land plants

Mark W. Chase et al.

TAXON (2007)

Article Multidisciplinary Sciences

Use of DNA barcodes to identify flowering plants

WJ Kress et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

I Ovcharenko et al.

GENOME RESEARCH (2005)

Article Biochemistry & Molecular Biology

Identification of birds through DNA barcodes

PDN Hebert et al.

PLOS BIOLOGY (2004)

Article Biology

Biological identifications through DNA barcodes

PDN Hebert et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2003)

Article Horticulture

Discrimination and genetic diversity of Cephalotaxus accessions using AFLP markers

DL Zhang et al.

JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE (2000)

Article Biochemistry & Molecular Biology

Phylogeny of taxaceae and cephalotaxaceae tenera inferred from chloroplast matK gene and nuclear rDNA ITS region

YC Cheng et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2000)