Gene Loss and Evolution of the Plastome

Co-Translational Protein Folding and Sorting in Chloroplasts

(2020) Fabian Ries et al.   Plants-Basel

PACVr: plastome assembly coverage visualization in R

(2020) Michael Gruenstaeudl et al.   BMC BIOINFORMATICS

Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas

(2020) José G. García-Cerdán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Stephan Greiner et al.   NUCLEIC ACIDS RESEARCH

Understanding evolution in Poales: Insights from Eriocaulaceae plastome

(2019) Ashwini M. Darshetkar et al.   PLoS One

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

Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis

(2018) Guiling Sun et al.   Nature Communications

Genome-wide identification of major protein families of cyanobacteria and genomic insight into the circadian rhythm

(2017) Tapan Kumar Mohanta et al.   EUROPEAN JOURNAL OF PHYCOLOGY

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes

(2017) Sean W. Graham et al.   NEW PHYTOLOGIST

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae

(2017) Monique Turmel et al.   Scientific Reports

Xenolog classification

(2016) Charlotte A. Darby et al.   BIOINFORMATICS

Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae

(2016) Claude Lemieux et al.   Frontiers in Plant Science

Universal Multiplexable matK Primers for DNA Barcoding of Angiosperms

(2016) Jacqueline Heckenhauer et al.   Applications in Plant Sciences

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

(2015) Henry Heberle et al.   BMC BIOINFORMATICS

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

(2015) Andan Zhu et al.   NEW PHYTOLOGIST

The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family

(2015) Choun-Sea Lin et al.   Scientific Reports

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms

(2014) Elizabeth C. Ruck et al.   Genome Biology and Evolution

Nuclear-encoded factors associated with the chloroplast transcription machinery of higher plants

(2014) Qing-Bo Yu et al.   Frontiers in Plant Science

The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms

(2013) Ji Ma et al.   GENE

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

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

(2013) S. Wicke et al.   PLANT CELL

Analysis of Essential Arabidopsis Nuclear Genes Encoding Plastid-Targeted Proteins

(2013) Linda J. Savage et al.   PLoS One

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer et al.   BIOINFORMATICS

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

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Plastid Biology: Focus on the Defining Organelle of Plants

(2011) K. W. Osteryoung et al.   PLANT PHYSIOLOGY

rbcL and matK Earn Two Thumbs Up as the Core DNA Barcode for Ferns

(2011) Fay-Wei Li et al.   PLoS One

New universal matK primers for DNA barcoding angiosperms

(2011) Jing YU et al.   Journal of Systematics and Evolution

Chloroplast RNA Metabolism

(2010) David B. Stern et al.   Annual Review of Plant Biology

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

The evolution of chloroplast genes and genomes in ferns

(2010) Paul G. Wolf et al.   PLANT MOLECULAR BIOLOGY

Identification of Nuclear Genes Encoding Chloroplast-Localized Proteins Required for Embryo Development in Arabidopsis

(2010) N. Bryant et al.   PLANT PHYSIOLOGY

Plastid ndh genes in plant evolution

(2010) Mercedes Martín et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects

(2010) Lei GAO et al.   Journal of Systematics and Evolution

Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: Selection toward a lower-cost strategy

(2009) Chung-Shien Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Glucose and Auxin Signaling Interaction in Controlling Arabidopsis thaliana Seedlings Root Growth and Development

(2009) Bhuwaneshwar S. Mishra et al.   PLoS One

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants?

(2008) C. A. Cullis et al.   ANNALS OF BOTANY

Genome Size Reduction in the Chicken Has Involved Massive Loss of Ancestral Protein-Coding Genes

(2008) A. L. Hughes et al.   MOLECULAR BIOLOGY AND EVOLUTION