Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes

(2022) Tanara P. Dalla Costa et al.   PLANTA

The complete plastomes of red fleshed pitaya (Selenicereus monacanthus) and three related Selenicereus species: insights into gene losses, inverted repeat expansions and phylogenomic implications

(2022) Qiulin Qin et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Genetic and evolutionary analyses of plastomes of the subfamily Cactoideae (Cactaceae) indicate relaxed protein biosynthesis and tRNA import from cytosol

(2021) Gleyson Morais da Silva et al.   Brazilian Journal of Botany

The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes

(2021) Jinfang Zheng et al.   Horticulture Research

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

(2021) William J Baker et al.   SYSTEMATIC BIOLOGY

Comparative chloroplast genomics of the genus Taxodium

(2020) Hao Duan et al.   BMC GENOMICS

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A complete chloroplast genome sequence of Gastrodia elata (Orchidaceae) represents high sequence variation in the species

(2020) Jongsun Park et al.   Mitochondrial DNA Part B-Resources

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

(2020) Matias Köhler et al.   Frontiers in Plant Science

Gene-targeted molecular phylogeny, phytochemical profiling, and antioxidant activity of nine species belonging to family Cactaceae

(2020) Heba H. Abouseadaa et al.   SAUDI JOURNAL OF BIOLOGICAL SCIENCES

Complete Chloroplast Genome of Rhipsalis baccifera, the only Cactus with Natural Distribution in the Old World: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies

(2020) Millicent Akinyi Oulo et al.   Plants-Basel

Plastid phylogenomic insights into the evolution of Caryophyllales

(2019) Gang Yao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics

(2019) Deserah D. Strand et al.   BIOCHEMICAL JOURNAL

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

Cryptic divergences in the genus Pisum L. (peas), as revealed by phylogenetic analysis of plastid genomes

(2018) Vera S. Bogdanova et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic Relationships and Evolutionary Trends in the Cactus Family

(2018) Pablo C Guerrero et al.   JOURNAL OF HEREDITY

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments

(2018) Ning Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution

(2018) Emily L. Wynn et al.   G3-Genes Genomes Genetics

Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae)

(2017) Xiao-Jian Qu et al.   Genome Biology and Evolution

Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion

(2017) ZhouXian Ni et al.   MOLECULES

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids

(2017) Choun-Sea Lin et al.   PLANT JOURNAL

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

(2017) Dario Copetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete Chloroplast Genome Sequences and Comparative Analysis of Chenopodium quinoa and C. album

(2017) Su-Young Hong et al.   Frontiers in Plant Science

Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues

(2016) Jean-René Arseneau et al.   Molecular Ecology Resources

Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes

(2016) Sonali Sachin Ranade et al.   MOLECULAR GENETICS AND GENOMICS

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

High speed BLASTN: an accelerated MegaBLAST search tool

(2015) Ying Chen et al.   NUCLEIC ACIDS RESEARCH

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

(2015) Hyoung Tae Kim et al.   PLoS One

The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms

(2013) Xuan Yi et al.   Genome Biology and Evolution

Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss

(2013) Thomas Braukmann et al.   JOURNAL OF EXPERIMENTAL BOTANY

Potential Functional Replacement of the Plastidic Acetyl-CoA Carboxylase Subunit (accD) Gene by Recent Transfers to the Nucleus in Some Angiosperm Lineages

(2013) M. Rousseau-Gueutin et al.   PLANT PHYSIOLOGY

Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)

(2013) Xi Li et al.   PLoS One

Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs

(2013) D. Mandal et al.   RNA

Angiosperm Responses to a Low-CO2 World: CAM and C4 Photosynthesis as Parallel Evolutionary Trajectories

(2012) Erika J. Edwards et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae−Opuntioideae)

(2012) C.M. Ritz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary constraints on the plastid tRNA set decoding methionine and isoleucine

(2012) Sibah Alkatib et al.   NUCLEIC ACIDS RESEARCH

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae)

(2011) J. Chris Blazier et al.   PLANT MOLECULAR BIOLOGY

Phylogenetic relationships and evolution of growth form in Cactaceae (Caryophyllales, Eudicotyledoneae)

(2010) T. Hernandez-Hernandez et al.   AMERICAN JOURNAL OF BOTANY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants

(2008) Kirsten Krause   CURRENT GENETICS