Plastid genome structure and phylogenomics of Nymphaeales: conserved gene order and new insights into relationships

Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased

(2016) Mark P. Simmons   CLADISTICS

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity

(2016) Jin Zhang et al.   Genome Biology and Evolution

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family

(2016) Saura R. Silva et al.   PLoS One

Chloroplast Phylogenomic Inference of Green Algae Relationships

(2016) Linhua Sun et al.   Scientific Reports

Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

(2015) Joseph F. Walker et al.   AMERICAN JOURNAL OF BOTANY

Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae

(2015) Natalie Cusimano et al.   NEW PHYTOLOGIST

The Root of Flowering Plants and Total Evidence

(2015) V. V. Goremykin et al.   SYSTEMATIC BIOLOGY

Towards a complete species tree of Nymphaea: shedding further light on subg. Brachyceras and its relationships to the Australian water-lilies

(2015) Thomas Borsch et al.   TELOPEA

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales)

(2014) William J D Iles et al.   BMC EVOLUTIONARY BIOLOGY

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Speciation in North American water lilies: evidence for the hybrid origin of the newly discovered Canadian endemic Nymphaea loriana sp. nov. (Nymphaeaceae) in a past contact zone

(2014) Thomas Borsch et al.   Botany

Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs

(2014) Jun-Bo Yang et al.   Molecular Ecology Resources

Another Look at the Root of the Angiosperms Reveals a Familiar Tale

(2014) Bryan T. Drew et al.   SYSTEMATIC BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae)

(2013) Hoang Dang Khoa Do et al.   GENE

Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates

(2013) Mao-Lun Weng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Disproportional Plastome-Wide Increase of Substitution Rates and Relaxed Purifying Selection in Genes of Carnivorous Lentibulariaceae

(2013) Susann Wicke et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

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

(2013) S. Wicke et al.   PLANT CELL

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

(2012) Chang Liu et al.   BMC GENOMICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

The Evolutionary Root of Flowering Plants

(2012) Vadim V. Goremykin et al.   SYSTEMATIC BIOLOGY

Sequencing and Analysis of Plastid Genome in Mycoheterotrophic Orchid Neottia nidus-avis

(2011) Maria D. Logacheva et al.   Genome Biology and Evolution

Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region

(2011) Michael J. Moore et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

A global picture of tRNA genes in plant genomes

(2011) Morgane Michaud et al.   PLANT JOURNAL

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

(2011) Susann Wicke et al.   PLANT MOLECULAR 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

(2009) Eeva M Soininen et al.   Frontiers in Zoology

The unusualOndinea, actually just another Australian water-lily ofNymphaeasubg.Anecphya (Nymphaeaceae)

(2009) Cornelia Löhne et al.   Willdenowia

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes

(2008) Rosemarie C. Haberle et al.   JOURNAL OF MOLECULAR EVOLUTION

Extensive Reorganization of the Plastid Genome of Trifolium subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions

(2008) Zhengqiu Cai et al.   JOURNAL OF MOLECULAR EVOLUTION

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY