The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant

(2016) Luis David Alcaraz et al.   PLoS One

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

Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification

(2015) Rolf Rutishauser   ANNALS OF BOTANY

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

ClicO FS: an interactive web-based service of Circos: Fig. 1.

(2015) Wei-Hien Cheong et al.   BIOINFORMATICS

Results from an online survey of family delimitation in angiosperms and ferns: recommendations to the Angiosperm Phylogeny Group for thorny problems in plant classification

(2015) Maarten J. M. Christenhusz et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The massive mitochondrial genome of the angiospermSilene noctiflorais evolving by gain or loss of entire chromosomes

(2015) Zhiqiang Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

(2015) Yayoi Takeuchi et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

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

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Widespread mitovirus sequences in plant genomes

(2015) Jeremy A. Bruenn et al.   PeerJ

Bacterial community associated with traps of the carnivorous plants Utricularia hydrocarpa and Genlisea filiformis

(2014) Fernanda A. Caravieri et al.   AQUATIC BOTANY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids

(2014) Seongjun Park et al.   BMC GENOMICS

Deep sequencing of the tobacco mitochondrial transcriptome reveals expressed ORFs and numerous editing sites outside coding regions

(2014) Benjamin T Grimes et al.   BMC GENOMICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes

(2014) James D. Stone et al.   MOLECULAR GENETICS AND GENOMICS

Handling tRNA introns, archaeal way and eukaryotic way

(2014) Tohru Yoshihisa   Frontiers in Genetics

The plant mitochondrial genome: Dynamics and maintenance

(2013) José M. Gualberto et al.   BIOCHIMIE

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure

(2013) Daniel B. Sloan   NEW PHYTOLOGIST

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

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

Reproductive biology and pollination ofUtricularia reniformisA.St.-Hil. (Lentibulariaceae)

(2013) D. Clivati et al.   PLANT BIOLOGY

Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade

(2013) Zhenxiang Xi et al.   PLoS Genetics

Microsatellite markers developed for Utricularia reniformis (Lentibulariaceae)

(2012) Débora Clivati et al.   AMERICAN JOURNAL OF BOTANY

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

(2012) Massimo Iorizzo et al.   BMC PLANT BIOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Plastid Sequences Contribute to Some Plant Mitochondrial Genes

(2012) D. Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

(2012) Daniel B. Sloan et al.   PLOS BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Multiple recent horizontal transfers of the cox1intron in Solanaceae and extended co-conversion of flanking exons

(2011) Maria V Sanchez-Puerta et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions

(2011) Sota Fujii et al.   BMC GENOMICS

Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome

(2011) Enrique Ibarra-Laclette et al.   BMC PLANT BIOLOGY

The Microbial Phyllogeography of the Carnivorous Plant Sarracenia alata

(2011) Margaret M. Koopman et al.   MICROBIAL ECOLOGY

Ecophysiological traits of terrestrial and aquatic carnivorous plants: are the costs and benefits the same?

(2011) Aaron M. Ellison et al.   OIKOS

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)

(2010) A. J. Alverson et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates

(2009) V. A. Albert et al.   JOURNAL OF EXPERIMENTAL BOTANY

Energetics and the evolution of carnivorous plants—Darwin's ‘most wonderful plants in the world’

(2009) Aaron M. Ellison et al.   JOURNAL OF EXPERIMENTAL BOTANY

Microbial community development in the traps of aquatic Utricularia species

(2008) Dagmara Sirová et al.   AQUATIC BOTANY

Frequent, Phylogenetically Local Horizontal Transfer of the cox1 Group I Intron in Flowering Plant Mitochondria

(2008) M. V. Sanchez-Puerta et al.   MOLECULAR BIOLOGY AND EVOLUTION