De Novo Hybrid Assembly of the Salvia miltiorrhiza Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of Salvia Species

Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza

(2021) Ying Ma et al.   Nature Communications

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Variation in protein gene and intron content among land plant mitogenomes

(2020) Jeffrey P. Mower   MITOCHONDRION

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

(2020) Chengjie Chen et al.   Molecular Plant

Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome

(2019) Varré et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   JOURNAL OF ECONOMIC ENTOMOLOGY

Multichromosomal structure of the onion mitochondrial genome and a transcript analysis

(2018) Mai Tsujimura et al.   MITOCHONDRION

Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes

(2018) Daniel B. Sloan et al.   PLANT CELL

ETCM: an encyclopaedia of traditional Chinese medicine

(2018) Hai-Yu Xu et al.   NUCLEIC ACIDS RESEARCH

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Saura R. Silva et al.   PLoS One

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

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

Mitogenomics of Hesperelaea, an extinct genus of Oleaceae

(2016) Céline Van de Paer et al.   GENE

GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution

(2016) Wenhu Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2016) Haibin Xu et al.   Molecular Plant

Whole Mitochondrial Genome Sequencing and Re-Examination of a Cytoplasmic Male Sterility-Associated Gene in Boro-Taichung-Type Cytoplasmic Male Sterile Rice

(2016) Tomohiko Kazama et al.   PLoS One

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

(2014) Andan Zhu 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

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

(2013) Jun Qian et al.   PLoS One

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella

(2013) D. W. Rice et al.   SCIENCE

Evidence against Equimolarity of Large Repeat Arrangements and a Predominant Master Circle Structure of the Mitochondrial Genome from a Monkeyflower (Mimulus guttatus) Lineage with Cryptic CMS

(2012) Jeffrey P. Mower et al.   Genome Biology and Evolution

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser 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

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

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

Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber

(2011) A. J. Alverson et al.   PLANT CELL

Apollo: a community resource for genome annotation editing

(2009) E. Lee et al.   BIOINFORMATICS

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Number matters: control of mammalian mitochondrial DNA copy number

(2009) Laura L. Clay Montier et al.   Journal of Genetics and Genomics