How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

(2013) Stephen L. Cameron   Annual Review of Entomology

The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex

(2013) Hua-Ling Wang et al.   BMC GENOMICS

The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny

(2013) S.T. Williams et al.   GENE

Mitogenomics at the base of Metazoa

(2013) Hans-Jürgen Osigus et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy

(2013) Julien Haran et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny

(2013) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing

(2013) Chih-Ming Hung et al.   PLoS One

Ancestral Gene Organization in the Mitochondrial Genome of Thyridosmylus langii (McLachlan, 1870) (Neuroptera: Osmylidae) and Implications for Lacewing Evolution

(2013) Jing Zhao et al.   PLoS One

Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

(2012) Sergey Ovchinnikov et al.   BMC EVOLUTIONARY BIOLOGY

The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing

(2012) Dick SJ Groenenberg et al.   BMC GENOMICS

Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

(2012) Leigh A. Nelson et al.   GENE

Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae)

(2012) Q.-Q. Sun et al.   GENETICS AND MOLECULAR RESEARCH

Description of complete mitochondrial genome of the black-veined white, Aporia crataegi (Lepidoptera: Papilionoidea), and comparison to papilionoid species

(2012) Jeong Sun Park et al.   JOURNAL OF ASIA-PACIFIC ENTOMOLOGY

Mitochondrial genomes reveal the global phylogeography and dispersal routes of the migratory locust

(2012) CHUAN MA et al.   MOLECULAR ECOLOGY

Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea)

(2012) Martijn J.T.N. Timmermans et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A mitochondrial genome phylogeny of termites (Blattodea: Termitoidae): Robust support for interfamilial relationships and molecular synapomorphies define major clades

(2012) Stephen L. Cameron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Multipartite Mitochondrial Genome of Liposcelis bostrychophila: Insights into the Evolution of Mitochondrial Genomes in Bilateral Animals

(2012) Dan-Dan Wei et al.   PLoS One

Selective Enrichment and Sequencing of Whole Mitochondrial Genomes in the Presence of Nuclear Encoded Mitochondrial Pseudogenes (Numts)

(2012) Jonci N. Wolff et al.   PLoS One

Complete Mitochondrial Genome of the Free-Living Earwig, Challia fletcheri (Dermaptera: Pygidicranidae) and Phylogeny of Polyneoptera

(2012) Xinlong Wan et al.   PLoS One

The First Mitochondrial Genome for the Fishfly Subfamily Chauliodinae and Implications for the Higher Phylogeny of Megaloptera

(2012) Yuyu Wang et al.   PLoS One

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

(2012) Ruibang Luo et al.   GigaScience

Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera)

(2011) Stephen L Cameron et al.   BMC GENOMICS

Mitochondrial Genome Sequences of Nematocera (Lower Diptera): Evidence of Rearrangement following a Complete Genome Duplication in a Winter Crane Fly

(2011) Andrew T. Beckenbach   Genome Biology and Evolution

The complete mitochondrial genome of the oriental fruit moth Grapholita molesta (Busck) (Lepidoptera: Tortricidae)

(2011) Ya-jun Gong et al.   MOLECULAR BIOLOGY REPORTS

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

(2011) Frank Jühling et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

(2011) Venu M. Margam et al.   PLoS One

The RNA-Seq approach to studying the expression of mosquito mitochondrial genes

(2010) M. Neira-Oviedo et al.   INSECT MOLECULAR BIOLOGY

Mitochondrial genome of the cotton bollwormHelicoverpa armigera(Lepidoptera: Noctuidae) and comparison with other Lepidopterans

(2010) Jiao Yin et al.   Mitochondrial DNA

Mitochondrial genomics in Orthoptera using MOSAS

(2010) Nathan C. Sheffield et al.   Mitochondrial DNA

MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies

(2010) Renato Lupi et al.   MITOCHONDRION

The complete mitochondrial genome of Spilonota lechriaspis Meyrick (Lepidoptera: Tortricidae)

(2010) Jin-Liang Zhao et al.   MOLECULAR BIOLOGY REPORTS

Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny

(2010) Benoit Nabholz et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa

(2010) Anke Braband et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

(2010) M. J. T. N. Timmermans et al.   NUCLEIC ACIDS RESEARCH

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

(2010) E. F. Kirkness et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics

(2010) HOJUN SONG et al.   SYSTEMATIC ENTOMOLOGY

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

(2010)   PLOS BIOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Characterization of mature mitochondrial transcripts in Drosophila, and the implications for the tRNA punctuation model in arthropods

(2009) James B. Stewart et al.   GENE

Evolution of the Mitochondrial Genomes of Gall Midges (Diptera: Cecidomyiidae): Rearrangement and Severe Truncation of tRNA Genes

(2009) Andrew T. Beckenbach et al.   Genome Biology and Evolution

The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus

(2009) R. Shao et al.   GENOME RESEARCH

The complete mitochondrial genome of the yellow coaster, Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini): sequence, gene organization and a unique tRNA translocation event

(2009) Jing Hu et al.   MOLECULAR BIOLOGY REPORTS

Phylogenetic approaches for the analysis of mitochondrial genome sequence data in the Hymenoptera – A lineage with both rapidly and slowly evolving mitochondrial genomes

(2009) Mark Dowton et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing

(2009) Tatiana Teixeira Torres et al.   NUCLEIC ACIDS RESEARCH

A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders

(2009) Stephen L. Cameron et al.   ZOOLOGICA SCRIPTA

The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs

(2008) Katja Domes et al.   BMC GENOMICS

Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda)

(2008) Aaron R Jex et al.   BMC GENOMICS

Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)

(2008) Jimeng Hua et al.   BMC GENOMICS

Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

(2008) D. C. S. G. Oliveira et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New Beetles

(2008) N. C. Sheffield et al.   MOLECULAR BIOLOGY AND EVOLUTION

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

(2008) H. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths

(2007) Stephen L. Cameron et al.   GENE