Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

Intraspecific rearrangement of mitochondrial genome suggests the prevalence of the tandem duplication-random loss (TDLR) mechanism in Quasipaa boulengeri

(2016) Yun Xia et al.   BMC GENOMICS

The complete mitochondrial genome ofLerema acciusand its phylogenetic implications

(2016) Qian Cong et al.   PeerJ

The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

(2015) David Roy Smith   Briefings in Functional Genomics

The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae)

(2015) Daniel A. Moreira et al.   GENE

Characterization of the mitochondrial genome ofAmolops tuberodepressus(Anura: Ranidae)

(2015) Chaohua Zhang et al.   Mitochondrial DNA

Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs

(2015) D. J. Machado et al.   Molecular Ecology Resources

Next-generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastriaspp.)

(2015) Z. T. Lounsberry et al.   Molecular Ecology Resources

The complete mitochondrial genome ofRhacophorus dennysi(Anura: Rhacophoridae) and phylogenetic analysis

(2015) Minyi Huang et al.   Mitochondrial DNA Part A

The complete mitogenome of Amolops loloensis and related phylogenetic relationship among Ranidae

(2015) Rui Xue et al.   Mitochondrial DNA Part A

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

(2015) Fábio Raposo do Amaral et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes

(2014) Han Gan et al.   BMC EVOLUTIONARY BIOLOGY

The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization

(2014) Yun Xia et al.   BMC GENOMICS

Complete mitochondrial genome ofAmolops mantzorum(Anura: Ranidae)

(2014) Xiang Shan et al.   Mitochondrial DNA

Complete mitochondrial genome of the Ye’s spiny-vented frogYerana yei(Anura: Dicroglossidae)

(2014) Zhuo Chen et al.   Mitochondrial DNA

The complete mitochondrial genome ofAmolops wuyiensis(Anura: Ranidae)

(2014) Minyi Huang et al.   Mitochondrial DNA

A phylogeographic evaluation of the Amolops mantzorum species group: Cryptic species and plateau uplift

(2014) Bin Lu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

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

(2014) STEPHEN L. CAMERON   SYSTEMATIC ENTOMOLOGY

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

(2013) Jan Y Poulsen et al.   BMC EVOLUTIONARY BIOLOGY

Afrobatrachian mitochondrial genomes: genome reorganization, gene rearrangement mechanisms, and evolutionary trends of duplicated and rearranged genes

(2013) Atsushi Kurabayashi et al.   BMC GENOMICS

Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

(2013) Nimrod D. Rubinstein et al.   Genome Biology and Evolution

The complete mitochondrial genome ofQuasipaa boulengeri(Anura: Dicroglossidae)

(2013) Xiang Shan et al.   Mitochondrial DNA

Efficient Sequencing of Anuran mtDNAs and a Mitogenomic Exploration of the Phylogeny and Evolution of Frogs

(2013) Peng Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke,Fasciolopsis buski(Lankester, 1857) Looss, 1899

(2013) Devendra Kumar Biswal et al.   PeerJ

Geological events play a larger role than Pleistocene climatic fluctuations in driving the genetic structure ofQuasipaa boulengeri(Anura: Dicroglossidae)

(2012) Fang Yan et al.   MOLECULAR ECOLOGY

MITOS: Improved de novo metazoan mitochondrial genome annotation

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

A European Melting Pot of Harbour Porpoise in the French Atlantic Coasts Inferred from Mitochondrial and Nuclear Data

(2012) Eric Alfonsi et al.   PLoS One

A De Novo Case of Floating Chromosomal Polymorphisms by Translocation in Quasipaa boulengeri (Anura, Dicroglossidae)

(2012) Liyan Qing et al.   PLoS One

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

(2012) Ruibang Luo et al.   GigaScience

Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results

(2011) Niina Haiminen et al.   PLoS One

Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh

(2010) Mohammad Shafiqul Alam et al.   GENES & GENETIC SYSTEMS

Complete mitochondrial DNA sequence of the endangered frog Odorrana ishikawae (family Ranidae) and unexpected diversity of mt gene arrangements in ranids

(2010) Atsushi Kurabayashi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

(2010) C. Lindqvist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete nucleotide sequence and gene organization of the mitochondrial genome of Paa spinosa (Anura: Ranoidae)

(2009) Yan Zhou et al.   GENE

Characterization of 67 Mitochondrial tRNA Gene Rearrangements in the Hymenoptera Suggests That Mitochondrial tRNA Gene Position Is Selectively Neutral

(2009) M. Dowton et al.   MOLECULAR BIOLOGY AND EVOLUTION

An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes

(2009) A. R. Jex et al.   NUCLEIC ACIDS RESEARCH

Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications

(2008) Zhumei Ren et al.   GENE

Relationship between mitochondrial gene rearrangements and stability of the origin of light strand replication

(2008) Miguel M. Fonseca et al.   GENETICS AND MOLECULAR BIOLOGY

Phylogeny, Recombination, and Mechanisms of Stepwise Mitochondrial Genome Reorganization in Mantellid Frogs from Madagascar

(2008) A. Kurabayashi et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois

(2008) Jing Che et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION