heuristically exploring mitochondrial rearrangements based on common intervals

start

start here and input data.

overview

CREx is a tool for comparisons of gene order data. it uses a data structure called strong common interval tree (Bérard et al. 2007) - also called pq-tree (Booth an Lueker 1976). it heuristically determines rearrangement scenarios to transform one gene order into the other. the main features of CREx are:

please cite:
Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter Stadler, and Martin Middendorf
CREx: Inferring Genomic Rearrangements Based on Common Intervals
Bioinformatics, 2007, 23(21):2957-2958 pdf link

documentation and examples

a short tutorial for the usage of CREx is presented here. the technical details of CREx and a short tutorial for the interpretation of the results are documented here. we have compiled a set of examples which demonstrates the capabilities of CREx.

contact

authors: matthias bernt, daniel merkle, martin middendorf
( parallel computing and complex systems group , university of leipzig ).
contact: bernt (at) informatik (dot) uni-leipzig (dot) de

see also:

Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter Stadler, Martin Schlegel
Evolution of Mitochondrial Gene Orders in Echinoderms
Molecular Phylogenetics and Evolution, 2008, 47(2):855-864 pdf

and:

Matthias Bernt, Daniel Merkle and Martin Middendorf
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree
Comparative Genomics, International Workshop, RECOMB-CG 2008, 2008, 5267, 143-157 link

obtaining input data for CREx

for generating a consistent set of gene orders you might use use our software for the automatic annotation of mitochondrial genomes MITOS.

gene order data for the comparison can also be obtained from MitoZoa

usage of CRex

MT Aguado, S Richter, R Sontowski, A Golombek, TH Struck, and C Bleidorn
Syllidae mitochondrial gene order is unusually variable for Annelida
Gene 2016 link

ND Rubinstein, T Feldstein, N Shenkar, F Botero-Castro, F Griggio, F Mastrototaro, F Delsuc, EJP Douzery, C Gissi, and D Huchon
Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes
Genome Biology and Evolution 2016 link

PG Foster, MA Staleri, A Waeschenbach, TD Littlewood
High-throughput multiplexed mitogenomics for Metazoa: prospects and limitations
In Next Generation Systematics 2016 link

L Bachmann, B Fromm, LP de Azambuja, WA Boeger
The mitochondrial genome of the egg-laying flatworm Aglaiogyrodactylus forficulatus (Platyhelminthes: Monogenoidea)
Parasites & Vectors 2016 link

J Zhang, TA Ruhlman, J Sabir, JC Blazier, ML Weng, S Park, and RK Jansen
Coevolution between nuclear encoded DNA replication, recombination and repair genes and plastid genome complexity
Genome Biology and Evolution 2016 link

XF Xue, JF Guo, Y Dong, XY Hong, R Shao
Mitochondrial genome evolution and tRNA truncation in Acariformes mites: new evidence from eriophyoid mites.
Scientific reports 2016 link

MJTN Timmermans, DC Lees, MJ Thompson, Sz. Sáfián, O Brattström
Mitogenomics of ’Old World Acraea’ butterflies reveals a highly divergent ‘Bematistes’.
Molecular Phylogenetics and Evolution 2015 link

M Stokkana, JA Jurado-Rivera, C Juan, D Jaume, and J Pons.
Mitochondrial genome rearrangements at low taxonomic levels: three distinct mitogenome gene orders in the genus Pseudoniphargus (Crustacea: Amphipoda).
Mitochondrial DNA 2015 link

MT Aguado, C Grande, M Gerth, C Bleidorn, C Noreña.
Characterization of the complete mitochondrial genomes from Polycladida (Platyhelminthes) using next-generation sequencing.
Gene 2015 link

YJ Luo, N Satoh, K Endo.
Mitochondrial gene order variation in the brachiopod Lingula anatina and its implications for mitochondrial evolution in lophotrochozoans.
Marine Genomics 2015 link

A Weigert, A Golombek, M Gerth, F Schwarz, TH Struck, C Bleidorn.
Evolution of mitochondrial gene order in Annelida.
Molecular Phylogenetics and Evolution 2015 link

GH Liu, RF Shao, XQ Cai, WW Li, XQ Zhu.
Gnathostoma spinigerum Mitochondrial Genome Sequence: a Novel Gene Arrangement and its Phylogenetic Position within the Class Chromadorea.
Scientific Reports 5, 12691 2015 link

I Atray, JS Bentur, S Nair.
The Asian Rice Gall Midge (Orseolia oryzae) Mitogenome Has Evolved Novel Gene Boundaries and Tandem Repeats That Distinguish Its Biotypes.
PLOS ONE 2015 link

MT Aguado, CJ Glasby, PC Schroeder, A Weigert, and C Bleidorn
The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata.
Scientific reports 5 2015 link

MH Tan, HM Gan, MB Schultz, CM Austin
MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes.
Molecular Phylogenetics and Evolution 2015 link

R Lin, C Liu, B Shen, M Bai, J Ling, G Chen, Z Mao, X Cheng and B Xie
Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales.
BMC Microbiology 15.1 (2015): 5 link

Heydari, M., Marashi, S. A., Tusserkani, R., and Sadeghi, M.
Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.
Biosystems 2014, 124, 86-94 link

M. Babbucci, A. Basso, A. Scupola, T. Patarnello, and E. Negrisolo
Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and Lepidoptera.
Genome Biology and Evolution 2014 link

M. Liu, Z. Zhang and Z. Peng
The mitochondrial genome of the water spider Argyroneta aquatica (Araneae: Cybaeidae).
Zoologica Scripta 2014 link

J Pons, MM Bauzà-Ribot, D Jaume, and C Juan
Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea).
BMC Genomics 2014, 15:566 link

M Mao, T Gibson, M Dowton
Evolutionary dynamics of the mitochondrial genome in the Evaniomorpha (Hymenoptera)–a group with an intermediate rate of gene rearrangement.
Genome Biology and Evolution, 2014 link

Shu-Jun Wei, Qian Li, Kees van Achterberg, Xue-Xin Chen
Two mitochondrial genomes from the families Bethylidae and Mutillidae: Independent rearrangement of protein-coding genes and higher-level phylogeny of the Hymenoptera.
Molecular Phylogenetics and Evolution 2014 link

Mao-Lun Weng, J. Chris Blazier, Madhumita Govindu, and Robert K. Jansen
Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation Between Genome Rearrangements, Repeats and Nucleotide Substitution Rates.
Mol Biol Evol. 2013 link

Nimrod D. Rubinstein et al.
Deep Sequencing of Mixed Total DNA Without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes
Genome Biology and Evolution 2013 link

A. Golombek, S. Tobergte, M. P. Nesnidal, G. Purschke, T. H. Struck
Mitochondrial genomes to the rescue - Diurodrilidae in the myzostomid trap
Molecular Phylogenetics and Evolution 2013 link

M. Perseke, A. Golombek, M. Schlegel, T. H. Struck
The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny
Molecular Phylogenetics and Evolution 2013, 66(3):898-905 link

Feng-Jiau Lin, Yuan Liu, Zhongli Sha, Ling M Tsang, Ka H Chu, Tin-Yam Chan, Ruiyu Liu and Zhaoxia Cui
Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes
BMC Genomics 2012, 13:631 link

Chen HX, Sun SC, Sundberg P, Ren WC, Norenburg JL
A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea.
BMC Genomics. 2012 13:139 link

L Krebes and R Bastrop
The mitogenome of Gammarus duebeni (Crustacea Amphipoda): A new gene order and non-neutral sequence evolution of tandem repeats in the control region
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics link

A Duò, R Bruggmann, S Zoller, M Bernt, CR Grünig
Mitochondrial genome evolution in species belonging to the Phialocephala fortinii sl-Acephala applanata species complex
BMC genomics 2012 13(1), 166 link

BL Webster and DTJ Littlewood
Mitochondrial gene order change in Schistosoma (Platyhelminthes: Digenea: Schistosomatidae)
International Journal for Parasitology 2012 42(3):313-321 link

M P Nesnidal, M Helmkampf, I Bruchhaus and B Hausdorf
The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships
BMC Genomics 2011, 12:572 link

M Wang, S Sun, C Li and X Shen
Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies
BMC Genomics 2011, 12:73 link

M Perseke, J Hetmank, M Bernt, P F Stadler, M Schlegel and D Bernhard
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
BMC Evolutionary Biology 2011, 11:134 link

A Mwinyi, X Bailly, S J Bourlat, U Jondelius, D Timothy J Littlewood and L Podsiadlowski
The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis
BMC Evolutionary Biology 2010, 10:309 link

T Stach, A Braband and L Podsiadlowski
Erosion of phylogenetic signal in tunicate mitochondrial genomes on different levels of analysis
Molecular Phylogenetics and Evolution 55(3):860-870, 2010 link

M Perseke, D Bernhard, G Fritzsch, F Brümmer, P F. Stadler and M Schlegel
Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata
Molecular Phylogenetics and Evolution 56(1):201-211, 2010 link

W Dermauw, T Van Leeuwen, B Vanholme and L Tirry
The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart): a novel gene arrangement among arthropods
BMC Genomics 2009, 10:107 link

C Bleidorn, N Hill, C Erséus and R Tiedemann
On the role of character loss in orbiniid phylogeny (Annelida): Molecules vs. morphology
Molecular Phylogenetics and Evolution 2009, 52(1):57-69 link

M M Bauzà-Ribot, D Jaume, C Juan and J Pons
The complete mitochondrial genome of the subterranean crustacean Metacrangonyx longipes (Amphipoda): A unique gene order and extremely short control region
Mitochondrial DNA 2009 20(4):88-99 link

Other studies citing CRex

Stephen L. Cameron
Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny.
Annual Review of Entomology 2014 Vol. 59: 95-117 link