CREx: inferring genomic rearrangements based on common intervals

Bernt, Matthias; Merkle, Daniel; Ramsch, Kai; Fritzsch, Guido; Perseke, Marleen; Bernhard, Detlef; Schlegel, Martin; Stadler, Peter F.; Middendorf, Martin

doi:10.1093/bioinformatics/btm468

Cited by 300 publications

(210 citation statements)

References 14 publications

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“…We used the program CREx (Bernt et al 2007) to deduce gene rearrangement scenarios in crustacean mitogenomes based on the detection of strong interval trees (STIs) on the CREx webserver (http://pacosy.informatik.uni-leipzig.de/crex). The STIs reflect genes that appear consecutively in several of the input gene orders, i.e.…”

Section: Gene Rearrangement Analysesmentioning

confidence: 99%

“…The descendants of a node (strong common interval) are simply the strong common intervals that it includes entirely. If the descendants of a node appear in the same order in both input gene orders, the node is called "linear increasing" (+); if the children of a node appear in exactly the opposite order, it is "linear decreasing" (-); otherwise the node is called prime (Bernt et al 2007). …”

Section: Gene Rearrangement Analysesmentioning

confidence: 99%

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The complete mitochondrial genome of the subterranean crustaceanMetacrangonyx longipes(Amphipoda): A unique gene order and extremely short control region

et al. 2009

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Metazoan mitochondrial genomes usually consist of the same gene set, but some taxonomic groups show a considerable variety in gene order and nucleotide composition. The mitochondrial genomes of 37 crustaceans are currently known. Within the malacostracan superorder Peracarida, only three partial mitogenome sequences and the complete sequence of Ligia oceanica (Isopoda) are available.Frequent translocation events have changed the mitochondrial gene order in crustaceans, providing an opportunity to study the patterns and mechanisms of mitogenome rearrangement and to determine their impact on phylogenetic reconstructions. Here we report the first complete nucleotide sequence of an amphipod species, Metacrangonyx longipes, belonging to a phylogenetically enigmatic family occurring in continental subterranean waters. The genome has 14,113 base pairs (bp) and contains the usual 13 protein coding genes and two rRNA subunits, but only 21 out of the typical 22 tRNA genes of Metazoa. This is the shortest mitogenome described thus far for a crustacean and also one of the richest in AT (76.03%). The genome compactness results from a very small control region of 76 bp, the occurrence of frequent gene overlap, and the absence of large non-coding fragments. Six of the protein-coding genes have unusual start codons.Comparison of individual protein coding genes with the sequences known for other crustaceans suggests that nad2, nad6, nad4L and atp8 show the highest divergence rates. Metacrangonyx longipes shows a unique crustacean mitogenome gene order, differing even from the condition found in Parhyale hawaiiensis (Amphipoda), whose coding sequence has also been completed in the present study.

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Section: Gene Rearrangement Analysesmentioning

confidence: 99%

Section: Gene Rearrangement Analysesmentioning

confidence: 99%

The complete mitochondrial genome of the subterranean crustaceanMetacrangonyx longipes(Amphipoda): A unique gene order and extremely short control region

et al. 2009

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“…Simple transposition can be explained by a duplication and random loss (drl) model (Moritz et al 1987; Boore 2000), whereas the inverted transposition can be described through the combination of these two mechanisms. The global rearrangement pattern can be further analysed through a tandem duplication and random loss (TDRL) mechanism (Bernt et al 2007; Bernt and Middendorf 2011). According to Bernt and Middendorf (2011), TDRL involves a tandem duplication of a continuous segment of genes such that the original segment and its copy are consecutive followed by the loss of one copy of each of the redundant genes.…”

Section: Introductionmentioning

confidence: 99%

Is It an Ant or a Butterfly? Convergent Evolution in the Mitochondrial Gene Order of Hymenoptera and Lepidoptera

Babbucci

Basso

Scupola³

et al. 2014

Genome Biology and Evolution

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Insect mitochondrial genomes (mtDNA) are usually double helical and circular molecules containing 37 genes that are encoded on both strands. The arrangement of the genes is not constant for all species, and produces distinct gene orders (GOs) that have proven to be diagnostic in defining clades at different taxonomic levels. In general, it is believed that distinct taxa have a very low chance of sharing identically arranged GOs. However, examples of identical, homoplastic local rearrangements occurring in distinct taxa do exist. In this study, we sequenced the complete mtDNAs of the ants Formica fusca and Myrmica scabrinodis (Formicidae, Hymenoptera) and compared their GOs with those of other Insecta. The GO of F. fusca was found to be identical to the GO of Dytrisia (the largest clade of Lepidoptera). This finding is the first documented case of an identical GO shared by distinct groups of Insecta, and it is the oldest known event of GO convergent evolution in animals. Both Hymenoptera and Lepidoptera acquired this GO early in their evolution. Using a phylogenetic approach combined with new bioinformatic tools, the chronological order of the evolutionary events that produced the diversity of the hymenopteran GOs was determined. Additionally, new local homoplastic rearrangements shared by distinct groups of insects were identified. Our study showed that local and global homoplasies affecting the insect GOs are more widespread than previously thought. Homoplastic GOs can still be useful for characterizing the various clades, provided that they are appropriately considered in a phylogenetic and taxonomic context.

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“…We used CREx (Bernt et al 2007) to conduct pairwise comparisons of the mitochondrial gene order. CREx determines the most parsimonious genome rearrangement scenario between the gene order of each pair of taxa including transpositions, reverse transpositions, reversals, and tandem-duplication-random-loss (tdrl) events.…”

Section: Mitochondrial Genome Annotation and Gene Order Analysesmentioning

confidence: 99%