Dataset Information

A method for computing an inventory of metazoan mitochondrial gene order rearrangements.

ABSTRACT:

Background

Changes in the order of mitochondrial genes are a good source of information for phylogenetic investigations. Phylogenetic hypotheses are often supported by parsimonious mitochondrial gene order rearrangement scenarios. CREx is a heuristic for computing short pairwise rearrangement scenarios for metazoan mitochondrial gene orders. Different from other methods, CREx considers four types of rearrangement operations: inversions, transpositions, inverse transpositions, and tandem duplication random loss operations.

Results

An extensive analysis of the CREx reconstructions for artificial data has been presented and it is shown how the quality of the reconstructed rearrangement scenarios depends on the type of rearrangement model and additional parameter values. Moreover, a fast method is proposed to apply CREx to a large number of gene orders to find likely rearrangement scenarios and store them in a graph structure called RI-Graph. This method is applied to analyse all known metazoan mitochondrial gene orders. It is shown that the obtained RI-Graph contains many rearrangement scenarios that are described in the literature.

Conclusions

The prospects and limitations of CREx have been analysed empirically and a comparison with the literature on gene order evolution highlights its benefits. The newly developed method to apply CREx to a large number of gene orders is successful in computing an RI-graph that contains many rearrangement scenarios for metazoan gene orders that have also been described in the literature. This shows that the new method is very helpful for a fast analysis of a large number of gene orders which is relevant due to the strongly increasing number of known gene orders.

SUBMITTER: Bernt M

PROVIDER: S-EPMC3283314 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature

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Publications

A method for computing an inventory of metazoan mitochondrial gene order rearrangements.

Bernt Matthias M Middendorf Martin M

BMC bioinformatics 20111005

<h4>Background</h4>Changes in the order of mitochondrial genes are a good source of information for phylogenetic investigations. Phylogenetic hypotheses are often supported by parsimonious mitochondrial gene order rearrangement scenarios. CREx is a heuristic for computing short pairwise rearrangement scenarios for metazoan mitochondrial gene orders. Different from other methods, CREx considers four types of rearrangement operations: inversions, transpositions, inverse transpositions, and tandem ...[more]

PMID: 22151086

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Project description:BackgroundRecent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae.ResultsThe L. longipenis mitogenome (15,433 bp) contains the standard 36 flatworm mitochondrial genes (atp8 is absent), whereas we failed to detect trnS1, trnC and trnG in L. spari (14,614 bp). Both mitogenomes exhibit unique gene orders (among the Monogenea), with a number of tRNA rearrangements. Both long non-coding regions contain a number of different (partially overlapping) repeat sequences. Intriguingly, these include putative tRNA pseudogenes in a tandem array (17 trnV pseudogenes in L. longipenis, 13 trnY pseudogenes in L. spari). Combined nucleotide diversity, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently showed that nad2, nad5 and nad4 were the most variable PCGs, whereas cox1, cox2 and cytb were the most conserved. Phylogenomic analysis showed that the newly sequenced species of the family Diplectanidae formed a sister-group with the Dactylogyridae + Capsalidae clade. Thus Dactylogyridea (represented by the Diplectanidae and Dactylogyridae) was rendered paraphyletic (with high statistical support) by the nested Capsalidea (represented by the Capsalidae) clade.ConclusionsOur results show that nad2, nad5 and nad4 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in the Diplectanidae. The unique gene order pattern further suggests discontinuous evolution of mitogenomic gene order arrangement in the Class Monogenea. This first report of paraphyly of the Dactylogyridea highlights the need to generate more molecular data for monogenean parasites, in order to be able to clarify their relationships using large datasets, as single-gene markers appear to provide a phylogenetic resolution which is too low for the task.

Project description:BackgroundComplete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. Ctenophora (comb jellies) is one such example, with only two complete mt sequences determined hitherto for this phylum, which encompasses ca. 150-200 described species. This lack of data derives from the extremely fast mt evolutionary rate in this lineage, complicating primer design and DNA amplification. Indeed, in the two ctenophore mt genomes sequenced to date, i.e. those of Mnemiopsis leidyi (order Lobata) and Pleurobrachia bachei (order Cydippida), both rRNA and protein coding genes exhibit an extraordinary size reduction and have highly derived sequences. Additionally, all tRNAs, and the atp6 and atp8 genes are absent. In order to determine whether these characteristics are shared by other ctenophores, we obtained the complete mt genomes of three benthic ctenophores belonging to the so far unsampled order of Platyctenida: Coeloplana loyai, Coeloplana yulianicorum and Vallicula multiformis.ResultsThe mt genomes of benthic ctenophores reveal the same peculiarities found in Mnemiopsis and Pleurobrachia, demonstrating that the fast evolutionary rate is a general trait of the ctenophore mt genomes. Our results also indicate that this high evolutionary rate not only affects the nucleotide substitution but also gene rearrangements. Indeed, gene order was highly rearranged among representatives of the different taxonomic orders in which it was close to random, but also quite variable within Platyctenida, in which the genera Coeloplana and Vallicula share only four conserved synteny blocks. However, the two congeneric Coeloplana species display exactly the same gene order. Because of the extreme evolutionary rate, our phylogenetic analyses were unable to resolve the phylogenetic position of ctenophores within metazoans or the relationships among the different Ctenophora orders. Comparative sequence-analyses allowed us to correct the annotation of the Pleurobrachia mt genome, confirming the absence of tRNAs, the presence of both rRNA genes, and the existence of a reassignment of codon TGA from tryptophan to serine for this species.ConclusionsSince Platyctenida is an early diverging lineage among Ctenophora, our findings suggest that the mt traits described above are ancestral characteristics of this phylum.

Dataset Information

A method for computing an inventory of metazoan mitochondrial gene order rearrangements.

Background

Results

Conclusions

Publications

A method for computing an inventory of metazoan mitochondrial gene order rearrangements.

Similar Datasets

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