GraphDNA: a Java program for graphical display of DNA composition analyses

Thomas, Jamie M.; Horspool, Daniel; Brown, Gordon D.; Tcherepanov, Vasily; Upton, Chris

doi:10.1186/1471-2105-8-21

Cited by 40 publications

(20 citation statements)

References 30 publications

(32 reference statements)

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“…Our analyses do not differentiate between the origin of replication on the heavy (OriH) vs. light (OriL) strand; however, based on previous analyses in closely related groups (see 63 ), we hypothesize that the Oris reported here are indicative of OriH.…”

Section: Resultsmentioning

confidence: 55%

“…We utilized the ‘DNA Walker’ graphing option within GraphDNA 63 available online via the Viral Bioinformatics Resource Center [virology.uvic.ca]) to search each mitogenomic chromosome for abrupt changes in base composition bias that are characteristic of both the heavy (OriH) and light (OriL) strand origins of replication (see 64 for usage of the DNA Walk within bamboo corals and black corals). We also searched each mitogenomic chromosome for repeats using the Tandem Repeats Finder online server (v 4.09 65 ) and E-QuickTandem (v 6.5.0 66 ).…”

Section: Methodsmentioning

confidence: 99%

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Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia

Stampar

Broe

Macrander

et al. 2019

Sci Rep

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Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia (“tube anemones”) remains one of the most enigmatic in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both Isarachnanthus nocturnus and Pachycerianthus magnus , the mitochondrial gene sequences could not be assembled into a single circular genome. Instead, our analyses suggest that both species have mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The inferred number of fragments and variation in gene order between species is much greater within Ceriantharia than among the lineages of Medusozoa. We identify origins of replication for each of the five putative chromosomes of the Isarachnanthus nocturnus mitogenome and for each of the eight putative chromosomes of the Pachycerianthus magnus mitogenome. At 80,923 bp, I. nocturnus now holds the record for the largest animal mitochondrial genome reported to date. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other Anthozoa. The presence of tRNA Met and tRNA Trp in both ceriantharian mitogenomes supports a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and any other cnidarian lineage, but phylogenetic analysis of the genes contained in the mitogenomes suggests that Ceriantharia is sister to a clade containing Octocorallia + Hexacorallia indicating a possible suppression of tRNA Trp in Octocorallia.

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Section: Resultsmentioning

confidence: 55%

Section: Methodsmentioning

confidence: 99%

Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia

Stampar

Broe

Macrander

et al. 2019

Sci Rep

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show abstract

“…Phylograms and gene orders were visualized in iTOL (Letunic & Bork, 2007), and annotated using files generated by PhyloSuite. Skews were calculated and plotted using PhyloSuite and GraphDNA (Thomas, Horspool, Brown, Tcherepanov, & Upton, 2007).…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda

Zhang

Zou

Hua

et al. 2019

Preprint

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The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different datasets often producing starkly incongruent phylogenetic hypotheses. We hypothesised that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different datasets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artefacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artefacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements can produce major compositional biases even on short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

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“…The next step is to identify motifs that are significantly over-represented in in comparison to the negative control dataset . Different scoring functions have been used in the literature to achieve this task, for example, the Fisher’s exact test P -value [ 18 ], the Z-score [ 11 ], the compound Poisson approximation [ 16 ], mutual information [ 19 – 21 ], and many other metrics [ 22 ]. Here, we use mutual information (MI) to first explore the lattice and simplify it, and then Fisher’s exact test to rank the selected motifs.…”

Section: Methodsmentioning

confidence: 99%

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

Saad¹,

Noé²,

Richard³

et al. 2018

BMC Bioinformatics

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BackgroundDiscovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because of the increasing number of potential applications. However, it remains a difficult challenge, especially with the huge quantity of data generated by high throughput sequencing technologies. To overcome this problem, existing tools use greedy algorithms and probabilistic approaches to find motifs in reasonable time. Nevertheless these approaches lack sensitivity and have difficulties coping with rare and subtle motifs.ResultsWe developed DiNAMO (for DNA MOtif), a new software based on an exhaustive and efficient algorithm for IUPAC motif discovery. We evaluated DiNAMO on synthetic and real datasets with two different applications, namely ChIP-seq peaks and Systematic Sequencing Error analysis. DiNAMO proves to compare favorably with other existing methods and is robust to noise.ConclusionsWe shown that DiNAMO software can serve as a tool to search for degenerate motifs in an exact manner using IUPAC models. DiNAMO can be used in scanning mode with sliding windows or in fixed position mode, which makes it suitable for numerous potential applications.Availabilityhttps://github.com/bonsai-team/DiNAMO.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2215-1) contains supplementary material, which is available to authorized users.

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GraphDNA: a Java program for graphical display of DNA composition analyses

Cited by 40 publications

References 30 publications

Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia

Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia

Mitochondrial architecture rearrangements produce asymmetrical nonadaptive mutational pressures that subvert the phylogenetic reconstruction in Isopoda

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

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