Gepard: a rapid and sensitive tool for creating dotplots on genome scale

Krumsiek, Jan; Arnold, Roland; Rattei, Thomas

doi:10.1093/bioinformatics/btm039

Cited by 638 publications

(574 citation statements)

References 10 publications

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“…Overall, 35 genes are different in the two genomes, corresponding to around 10% of both genomes. Furthermore, using dot plots (created with the Gepard program [61]), we compared genome synteny between the two genomes infecting Choristoneura species (CBEV and CREV) (Fig. 5a) and between genomes of two different chordopoxvirus species belonging to the same genus (Tanapox virus and Yaba monkey tumor virus, both species of the Yatapoxvirus genus) (Fig.…”

Section: Discussionmentioning

confidence: 99%

New Insights into the Evolution of Entomopoxvirinae from the Complete Genome Sequences of Four Entomopoxviruses Infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata

Thézé

Takatsuka

Li³

et al. 2013

J Virol

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dPoxviruses are nucleocytoplasmic large DNA viruses encompassing two subfamilies, the Chordopoxvirinae and the Entomopoxvirinae, infecting vertebrates and insects, respectively. While chordopoxvirus genomics have been widely studied, only two entomopoxvirus (EPV) genomes have been entirely sequenced. We report the genome sequences of four EPVs of the Betaentomopoxvirus genus infecting the Lepidoptera: Adoxophyes honmai EPV (AHEV), Choristoneura biennis EPV (CBEV), Choristoneura rosaceana EPV (CREV), and Mythimna separata EPV (MySEV). The genomes are 80% AT rich, are 228 to 307 kbp long, and contain 247 to 334 open reading frames (ORFs). Most genes are homologous to those of Amsacta moorei entomopoxvirus and encode several protein families repeated in tandem in terminal regions. Some genomes also encode proteins of unknown functions with similarity to those of other insect viruses. Comparative genomic analyses highlight a high colinearity among the lepidopteran EPV genomes and little gene order conservation with other poxvirus genomes. As with previously sequenced EPVs, the genomes include a relatively conserved central region flanked by inverted terminal repeats. Protein clustering identified 104 core EPV genes. Among betaentomopoxviruses, 148 core genes were found in relatively high synteny, pointing to low genomic diversity. Whole-genome and spheroidin gene phylogenetic analyses showed that the lepidopteran EPVs group closely in a monophyletic lineage, corroborating their affiliation with the Betaentomopoxvirus genus as well as a clear division of the EPVs according to the orders of insect hosts (Lepidoptera, Coleoptera, and Orthoptera). This suggests an ancient coevolution of EPVs with their insect hosts and the need to revise the current EPV taxonomy to separate orthopteran EPVs from the lepidopteran-specific betaentomopoxviruses so as to form a new genus. Poxviruses are large double-stranded DNA (dsDNA) viruses infecting a wide range of animals. They belong to the phylogenetically related group of viruses termed nucleocytoplasmic large DNA viruses (NCLDV) (1). They harbor linear dsDNA genomes with inverted terminal repeats (ITRs) (2). Poxvirus genomes are 130 to 375 kbp long and replicate in the cytoplasm (3). The family Poxviridae includes two subfamilies: the Chordopoxvirinae, infecting vertebrates, and the Entomopoxvirinae, infecting insects. The chordopoxviruses are classified into nine genera, including Orthopoxvirus and Avipoxvirus (4), and have been the subjects of the main body of research on poxviruses (5, 6). The entomopoxviruses (EPVs) are currently divided into three genera based on host range and virion morphology: Alphaentomopoxvirus, infecting coleopterans; Betaentomopoxvirus, infecting lepidopterans and orthopterans; and Gammaentomopoxvirus, infecting dipterans (4). However, the lack of genomic data has precluded the integration of unifying genetic criteria into this classification. That is why the orthopteran EPV Melanoplus sanguinipes entomopoxvirus was removed from the Betaentomopoxvirus ...

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Section: Discussionmentioning

confidence: 99%

New Insights into the Evolution of Entomopoxvirinae from the Complete Genome Sequences of Four Entomopoxviruses Infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata

Thézé

Takatsuka

Li³

et al. 2013

J Virol

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“…This reconstruction indicated clearly that the tail tube was composed of 34 stacked hexamers, including the tail terminator hexamer, at the interface with the connector, and the 33 MTP (ORF62) hexamers form the rest of the tube. In a subsequent step, we boxed short tail Table S1 in the supplemental material using Gepard (75). (B) Phylogenetic tree based on the nucleotide genome of Araucaria and its 8 closest mycobacteriophages using the neighbor joining method.…”

Section: Genome Characteristics Of Mycobacteriophagementioning

confidence: 99%

The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria

Sassi

Bebeacua

Drancourt

et al. 2013

J Virol

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The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ϳ3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis. M. abscessus subsp. bolletii was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the M. abscessus subsp. bolletii prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to Siphoviridae and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram ؊ ) or Gram ؉ bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.

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“…Ks and Ka were estimated using an evolutionary pathway approach (Nei and Gojobori, 1986) implemented in PAML (Yang, 1997). Gepard (Krumsiek et al, 2007), implementing a suffix tree algorithm, was used to make the dot plots of homeologous sequences (word size set to be 16 bp).…”

Section: Evolutionary Analysismentioning

confidence: 99%

Seventy Million Years of Concerted Evolution of a Homoeologous Chromosome Pair, in Parallel, in Major Poaceae Lineages

2011

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Whole genome duplication ;70 million years ago provided raw material for Poaceae (grass) diversification. Comparison of rice (Oryza sativa), sorghum (Sorghum bicolor), maize (Zea mays), and Brachypodium distachyon genomes revealed that one paleoduplicated chromosome pair has experienced very different evolution than all the others. For tens of millions of years, the two chromosomes have experienced illegitimate recombination that has been temporally restricted in a stepwise manner, producing structural stratification in the chromosomes. These strata formed independently in different grass lineages, with their similarities (low sequence divergence between paleo-duplicated genes) preserved in parallel for millions of years since the divergence of these lineages. The pericentromeric region of this homeologous chromosome pair accounts for two-thirds of the gene content differences between the modern chromosomes. Both intriguing and perplexing is a distal chromosomal region with the greatest DNA similarity between surviving duplicated genes but also with the highest concentration of lineage-specific gene pairs found anywhere in these genomes and with a significantly elevated gene evolutionary rate. Intragenomic similarity near this chromosomal terminus may be important in hom(e)ologous chromosome pairing. Chromosome structural stratification, together with enrichment of autoimmune response-related (nucleotide binding site-leucine-rich repeat) genes and accelerated DNA rearrangement and gene loss, confer a striking resemblance of this grass chromosome pair to the sex chromosomes of other taxa.

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Gepard: a rapid and sensitive tool for creating dotplots on genome scale

Abstract: Both source codes and executable binaries are available at http://mips.gsf.de/services/analysis/gepard

Cited by 638 publications

References 10 publications

New Insights into the Evolution of Entomopoxvirinae from the Complete Genome Sequences of Four Entomopoxviruses Infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata

New Insights into the Evolution of Entomopoxvirinae from the Complete Genome Sequences of Four Entomopoxviruses Infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata

The First Structure of a Mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria

Seventy Million Years of Concerted Evolution of a Homoeologous Chromosome Pair, in Parallel, in Major Poaceae Lineages

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