A New Enterobacter cloacae Bacteriophage EC151 Encodes the Deazaguanine DNA Modification Pathway and Represents a New Genus within the Siphoviridae Family

A novel Enterobacter cloacae phage, EC151, was isolated and characterized. Electron microscopy revealed that EC151 has a siphovirus-like virion morphology. The EC151 nucleotide sequence shows limited similarity to other phage genomes deposited in the NCBI GenBank database. The size of the EC151 genome is 60,753 bp and contains 58 putative genes. Thirty-nine of them encode proteins of predicted function, 18 are defined as hypothetical proteins, and one ORF identifies as the tRNA-Ser-GCT-encoding gene. Six ORFs were predicted to be members of the deazaguanine DNA modification pathway, including the preQ0 transporter. Comparative proteomic phylogenetic analysis revealed that phage EC151 represents a distinct branch within a group of sequences containing clades formed by members of the Seuratvirus, Nonagvirus, and Vidquintavirus genera. In addition, the EC151 genome showed gene synteny typical of the Seuratvirus, Nonagvirus, and Nipunavirus phages. The average genetic distances of EC151/Seuratvirus, EC151/Nonagvirus, and EC151/Vidquintavirus are approximately equal to those between the Seuratvirus, Nonagvirus, and Vidquintavirus genera (~0.7 substitutions per site). Therefore, EC151 may represent a novel genus within the Siphoviridae family. The origin of the deazaguanine DNA modification pathway in the EC151 genome can be traced to Escherichia phages from the Seuratvirus genus.

The mitochondrial genome of Ophiostoma himal-ulmi and comparison with other Dutch elm disease causing fungi.

The mitochondrial genome of Ophiostoma himal-ulmi, a species endemic to the Western Himalayas and a member of the Dutch elm disease-causing fungi, has been sequenced and characterized. The mitochondrial genome was compared with other available genomes for members of the Ophiostomatales, including other agents of Dutch elm disease (Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi and Ophiostoma novo-ulmi subspecies americana) and it was noted that gene synteny is highly conserved and variability among members of the Dutch-elm disease-causing fungi is primarily due to the number of intron insertions. Among the Dutch elm disease-causing fungi examined, O. himal-ulmi has the largest mitochondrial genomes ranging from 94 934 bp to 111 712 bp due to the expansion of the number of introns.

A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

The Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae).

Balon Balığı (Fugu rubripes)’nda Katalaz Geninin Biyoinformatik Analizleri

In this study, bioinformatics analysis of fugu (Fugu rubripes) catalase (cat) gene was performed. Molecular biology science is developing rapidly in parallel with the increasing importance of bioinformatics, thanks to the developed techniques in recent years. In this bioinformatics-based study wich enables the effective identification and characterization of genes in living organisms using online genome databases and statistics and storage, organization and sharing of the ever-increasing genetic data we designed the conserved gene synteny and gene structure and detected the identiy-similarity ratios between fugu and the other telosts and tetrapods. NCBI-GeneBank, EMBL, ENSEML and UNIPROT databases have been used for all these bioinformatics studies. Bioedit and Mega programs were used to perform the analysis and evaluate the data obtained from all these databases. In silico analysis such as the identification and characterization of fugu cat gene, exons-introns organization, phylogenetic tree and gene synteny were completed in this study and presented with tables and figures.

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Conclusions Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

Screening for mouse genes lost in mammals with long lifespans

Background Gerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate species can be due, among other things, to the loss of particular genes that are present in short-lived species of the same orders. These genes can also explain the widely different rates of aging among diverse species as well as why similarly sized rodents or primates sometimes have anomalous life expectancies (e.g., naked mole-rats and humans). Here, we consider the gene loss in the context of the prediction of Williams’ theory that concerns the reallocation of physiological resources of an organism between active reproduction (r-strategy) and self-maintenance (K-strategy). We have identified such lost genes using an original computer-aided approach; the software considers the loss of a gene as disruptions in gene orthology, local gene synteny or both. Results A method and software identifying the genes that are absent from a predefined set of species but present in another predefined set of species are suggested. Examples of such pairs of sets include long-lived vs short-lived, homeothermic vs poikilothermic, amniotic vs anamniotic, aquatic vs terrestrial, and neotenic vs nonneotenic species, among others. Species are included in one of two sets according to the property of interest, such as longevity or homeothermy. The program is universal towards these pairs, i.e., towards the underlying property, although the sets should include species with quality genome assemblies. Here, the proposed method was applied to study the longevity of Euarchontoglires species. It largely predicted genes that are highly expressed in the testis, epididymis, uterus, mammary glands, and the vomeronasal and other reproduction-related organs. This agrees with Williams’ theory that hypothesizes a species transition from r-strategy to K-strategy. For instance, the method predicts the mouse gene Smpd5, which has an expression level 20 times greater in the testis than in organs unrelated to reproduction as experimentally demonstrated elsewhere. At the same time, its paralog Smpd3 is not predicted by the program and is widely expressed in many organs not specifically related to reproduction. Conclusions The method and program, which were applied here to screen for gene losses that can accompany increased lifespan, were also applied to study reduced regenerative capacity and development of the telencephalon, neoteny, etc. Some of these results have been carefully tested experimentally. Therefore, we assume that the method is widely applicable.

PACVr: Plastome Assembly Coverage Visualization in R

ABSTRACTBackgroundThe circular, quadripartite structure of plastid genomes which includes two inverted repeat regions renders the automatic assembly of plastid genomes challenging. The correct assembly of plastid genomes is a prerequisite for the validity of subsequent analyses on plastid genome structure and evolution. Plastome-based phylogenetic or population genetic investigations, for example, require the precise identification of DNA sequence and length to determine the location of nucleotide polymorphisms. The average coverage depth of a genome assembly is often used as an indicator for assembly quality. Visualizing coverage depth across a draft genome allows users to inspect the quality of the assembly and, where applicable, identify regions of reduced assembly confidence. Based on such visualizations, users can conduct a local re-assembly or other forms of targeted error correction. Few, if any, contemporary software tools can visualize the coverage depth of a plastid genome assembly while taking its quadripartite structure into account, despite the interplay between genome structure and assembly quality. A software tool is needed that visualizes the coverage depth of a plastid genome assembly on a circular, quadripartite map of the plastid genome.ResultsWe introduce ‘PACVr’, an R package that visualizes the coverage depth of a plastid genome assembly in relation to the circular, quadripartite structure of the genome as well as to the individual plastome genes. The tool allows visualizations on different scales using a variable window approach and also visualizes the equality of gene synteny in the inverted repeat regions of the plastid genome, thus providing an additional measure of assembly quality. As a tool for plastid genomics, PACVr provides the functionality to identify regions of coverage depth above or below user-defined threshold values and helps to identify non-identical IR regions. To allow easy integration into bioinformatic workflows, PACVr can be directly invoked from a Unix shell, thus facilitating its use in automated quality control. We illustrate the application of PACVr on two empirical datasets and compare the resulting visualizations with alternative software tools for displaying plastome sequencing coverage.ConclusionsPACVr provides a user-friendly tool to visualize (a) the coverage depth of a plastid genome assembly on a circular, quadripartite plastome map and in relation to individual plastome genes, and (b) the equality of gene synteny in the inverted repeat regions. It, thus, contributes to optimizing plastid genome assemblies and increasing the reliability of publicly available plastome sequences, especially in light of incongruence among the visualization results of alternative software tools. The software, example datasets, technical documentation, and a tutorial are available with the package at https://github.com/michaelgruenstaeudl/PACVr.

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

BackgroundNew sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.ResultsWe employed three gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: six with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and three with new assemblies based on re-scaffolding or Pacific Biosciences long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: seven for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further seven with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.ConclusionsExperimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our comparisons show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.