Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

Since the discovery of Mimivirus, viruses with large genomes encoding components of the translation machinery and other cellular processes have been described as belonging to the nucleocytoplasmic large DNA viruses. Recently, genome-resolved metagenomics led to the discovery of more than 40 viruses that have been grouped together in a proposed viral subfamily named Klosneuvirinae. Members of this group had genomes of up to 2.4Mb in size and featured an expanded array of translation system genes. Yet, despite the large diversity of the Klosneuvirinae in metagenomic data, there are currently only two isolates available. Here, we report the isolation of a novel giant virus known as Fadolivirus from an Algerian sewage site and provide morphological data throughout its replication cycle in amoeba and a detailed genomic characterization. The Fadolivirus genome, which is more than 1.5Mb in size, encodes 1,452 predicted proteins and phylogenetic analyses place this viral isolate as a near relative of the metagenome assembled Klosneuvirus and Indivirus. The genome encodes for 66 tRNAs, 23 aminoacyl-tRNA synthetases and a wide range of transcription factors, surpassing Klosneuvirus and other giant viruses. The Fadolivirus genome also encodes putative vacuolar-type proton pumps with the domains D and A, potentially constituting a virus-derived system for energy generation. The successful isolation of Fadolivirus will enable future hypothesis-driven experimental studies providing deeper insights into the biology of the Klosneuvirinae.

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Novel Cell-Virus-Virophage Tripartite Infection Systems Discovered in the Freshwater Lake Dishui Lake in Shanghai, China

Journal of Virology ◽

10.1128/jvi.00149-20 ◽

2020 ◽

Vol 94 (11) ◽

Cited By ~ 1

Author(s):

Shengzhong Xu ◽

Liang Zhou ◽

Xiaosha Liang ◽

Yifan Zhou ◽

Hao Chen ◽

...

Keyword(s):

Green Algae ◽

Green Alga ◽

Phylogenetic Analyses ◽

Freshwater Lake ◽

Metagenomic Data ◽

Data Sets ◽

Data Set ◽

Dna Viruses ◽

Oligonucleotide Frequency ◽

Dsdna Viruses

ABSTRACT Virophages are small parasitic double-stranded DNA (dsDNA) viruses of giant dsDNA viruses infecting unicellular eukaryotes. Except for a few isolated virophages characterized by parasitization mechanisms, features of virophages discovered in metagenomic data sets remain largely unknown. Here, the complete genomes of seven virophages (26.6 to 31.5 kbp) and four large DNA viruses (190.4 to 392.5 kbp) that coexist in the freshwater lake Dishui Lake, Shanghai, China, have been identified based on environmental metagenomic investigation. Both genomic and phylogenetic analyses indicate that Dishui Lake virophages (DSLVs) are closely related to each other and to other lake virophages, and Dishui Lake large DNA viruses are affiliated with the micro-green alga-infecting Prasinovirus of the Phycodnaviridae (named Dishui Lake phycodnaviruses [DSLPVs]) and protist (protozoan and alga)-infecting Mimiviridae (named Dishui Lake large alga virus [DSLLAV]). The DSLVs possess more genes with closer homology to that of large alga viruses than to that of giant protozoan viruses. Furthermore, the DSLVs are strongly associated with large green alga viruses, including DSLPV4 and DSLLAV1, based on codon usage as well as oligonucleotide frequency and correlation analyses. Surprisingly, a nonhomologous CRISPR-Cas like system is found in DSLLAV1, which appears to protect DSLLAV1 from the parasitization of DSLV5 and DSLV8. These results suggest that novel cell-virus-virophage (CVv) tripartite infection systems of green algae, large green alga virus (Phycodnaviridae- and Mimiviridae-related), and virophage exist in Dishui Lake, which will contribute to further deep investigations of the evolutionary interaction of virophages and large alga viruses as well as of the essential roles that the CVv plays in the ecology of algae. IMPORTANCE Virophages are small parasitizing viruses of large/giant viruses. To our knowledge, the few isolated virophages all parasitize giant protozoan viruses (Mimiviridae) for propagation and form a tripartite infection system with hosts, here named the cell-virus-virophage (CVv) system. However, the CVv system remains largely unknown in environmental metagenomic data sets. In this study, we systematically investigated the metagenomic data set from the freshwater lake Dishui Lake, Shanghai, China. Consequently, four novel large alga viruses and seven virophages were discovered to coexist in Dishui Lake. Surprisingly, a novel CVv tripartite infection system comprising green algae, large green alga viruses (Phycodnaviridae- and Mimiviridae-related), and virophages was identified based on genetic link, genomic signature, and CRISPR system analyses. Meanwhile, a nonhomologous CRISPR-like system was found in Dishui Lake large alga viruses, which appears to protect the virus host from the infection of Dishui Lake virophages (DSLVs). These findings are critical to give insight into the potential significance of CVv in global evolution and ecology.

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Multiple evolutionary origins of giant viruses

F1000Research ◽

10.12688/f1000research.16248.1 ◽

2018 ◽

Vol 7 ◽

pp. 1840 ◽

Cited By ~ 28

Author(s):

Eugene V. Koonin ◽

Natalya Yutin

Keyword(s):

Life Forms ◽

Translation System ◽

Dna Viruses ◽

Evolutionary Forces ◽

Evolutionary Origins ◽

Cellular Life ◽

Giant Viruses ◽

Nucleocytoplasmic Large Dna Viruses ◽

Phylogenomic Analyses ◽

Definition Of

The nucleocytoplasmic large DNA viruses (NCLDVs) are a monophyletic group of diverse eukaryotic viruses that reproduce primarily in the cytoplasm of the infected cells and include the largest viruses currently known: the giant mimiviruses, pandoraviruses, and pithoviruses. With virions measuring up to 1.5 μm and genomes of up to 2.5 Mb, the giant viruses break the now-outdated definition of a virus and extend deep into the genome size range typical of bacteria and archaea. Additionally, giant viruses encode multiple proteins that are universal among cellular life forms, particularly components of the translation system, the signature cellular molecular machinery. These findings triggered hypotheses on the origin of giant viruses from cells, likely of an extinct fourth domain of cellular life, via reductive evolution. However, phylogenomic analyses reveal a different picture, namely multiple origins of giant viruses from smaller NCLDVs via acquisition of multiple genes from the eukaryotic hosts and bacteria, along with gene duplication. Thus, with regard to their origin, the giant viruses do not appear to qualitatively differ from the rest of the virosphere. However, the evolutionary forces that led to the emergence of virus gigantism remain enigmatic.

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Evaluating species in Botryosphaeriales

Persoonia - Molecular Phylogeny and Evolution of Fungi ◽

10.3767/persoonia.2021.46.03 ◽

2021 ◽

Author(s):

W. Zhang ◽

J.Z. Groenewald ◽

L. Lombard ◽

R.K. Schumacher ◽

A.J.L. Phillips ◽

...

Keyword(s):

South Africa ◽

Woody Plants ◽

Phylogenetic Analyses ◽

Culture Collection ◽

Morphological Data ◽

Culture Collections ◽

Future Studies ◽

The Past ◽

Wide Range ◽

Solid Foundation

The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.

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Using morphology to infer physiology: case studies on rorqual whales (Balaenopteridae)

Canadian Journal of Zoology ◽

10.1139/cjz-2014-0311 ◽

2015 ◽

Vol 93 (9) ◽

pp. 687-700 ◽

Cited By ~ 8

Author(s):

Jeremy A. Goldbogen ◽

Robert E. Shadwick ◽

Margo A. Lillie ◽

Marina A. Piscitelli ◽

Jean Potvin ◽

...

Keyword(s):

Experimental Studies ◽

Model Systems ◽

Morphological Data ◽

Sensory Physiology ◽

Aquatic Life ◽

Baleen Whales ◽

Physiological Processes ◽

Morphological Studies ◽

Large Size ◽

Wide Range

Whales are important model systems for understanding the physiological and ecological consequences of extreme body size. However, whales are also some of the most difficult animals to study because their large size precludes experimental studies under controlled conditions. Here we review a wide range of morphological studies that enable greater inference of physiological processes. In particular, we focus on baleen whales that exhibit extensive diving and foraging adaptations. Using morphological data, we (i) explore the biomechanics and sensory physiology of lunge-feeding rorqual whales (Balaenopteridae), (ii) determine the effects of scale and diving pressures on the circulatory physiology of fin whales (Balaenoptera physalus (L., 1758)), and (iii) better understand the adaptations of the cetacean respiratory system that facilitate a fully aquatic life history. These studies underscore the value of understanding functional morphology in animals that cannot be studied using traditional laboratory techniques.

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Discovery of viral myosin genes with complex evolutionary history within plankton

10.1101/2021.03.14.435220 ◽

2021 ◽

Author(s):

Soichiro Kijima ◽

Tom O. Delmont ◽

Urara Miyazaki ◽

Morgan Gaia ◽

Hisashi Endo ◽

...

Keyword(s):

Evolutionary History ◽

Viral Particle ◽

Phylogenetic Analyses ◽

Viral Proteins ◽

The Other ◽

Dna Viruses ◽

Nucleocytoplasmic Large Dna Viruses ◽

The One ◽

Complex Evolutionary History

AbstractNucleocytoplasmic large DNA viruses (NCLDVs) infect diverse eukaryotes and form a group of viruses with capsids encapsulating large genomes. Recent studies are increasingly revealing a spectacular array of functions encoded in their genomes, including genes for energy metabolisms, nutrient uptake, as well as cytoskeleton. Here, we report the discovery of genes homologous to myosins, the major eukaryotic motor proteins previously unrecognized in the virosphere, in environmental genomes of NCLDVs from the surface of the oceans. Interestingly, these genes were often accompanied by kinesin genes in the environmental genomes, suggesting a role of these viral proteins in the intracellular viral particle transport. Phylogenetic analyses indicate that most viral myosins (named “virmyosins”) belong to the Imitervirales order, except for one belonging to the Phycodnaviridae family. On the one hand, the phylogenetic positions of virmyosin-encoding Imitervirales are scattered within the Imitervirales. On the other hand, Imitervirales virmyosin genes form a monophyletic group in the phylogeny of diverse myosin sequences. Furthermore, phylogenetic trends for the virmyosin genes and viruses containing them were incongruent. Based on these results, we argue that multiple transfers of myosin homologs have occurred not only from eukaryotes to viruses but also between viruses, supposedly during co-infections of the same host.

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Cladistics and rates of morphological evolution: computation and comparison

The Paleontological Society Special Publications ◽

10.1017/s2475262200006213 ◽

1992 ◽

Vol 6 ◽

pp. 61-61

Author(s):

Richard Cloutier ◽

Timothy Rowe

Keyword(s):

Morphological Evolution ◽

Average Rate ◽

Relative Rate ◽

Phylogenetic Analyses ◽

Evolutionary Rates ◽

Data Matrix ◽

Morphological Data ◽

Geological Time Scale ◽

Rates Of Evolution ◽

Wide Range

For the part fifty years, the concept of evolutionary rates has been developed largely in an evolutionary or phenetic framework. Many authors discussed rates, but under previous systematic paradigms no standardized methods developed to provide a uniform and general framework in which temporal properties of different lineages could be objectively measured and compared.We review recently developed methods for measuring rate-related properties of lineages that are based on phylogenetic analyses. Rate measurements are made directly from phylogenetic data matrices and cladograms. Because they benefit from the standardized procedures required to compile a data matrix, these methods are potentially exportable to a wide range of phylogenetic studies. Four potential factors relevant to the study of evolutionary rates in a cladistic framework have been analyzed with these methods: (1) morphological changes, (2) age and duration, (3) cladogenesis, and (4) species-diversity. We investigate interactions among these factors.Underlying assumptions in using a cladogram to calculate rates of evolution are: (1) the tree reflects the history of the group, and (2) the distributions of character states on the tree reflects the true distribution of character states during the evolution of the group. The calculation of rates from a cladogram requires that: (1) the cladograms are derived from parsimony analysis (e.g., PAUP, HENNIG86) of species coded for discrete character states; (2) the phylogenetic pattern (or branching sequence) is superimposed on a geological time scale in which each species is mapped according to its geological age (temporal cladogram); (3) phylogenetic pathways (unidirectional series of consecutive cladogenetic events) are determined in such a manner that the selected origin is a hypothetical ancestor to the terminal taxa selected; and (4) rates are calculated along selected phylogenetic pathways.Rates may be calculated as the number of changes—including autapomorphies, synapomorphies, and homoplasies—per unit of time. Alternatively, relative measures of rate may be obtained by comparing the average number of changes for an entire data matrix with changes in data subsets within the matrix. Five types of rates of morphological evolution can be determined and quantified along a phylogenetic pathway: (1) rate between two consecutive cladogenetic events, (2) rate during a geological period, (3) rate during a fixed period of time in millions of years, (4) relative rates of change for different morphological data subsets, such as dentition versus skeleton, and (5) relative rate along a selected segment of the cladogram, compared to the average rate measured for the cladogram as a whole. Various methods for comparing rates are investigated, such as Spearman Rank correlation, Fourier analysis, time series, and homoplasy index.Classic examples of rates of morphological evolution were previously taken from bivalves, echinoderms, lungfishes, coelacanths, and mammals. In the present study, rates of evolution within and/or between the Dipnoi (lungfishes), the Actinistia (coelacanths), and the Mammalia are calculated and compared.

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Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton

Frontiers in Microbiology ◽

10.3389/fmicb.2021.683294 ◽

2021 ◽

Vol 12 ◽

Author(s):

Soichiro Kijima ◽

Tom O. Delmont ◽

Urara Miyazaki ◽

Morgan Gaia ◽

Hisashi Endo ◽

...

Keyword(s):

Intracellular Trafficking ◽

Evolutionary History ◽

Intracellular Transport ◽

Motor Proteins ◽

Phylogenetic Analyses ◽

Dna Viruses ◽

Viral Particles ◽

Nucleocytoplasmic Large Dna Viruses ◽

The One ◽

Complex Evolutionary History

Nucleocytoplasmic large DNA viruses (NCLDVs) infect diverse eukaryotes and form a group of viruses with capsids encapsulating large genomes. Recent studies are increasingly revealing a spectacular array of functions encoded in their genomes, including genes for energy metabolisms, nutrient uptake, as well as cytoskeleton. Here, we report the discovery of genes homologous to myosins, the major eukaryotic motor proteins previously unrecognized in the virosphere, in environmental genomes of NCLDVs from the surface of the oceans. Phylogenetic analyses indicate that most viral myosins (named “virmyosins”) belong to the Imitervirales order, except for one belonging to the Phycodnaviridae family. On the one hand, the phylogenetic positions of virmyosin-encoding Imitervirales are scattered within the Imitervirales. On the other hand, Imitervirales virmyosin genes form a monophyletic group in the phylogeny of diverse myosin sequences. Furthermore, phylogenetic trends for the virmyosin genes and viruses containing them were incongruent. Based on these results, we argue that multiple transfers of myosin homologs have occurred not only from eukaryotes to viruses but also between viruses, supposedly during co-infections of the same host. Like other viruses that use host motor proteins for their intracellular transport or motility, these viruses may use the virally encoded myosins for the intracellular trafficking of giant viral particles.

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Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses

mSphere ◽

10.1128/msphere.01298-20 ◽

2021 ◽

Vol 6 (2) ◽

Author(s):

Lingjie Meng ◽

Hisashi Endo ◽

Romain Blanc-Mathieu ◽

Samuel Chaffron ◽

Rodrigo Hernández-Velázquez ◽

...

Keyword(s):

Large Scale ◽

Positive Likelihood Ratio ◽

Prediction Performance ◽

Marine Environments ◽

Sequencing Data ◽

Dna Viruses ◽

Host Interactions ◽

Wide Range ◽

Nucleocytoplasmic Large Dna Virus ◽

Nucleocytoplasmic Large Dna Viruses

ABSTRACT Nucleocytoplasmic large DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, the knowledge of their hosts is limited because only a few NCLDVs have been isolated so far. Taking advantage of the recent large-scale marine metagenomics census, in silico host prediction approaches are expected to fill the gap and further expand our knowledge of virus-host relationships for unknown NCLDVs. In this study, we built co-occurrence networks of NCLDVs and eukaryotic taxa to predict virus-host interactions using Tara Oceans sequencing data. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we benchmarked several co-occurrence approaches and demonstrated an increase in the odds ratio of predicting true positive relationships 4-fold compared to random host predictions. To further refine host predictions from high-dimensional co-occurrence networks, we developed a phylogeny-informed filtering method, Taxon Interaction Mapper, and showed it further improved the prediction performance by 12-fold. Finally, we inferred virophage-NCLDV networks to corroborate that co-occurrence approaches are effective for predicting interacting partners of NCLDVs in marine environments. IMPORTANCE NCLDVs can infect a wide range of eukaryotes, although their life cycle is less dependent on hosts compared to other viruses. However, our understanding of NCLDV-host systems is highly limited because few of these viruses have been isolated so far. Co-occurrence information has been assumed to be useful to predict virus-host interactions. In this study, we quantitatively show the effectiveness of co-occurrence inference for NCLDV host prediction. We also improve the prediction performance with a phylogeny-guided method, which leads to a concise list of candidate host lineages for three NCLDV families. Our results underpin the usage of co-occurrence approaches for the metagenomic exploration of the ecology of this diverse group of viruses.

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Image Statistics Preserving Encrypt-then-Compress Scheme Dedicated for JPEG Compression Standard

Entropy ◽

10.3390/e23040421 ◽

2021 ◽

Vol 23 (4) ◽

pp. 421

Author(s):

Dariusz Puchala ◽

Kamil Stokfiszewski ◽

Mykhaylo Yatsymirskyy

Keyword(s):

Statistical Analysis ◽

Image Encryption ◽

Experimental Studies ◽

Quality Measures ◽

Input Image ◽

Jpeg Compression ◽

Image Statistics ◽

Compression Stage ◽

Wide Range ◽

The Impact

In this paper, the authors analyze in more details an image encryption scheme, proposed by the authors in their earlier work, which preserves input image statistics and can be used in connection with the JPEG compression standard. The image encryption process takes advantage of fast linear transforms parametrized with private keys and is carried out prior to the compression stage in a way that does not alter those statistical characteristics of the input image that are crucial from the point of view of the subsequent compression. This feature makes the encryption process transparent to the compression stage and enables the JPEG algorithm to maintain its full compression capabilities even though it operates on the encrypted image data. The main advantage of the considered approach is the fact that the JPEG algorithm can be used without any modifications as a part of the encrypt-then-compress image processing framework. The paper includes a detailed mathematical model of the examined scheme allowing for theoretical analysis of the impact of the image encryption step on the effectiveness of the compression process. The combinatorial and statistical analysis of the encryption process is also included and it allows to evaluate its cryptographic strength. In addition, the paper considers several practical use-case scenarios with different characteristics of the compression and encryption stages. The final part of the paper contains the additional results of the experimental studies regarding general effectiveness of the presented scheme. The results show that for a wide range of compression ratios the considered scheme performs comparably to the JPEG algorithm alone, that is, without the encryption stage, in terms of the quality measures of reconstructed images. Moreover, the results of statistical analysis as well as those obtained with generally approved quality measures of image cryptographic systems, prove high strength and efficiency of the scheme’s encryption stage.

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Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽

10.1093/genetics/159.3.1103 ◽

2001 ◽

Vol 159 (3) ◽

pp. 1103-1115 ◽

Cited By ~ 1

Author(s):

Hongguang Shao ◽

Zhijian Tu

Keyword(s):

Phylogenetic Analyses ◽

Mosquito Species ◽

Open Reading Frames ◽

Inverted Repeats ◽

Sequence Comparisons ◽

Wide Range ◽

Multiple Copies ◽

Catalytic Motif ◽

Open The Doors ◽

Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

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