Genomic Abundance Research Articles

Drivers of within-host genetic diversity in acute infections of viruses.

Genetic diversity is the fuel of evolution and facilitates adaptation to novel environments. However, our understanding of what drives differences in the genetic diversity during the early stages of viral infection is somewhat limited. Here, we use ultra-deep sequencing to interrogate 43 clinical samples taken from early infections of the human-infecting viruses HIV, RSV and CMV. Hundreds to thousands of virus templates were sequenced per sample, allowing us to reveal dramatic differences in within-host genetic diversity among virus populations. We found that increased diversity was mostly driven by presence of multiple divergent genotypes in HIV and CMV samples, which we suggest reflect multiple transmitted/founder viruses. Conversely, we detected an abundance of low frequency hyper-edited genomes in RSV samples, presumably reflecting defective virus genomes (DVGs). We suggest that RSV is characterized by higher levels of cellular co-infection, which allow for complementation and hence elevated levels of DVGs.

Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of Dictyostelium discoideum.

We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium discoideum, a key model organism in molecular, cellular, evolutionary and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. discoideum to evolve an extremely low base-substitution mutation rate.

CRISPR/Cas9-mediated VvPR4b editing decreases downy mildew resistance in grapevine (Vitis vinifera L.)

Downy mildew of grapevine (Vitis vinifera L.), caused by the oomycete pathogen Plasmopara viticola, is one of the most serious concerns for grape production worldwide. It has been widely reported that the pathogenesis-related 4 (PR4) protein plays important roles in plant resistance to diseases. However, little is known about the role of PR4 in the defense of grapevine against P. viticola. In this study, we engineered loss-of-function mutations in the VvPR4b gene from the cultivar “Thompson Seedless” using the CRISPR/Cas9 system and evaluated the consequences for downy mildew resistance. Sequencing results showed that deletions were the main type of mutation introduced and that no off-target events occurred. Infection assays using leaf discs showed that, compared to wild-type plants, the VvPR4b knockout lines had increased susceptibility to P. viticola. This was accompanied by reduced accumulation of reactive oxygen species around stomata. Measurement of the relative genomic abundance of P. viticola in VvPR4b knockout lines also demonstrated that the mutants had increased susceptibility to the pathogen. Our results confirm that VvPR4b plays an active role in the defense of grapevine against downy mildew.

An ECF41 family σ factor controls motility and biogenesis of lateral flagella in Azospirillum brasilense Sp245.

ECF41 is a large family of bacterial extra-cytoplasmic function (ECF) σ factors. Their role in bacterial physiology or behavior, however, is not known. One of the 10 ECF σ factors encoded in the genome of Azospirillum brasilense Sp245, RpoE10, exhibits characteristic features of the typical ECF41-type σ factors. Inactivation of rpoE10 in A. brasilense Sp245 led to an increase in motility that could be complemented by the expression of rpoE10 By comparing the number of lateral flagella, transcriptome and proteome of A. brasilense Sp245 with its rpoE10::km mutant, we show here that this ECF41-type σ factor is involved in the negative regulation of swimming motility and biogenesis of lateral flagella of A. brasilense Sp245. The genome of A. brasilense Sp245 also encodes two OmpR-type regulators (LafR1 and LafR2), and three flagellins including Laf1, the major flagellin of lateral flagella. Elevated levels of laf1 transcripts and Laf1 protein in the rpoE10::km mutant indicated that RpoE10 negatively regulates the expression of Laf1. The elevated level of LafR1 in the rpoE10::km mutant indicated that LafR1 is also negatively regulated by RpoE10. The loss of motility and Laf1 in the lafR1::km mutant, complemented by lafR1 expression, showed that LafR1 is a positive regulator of Laf1 and motility in A. brasilense In addition, upregulation of laf1::lacZ and lafR1::lacZ fusions by RpoE10, and downregulation of the laf1::lacZ fusion by LafR1 suggests that RpoE10 negatively regulates swimming motility and the expression of LafR1 and Laf1. However, LafR1 positively regulates the swimming motility and Laf1 expression.Importance: Among extra-cytoplasmic function (ECF) σ factors, ECF41-type σ factors are unique due to the presence of a large C-terminal extension in place of a cognate anti- σ factor, which regulates their activity. Despite wide distribution and abundance in bacterial genomes, their physiological or behavioural roles are not known. We show here an indirect negative role of an ECF41-type of σ factor in the expression of lateral flagellar genes and motility in A.brasilense This study suggests that the motility of A. brasilense might be controlled by a regulatory cascade involving RpoE10, an unknown repressor, LafR1 and lateral flagellar genes including Laf1.

Supernumerary B Chromosomes and Plant Genome Changes: A Snapshot of Wild Populations of Aegilops speltoides Tausch (Poaceae, Triticeae).

In various eukaryotes, supernumerary B chromosomes (Bs) are an optional genomic component that affect their integrity and functioning. In the present study, the impact of Bs on the current changes in the genome of goatgrass, Aegilops speltoides, was addressed. Individual plants from contrasting populations with and without Bs were explored using fluorescence in situ hybridization. In parallel, abundances of the Ty1-copia, Ty3-gypsy, and LINE retrotransposons (TEs), and the species-specific Spelt1 tandem repeat (TR) in vegetative and generative spike tissues were estimated by real-time quantitative PCR. The results revealed: (i) ectopic associations between Bs and the regular A chromosomes, and (ii) cell-specific rearrangements of Bs in both mitosis and microgametogenesis. Further, the copy numbers of TEs and TR varied significantly between (iii) genotypes and (iv) different spike tissues in the same plant(s). Finally, (v) in plants with and without Bs from different populations, genomic abundances and/or copy number dynamics of TEs and TR were similar. These findings indicate that fluctuations in TE and TR copy numbers are associated with DNA damage and repair processes during cell proliferation and differentiation, and ectopic recombination is one of the mechanisms by which Bs play a role in genome changes.

Iflavirus Covert Infection Increases Susceptibility to Nucleopolyhedrovirus Disease in Spodoptera exigua.

Naturally occurring covert infections in lepidopteran populations can involve multiple viruses with potentially different transmission strategies. In this study, we characterized covert infection by two RNA viruses, Spodoptera exigua iflavirus 1 (SeIV-1) and Spodoptera exigua iflavirus 2 (SeIV-2) (family Iflaviridae) that naturally infect populations of Spodoptera exigua, and examined their influence on susceptibility to patent disease by the nucleopolyhedrovirus Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) (family Baculoviridae). The abundance of SeIV-1 genomes increased up to ten-thousand-fold across insect developmental stages after surface contamination of host eggs with a mixture of SeIV-1 and SeIV-2 particles, whereas the abundance of SeIV-2 remained constant across all developmental stages. Low levels of SeIV-2 infection were detected in all groups of insects, including those that hatched from surface-decontaminated egg masses. SeIV-1 infection resulted in reduced larval weight gain, and an unbalanced sex ratio, whereas larval developmental time, pupal weight, and adult emergence and fecundity were not significantly affected in infected adults. The inoculation of S. exigua egg masses with iflavirus, followed by a subsequent infection with SeMNPV, resulted in an additive effect on larval mortality. The 50% lethal concentration (LC50) of SeMNPV was reduced nearly 4-fold and the mean time to death was faster by 12 h in iflavirus-treated insects. These results suggest that inapparent iflavirus infections may be able to modulate the host response to a new pathogen, a finding that has particular relevance to the use of SeMNPV as the basis for biological pest control products.

Functional Significance of Satellite DNAs: Insights From Drosophila.

Since their discovery more than 60 years ago, satellite repeats are still one of the most enigmatic parts of eukaryotic genomes. Being non-coding DNA, satellites were earlier considered to be non-functional “junk,” but recently this concept has been extensively revised. Satellite DNA contributes to the essential processes of formation of crucial chromosome structures, heterochromatin establishment, dosage compensation, reproductive isolation, genome stability and development. Genomic abundance of satellites is under stabilizing selection owing of their role in the maintenance of vital regions of the genome – centromeres, pericentromeric regions, and telomeres. Many satellites are transcribed with the generation of long or small non-coding RNAs. Misregulation of their expression is found to lead to various defects in the maintenance of genomic architecture, chromosome segregation and gametogenesis. This review summarizes our current knowledge concerning satellite functions, the mechanisms of regulation and evolution of satellites, focusing on recent findings in Drosophila. We discuss here experimental and bioinformatics data obtained in Drosophila in recent years, suggesting relevance of our analysis to a wide range of eukaryotic organisms.

N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA

N6-Methyldeoxyadenosine (6mA) has recently been shown to exist and play regulatory roles in eukaryotic genomic DNA (gDNA). However, the biological functions of 6mA in mammals have yet to be adequately explored, largely due to its low abundance in most mammalian genomes. Here, we report that mammalian mitochondrial DNA (mtDNA) is enriched for 6mA. The level of 6mA in HepG2 mtDNA is at least 1,300-fold higher than that in gDNA under normal growth conditions, corresponding to approximately four 6mA modifications on each mtDNA molecule. METTL4, a putative mammalian methyltransferase, can mediate mtDNA 6mA methylation, which contributes to attenuated mtDNA transcription and a reduced mtDNA copy number. Mechanistically, the presence of 6mA could repress DNA binding and bending by mitochondrial transcription factor (TFAM). Under hypoxia, the 6mA level in mtDNA could be further elevated, suggesting regulatory roles for 6mA in mitochondrial stress response. Our study reveals DNA 6mA as a regulatory mark in mammalian mtDNA.

Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa.

Background and AimsDespite their abundant odd-ploidy (2n = 5x = 35), dogroses (Rosa sect. Caninae) are capable of sexual reproduction due to their unique meiosis. During canina meiosis, two sets of chromosomes form bivalents and are transmitted by male and female gametes, whereas the remaining chromosomes form univalents and are exclusively transmitted by the egg cells. Thus, the evolution of chromosomes is expected to be driven by their behaviour during meiosis.MethodsTo gain insight into differential chromosome evolution, fluorescence in situ hybridization was conducted for mitotic and meiotic chromosomes in four dogroses (two subsections) using satellite and ribosomal DNA probes. By exploiting high-throughput sequencing data, we determined the abundance and diversity of the satellite repeats in the genus Rosa by analysing 20 pentaploid, tetraploid and diploid species in total.Key ResultsA pericentromeric satellite repeat, CANR4, was found in all members of the genus Rosa, including the basal subgenera Hulthemia and Hesperhodos. The satellite was distributed across multiple chromosomes (5–20 sites per mitotic cell), and its genomic abundance was higher in pentaploid dogroses (2.3 %) than in non-dogrose species (1.3 %). In dogrose meiosis, univalent chromosomes were markedly enriched in CANR4 repeats based on both the number and the intensity of the signals compared to bivalent-forming chromosomes. Single-nucleotide polymorphisms and cluster analysis revealed high intragenomic homogeneity of the satellite in dogrose genomes.ConclusionsThe CANR4 satellite arose early in the evolution of the genus Rosa. Its high content and extraordinary homogeneity in dogrose genomes is explained by its recent amplification in non-recombining chromosomes. We hypothesize that satellite DNA expansion may contribute to the divergence of univalent chromosomes in Rosa species with non-symmetrical meiosis.

Deoxyinosine and 7-Deaza-2-Deoxyguanosine as Carriers of Genetic Information in the DNA of Campylobacter Viruses.

Several reports have demonstrated that Campylobacter bacteriophage DNA is refractory to manipulation, suggesting that these phages encode modified DNA. The characterized Campylobacter jejuni phages fall into two phylogenetic groups within the Myoviridae: the genera Firehammervirus and Fletchervirus Analysis of genomic nucleosides from several of these phages by high-pressure liquid chromatography-mass spectrometry confirmed that 100% of the 2'-deoxyguanosine (dG) residues are replaced by modified bases. Fletcherviruses replace dG with 2'-deoxyinosine, while the firehammerviruses replace dG with 2'-deoxy-7-amido-7-deazaguanosine (dADG), noncanonical nucleotides previously described, but a 100% base substitution has never been observed to have been made in a virus. We analyzed the genome sequences of all available phages representing both groups to elucidate the biosynthetic pathway of these noncanonical bases. Putative ADG biosynthetic genes are encoded by the Firehammervirus phages and functionally complement mutants in the Escherichia coli queuosine pathway, of which ADG is an intermediate. To investigate the mechanism of DNA modification, we isolated nucleotide pools and identified dITP after phage infection, suggesting that this modification is made before nucleotides are incorporated into the phage genome. However, we were unable to observe any form of dADG phosphate, implying a novel mechanism of ADG incorporation into an existing DNA strand. Our results imply that Fletchervirus and Firehammervirus phages have evolved distinct mechanisms to express dG-free DNA.IMPORTANCE Bacteriophages are in a constant evolutionary struggle to overcome their microbial hosts' defenses and must adapt in unconventional ways to remain viable as infectious agents. One mode of adaptation is modifying the viral genome to contain noncanonical nucleotides. Genome modification in phages is becoming more commonly reported as analytical techniques improve, but guanosine modifications have been underreported. To date, two genomic guanosine modifications have been observed in phage genomes, and both are low in genomic abundance. The significance of our research is in the identification of two novel DNA modification systems in Campylobacter-infecting phages, which replace all guanosine bases in the genome in a genus-specific manner.

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

Single nucleotide polymorphisms (SNPs) have been proved to be powerful markers in genetic analysis due to their high abundance and polymorphism in plant genomes. The recently developed high-resolution melting (HRM) analysis method provides a novel, quick, and close-tube PCR approach to analyze SNP variations. In present study, 101 HRM-based SNP markers from 20 soybean chromosomes were developed for genotyping vegetable soybean cultivar ‘Zhexian No.9’ with ‘Williams 82’ as reference. 33.7% of these markers were polymorphic between ‘Zhexian No.9’ and ‘Williams 82’. Polymorphic markers were found on 85% (17 of 20) of the soybean chromosomes when comparing ‘Zhexian No.9’ and ‘Williams 82’. Finally, an array of 101 in-sequence nucleotide letters was generated as the first precise SNP fingerprint of ‘Zhexian No.9’. The described marker-developing methodology could be used in other crops with known genomic information.

Interspecific hybridisation and LTR-retrotransposon mobilisation-related structural variation in plants: A case study

The dynamics of long-terminal-repeat retrotransposons in two poplar species (Populus deltoides and P. nigra) and in an interspecific hybrid, recently synthesized, were investigated by analyzing the genomic abundance and transcription levels of a collection of 828 full-length retroelements identified in the genome sequence of P. trichocarpa, all occurring also in the genomes of P. deltoides and P. nigra. Overall, genomic abundance and transcription levels of many retrotransposons in the hybrid resulted higher or lower than expected by calculating the mean of the parental values. A bioinformatics procedure was established to ascertain the occurrence of the same retrotransposon loci in the three genotypes. The results indicated that retrotransposon abundance variations between the hybrid and the mean value of the parents were due to i) co-segregation of retrotransposon high- or low-abundant haplotypes; ii) new retroelement insertions; iii) retrotransposon loss. Concerning retrotransposon expression, this was generally low, with only 14/828 elements over- or under-expressed in the hybrid than expected by calculating the mean of the parents. It is concluded that interspecific hybridisation between the two poplar species determine quantitative variation and differential expression of some retrotransposons, with possible consequences for the genetic differentiation of the hybrid.

Analysis of Paramyxovirus Transcription and Replication by High-Throughput Sequencing.

We have developed a high-throughput sequencing (HTS) workflow for investigating paramyxovirus transcription and replication. We show that sequencing of oligo(dT)-selected polyadenylated mRNAs, without considering the orientation of the RNAs from which they had been generated, cannot accurately be used to analyze the abundance of viral mRNAs because genomic RNA copurifies with the viral mRNAs. The best method is directional sequencing of infected cell RNA that has physically been depleted of ribosomal and mitochondrial RNA followed by bioinformatic steps to differentiate data originating from genomes from viral mRNAs and antigenomes. This approach has the advantage that the abundance of viral mRNA (and antigenomes) and genomes can be analyzed and quantified from the same data. We investigated the kinetics of viral transcription and replication during infection of A549 cells with parainfluenza virus type 2 (PIV2), PIV3, PIV5, or mumps virus and determined the abundances of individual viral mRNAs and readthrough mRNAs. We found that the mRNA abundance gradients differed significantly between all four viruses but that for each virus the pattern remained relatively stable throughout infection. We suggest that rapid degradation of non-poly(A) mRNAs may be primarily responsible for the shape of the mRNA abundance gradient in parainfluenza virus 3, whereas a combination of this factor and disengagement of RNA polymerase at intergenic sequences, particularly those at the NP:P and P:M gene boundaries, may be responsible in the other viruses.IMPORTANCE High-throughput sequencing (HTS) of virus-infected cells can be used to study in great detail the patterns of virus transcription and replication. For paramyxoviruses, and by analogy for all other negative-strand RNA viruses, we show that directional sequencing must be used to distinguish between genomic RNA and mRNA/antigenomic RNA because significant amounts of genomic RNA copurify with poly(A)-selected mRNA. We found that the best method is directional sequencing of total cell RNA, after the physical removal of rRNA (and mitochondrial RNA), because quantitative information on the abundance of both genomic RNA and mRNA/antigenomes can be simultaneously derived. Using this approach, we revealed new details of the kinetics of virus transcription and replication for parainfluenza virus (PIV) type 2, PIV3, PIV5, and mumps virus, as well as on the relative abundance of the individual viral mRNAs.

Identification of diverse arthropod associated viruses in native Australian fleas

Fleas are important vectors of zoonotic disease. However, little is known about the natural diversity and abundance of flea viruses, particularly in the absence of disease associations, nor the evolutionary relationships among those viruses found in different parasitic vector species. Herein, we present the first virome scale study of fleas, based on the meta-transcriptomic analysis of 52 fleas collected along the eastern coast of Australia. Our analysis revealed 18 novel RNA viruses belonging to nine viral families with diverse genome organizations, although the majority (72%) possessed single-stranded positive-sense genomes. Notably, a number of the viruses identified belonged to the same phylogenetic groups as those observed in ticks sampled at the same locations, although none were likely associated with mammalian infection. Overall, we identified high levels of genomic diversity and abundance of viruses in the flea species studied, and established that fleas harbor viruses similar to those seen to other vectors.

Chromosomal and Genomic Dynamics of Satellite DNAs in Characidae (Characiformes, Teleostei) Species.

Satellite DNAs (satDNAs) are tandemly repeated DNA sequences with great abundance in eukaryotic genomes. A single species may carry up to hundreds of satDNA families, which is collectively called as "satellitome," each showing its own dynamics and evolution rates. In this context, all live species contain a satDNA library that may be partially or totally shared with other related species/populations. In the late few years, next-generation sequencing (NGS) and novel bioinformatic tools facilitated the massive characterization of these sequences at low costs, and consequently, comparing satDNAs between species. In this study, we characterized two novel satDNAs (MsaSat03-80 and MsaSat04-142) in three characid fish (Astyanax paranae and Astyanax fasciatus and two populations of Moenkhausia sanctaefilomenae) and mapped their chromosomal location to unveil the evolutionary dynamics of satDNA repeats in those species. Our results evidenced that MsaSat03 is present in the genomes of all analyzed species, but is clustered only in the chromosomes of M. sanctaefilomenae, exhibiting a conserved number and location of sites. Conversely, MsaSat04 sequences is restricted to M. sanctaefilomenae and shows a differential distribution between the two analyzed populations. Altogether, our analyses point to a complex history of satDNA families in characid fish and the utility of NGS data for comparative satDNA analysis.

In silico mining and FISH mapping of a chromosome-specific satellite DNA in Capsicum annuum L.

A large proportion of eukaryote nuclear genomes is composed of repetitive DNA. Tracing the dynamics of repetitive elements in the genomes of related taxa can reveal important information about their phylogenic relationships as well as traits that have become distinct to a lineage. Study the genomic abundance and chromosomal location of repetitive DNA in Capsicum annuum L. to understand the repeat dynamics. We quantified repeated DNA content in the C. annuum genome using the RepeatExplorer pipeline. About 42% of the C. annuum genome dataset comprised repetitive elements. Of these, 0.011, 0.98, 3.09, and 0.024% represented high and low confidence satellite repeats, putative long-terminal repeats (LTRs), and rDNA sequences, respectively. One novel high confidence 167-bp satellite repeat with a genomic proportion of 0.011%, Ca167TR, was identified. Furthermore, FISH with Ca167TR on metaphase chromosomes of C. annuum revealed signals in the subtelomeric regions of the short and long arms of chromosome 3 and 4, respectively. Further understanding of the origin and associated functions of Ca167TR and other repeats in Capsicum will give us insights into the genomic relationships and functions of the genome.

An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE)

BackgroundImmune checkpoint inhibitors (ICIs) demonstrate unprecedented efficacy in multiple malignancies; however, the mechanisms of sensitivity and resistance are poorly understood and predictive biomarkers are scarce. INSPIRE is a phase 2 basket study to evaluate the genomic and immune landscapes of peripheral blood and tumors following pembrolizumab treatment.MethodsPatients with incurable, locally advanced or metastatic solid tumors that have progressed on standard therapy, or for whom no standard therapy exists or standard therapy was not deemed appropriate, received 200 mg pembrolizumab intravenously every three weeks. Blood and tissue samples were collected at baseline, during treatment, and at progression. One core biopsy was used for immunohistochemistry and the remaining cores were pooled and divided for genomic and immune analyses. Univariable analysis of clinical, genomic, and immunophenotyping parameters was conducted to evaluate associations with treatment response in this exploratory analysis.ResultsEighty patients were enrolled from March 21, 2016 to June 1, 2017, and 129 tumor and 382 blood samples were collected. Immune biomarkers were significantly different between the blood and tissue. T cell PD-1 was blocked (≥98%) in the blood of all patients by the third week of treatment. In the tumor, 5/11 (45%) and 11/14 (79%) patients had T cell surface PD-1 occupance at weeks six and nine, respectively. The proportion of genome copy number alterations and abundance of intratumoral 4-1BB+ PD-1+ CD8 T cells at baseline (P < 0.05), and fold-expansion of intratumoral CD8 T cells from baseline to cycle 2–3 (P < 0.05) were associated with treatment response.ConclusionThis study provides technical feasibility data for correlative studies. Tissue biopsies provide distinct data from the blood and may predict response to pembrolizumab.

The long isoform of ZAP widely restricts Paramyxoviruses

Paramyxoviruses (PVs) are negative-sense RNA viruses that are important in human and animal health, and can cause severe zoonotic diseases. We screened a wide range of animal and human PV matrix proteins for host interactions, and found that the long (L) isoform of the host protein ZAP (zinc-finger antiviral protein) interacted with all the tested viral matrixes. ZAP-L is constitutively expressed, has a prenlyation motif for membrane-localization, and primarily mediates antiviral activity by binding and degrading viral RNAs through the exosome complex. However, ZAP restriction of PVs has not been demonstrated in the literature. We found that knockdown of ZAP-L results in increased replication of a panel of five human and animal PVs. Overexpression of ZAP-L (but not ZAP-short) restricts replication of PVs in a reciprocal pattern – with the notable exception of Sendai virus (SeV) – and as with other viruses, mutating the prenylation motif of ZAP-L abolishes restriction. RT-qPCR of PV RNAs and pulled-down RNAs does not indicate specific targeting of a viral transcript by ZAP-L, although overall genome abundance is reduced. Finally, immunoprecipitation of ZAP shows an additional RNA-independent interaction between ZAP-L and SeV-nucleocapsid not found with HPIV3-nucleocapsid, a closely-related PV. Thus, we have observed that ZAP-L interacts with the matrix of, and restricts replication of, a wide range of paramyxoviruses. A PV that is not restricted (SeV), has an additional interaction with ZAP via its nucleocapsid protein that may ameliorate ZAP restriction. Investigating ZAP-related restriction differences between closely-related PVs may shed light on anti-viral mechanisms of ZAP.

Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.

To address the question of how microbial diversity and function in the oral cavities of children relates to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. Caries phenotypes contained statistically significant enrichments in specific genome abundances and distinct community composition profiles, including strain-level changes. Metabolic pathways that are statistically associated with caries include several sugar-associated phosphotransferase systems, antimicrobial resistance, and metal transport. Numerous closely related previously uncharacterized microbes had substantial variation in central metabolism, including the loss of biosynthetic pathways resulting in auxotrophy, changing the ecological role. We also describe the first complete Gracilibacteria genomes from the human microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.IMPORTANCE Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing, we constructed a genome encyclopedia describing the core supragingival plaque microbiome. This unveiled several new previously uncharacterized but ubiquitous microbial lineages in the oral microbiome. Caries is a microbial community metabolic disorder that cannot be described by a single etiology, and our results provide the information needed for next-generation diagnostic tools and therapeutics for caries.

Phylogenetic signal of genomic repeat abundances can be distorted by random homoplasy: a case study from hominid primates

Phylogenetic signal of genomic repeat abundances can be distorted by random homoplasy: a case study from hominid primates