scholarly journals Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples

Viruses ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 749 ◽  
Author(s):  
Melanie Hiltbrunner ◽  
Gerald Heckel
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Common Vole ◽  
Natural Host ◽  
Sequence Information ◽  
Coding Region ◽  
Sequence Capture ◽  
Genome Wide ◽  
The Impact

Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.

Bacterial origin of thymidylate and folate metabolism in Asgard Archaea

2021 ◽  
Author(s):  
Jonathan Filee ◽  
Hubert J. Becker ◽  
Lucille Mellottee ◽  
Zhihui LI ◽  
Jean-Christophe Lambry ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Phylogenetic Trees ◽  
De Novo ◽  
Horizontal Transmission ◽  
Folate Metabolism ◽  
Ecological Niches ◽  
Sequence Information ◽  
Amino Acid Utilization ◽  
Genome Wide

Little is known about the evolution and biosynthetic function of DNA precursor and the folate metabolism in the Asgard group of archaea. As Asgard occupy a key position in the archaeal and eukaryotic phylogenetic trees, we have exploited very recently emerged genome and metagenome sequence information to investigate these central metabolic pathways. Our genome-wide analyses revealed that the recently cultured Asgard archaeon Candidatus Prometheoarchaeum syntrophicum strain MK-D1 (Psyn) contains a complete folate-dependent network for the biosynthesis of DNA/RNA precursors, amino acids and syntrophic amino acid utilization. Altogether our experimental and computational data suggest that phylogenetic incongruences of functional folate-dependent enzymes from Asgard archaea reflect their persistent horizontal transmission from various bacterial groups, which has rewired the key metabolic reactions in an important and recently identified archaeal phylogenetic group. We also experimentally validated the functionality of the lateral gene transfer of Psyn thymidylate synthase ThyX. This enzyme uses bacterial-like folates efficiently and is inhibited by mycobacterial ThyX inhibitors. Our data raise the possibility that the thymidylate metabolism, required for de novo DNA synthesis, originated in bacteria and has been independently transferred to archaea and eukaryotes. In conclusion, our study has revealed that recent prevalent lateral gene transfer has markedly shaped the evolution of Asgard archaea by allowing them to adapt to specific ecological niches.

scholarly journals Contribution of retrotransposition to developmental disorders

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Eugene J. Gardner ◽  
Elena Prigmore ◽  
Giuseppe Gallone ◽  
Petr Danecek ◽  
Kaitlin E. Samocha ◽  
...  
Keyword(s):  
Developmental Disorders ◽  
De Novo ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Protein Coding ◽  
Genome Wide ◽  
De Novo Gene ◽  
The Impact ◽  
Transcribed Sequences

Abstract Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient’s symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

scholarly journals The Needle in the Haystack—Searching for Genetic and Epigenetic Differences in Monozygotic Twins Discordant for Tetralogy of Fallot

2020 ◽  
Vol 7 (4) ◽  
pp. 55
Author(s):  
Marcel Grunert ◽  
Sandra Appelt ◽  
Paul Grossfeld ◽  
Silke R. Sperling
Keyword(s):  
Tetralogy Of Fallot ◽  
High Throughput Sequencing ◽  
Heart Defects ◽  
Monozygotic Twins ◽  
Disease Status ◽  
Epigenetic Alterations ◽  
Structural Genomic ◽  
Genome Wide ◽  
Underlying Causes ◽  
The Impact

Congenital heart defects (CHDs) are the most common birth defect in human with an incidence of almost 1% of all live births. Most cases have a multifactorial origin with both genetics and the environment playing a role in its development and progression. Adding an epigenetic component to this aspect is exemplified by monozygotic twins which share the same genetic background but have a different disease status. As a result, the interplay between the genetic, epigenetic and the environmental conditions might contribute to the etiology and phenotype. To date, the underlying causes of the majority of CHDs remain poorly understood. In this study, we performed genome-wide high-throughput sequencing to examine the genetic, structural genomic and epigenetic differences of two identical twin pairs discordant for Tetralogy of Fallot (TOF), representing the most common cyanotic form of CHDs. Our results show the almost identical genetic and structural genomic identity of the twins. In contrast, several epigenetic alterations could be observed given by DNA methylation changes in regulatory regions of known cardiac-relevant genes. Overall, this study provides first insights into the impact of genetic and especially epigenetic factors underlying monozygotic twins discordant for CHD like TOF.

scholarly journals Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Margie Kinnersley ◽  
Katja Schwartz ◽  
Dong-Dong Yang ◽  
Gavin Sherlock ◽  
Frank Rosenzweig
Keyword(s):  
High Frequency ◽  
High Throughput Sequencing ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Allelic Diversity ◽  
Microbial Evolution ◽  
De Novo Mutations ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
The Impact

Abstract Background Microbial evolution experiments can be used to study the tempo and dynamics of evolutionary change in asexual populations, founded from single clones and growing into large populations with multiple clonal lineages. High-throughput sequencing can be used to catalog de novo mutations as potential targets of selection, determine in which lineages they arise, and track the fates of those lineages. Here, we describe a long-term experimental evolution study to identify targets of selection and to determine when, where, and how often those targets are hit. Results We experimentally evolved replicate Escherichia coli populations that originated from a mutator/nonsense suppressor ancestor under glucose limitation for between 300 and 500 generations. Whole-genome, whole-population sequencing enabled us to catalog 3346 de novo mutations that reached > 1% frequency. We sequenced the genomes of 96 clones from each population when allelic diversity was greatest in order to establish whether mutations were in the same or different lineages and to depict lineage dynamics. Operon-specific mutations that enhance glucose uptake were the first to rise to high frequency, followed by global regulatory mutations. Mutations related to energy conservation, membrane biogenesis, and mitigating the impact of nonsense mutations, both ancestral and derived, arose later. New alleles were confined to relatively few loci, with many instances of identical mutations arising independently in multiple lineages, among and within replicate populations. However, most never exceeded 10% in frequency and were at a lower frequency at the end of the experiment than at their maxima, indicating clonal interference. Many alleles mapped to key structures within the proteins that they mutated, providing insight into their functional consequences. Conclusions Overall, we find that when mutational input is increased by an ancestral defect in DNA repair, the spectrum of high-frequency beneficial mutations in a simple, constant resource-limited environment is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever go to fixation.

scholarly journals Genome-Wide Patterns of Intrahuman Dengue Virus Diversity Reveal Associations with Viral Phylogenetic Clade and Interhost Diversity

2012 ◽  
Vol 86 (16) ◽  
pp. 8546-8558 ◽  
Author(s):  
Poornima Parameswaran ◽  
Patrick Charlebois ◽  
Yolanda Tellez ◽  
Andrea Nunez ◽  
Elizabeth M. Ryan ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Dengue Virus ◽  
Strong Association ◽  
Viral Fitness ◽  
Envelope Gene ◽  
Specific Method ◽  
Coding Region ◽  
Virus Diversity ◽  
Genome Wide ◽  
The Impact

Analogous to observations in RNA viruses such as human immunodeficiency virus, genetic variation associated with intrahost dengue virus (DENV) populations has been postulated to influence viral fitness and disease pathogenesis. Previous attempts to investigate intrahost genetic variation in DENV characterized only a few viral genes or a limited number of full-length genomes. We developed a whole-genome amplification approach coupled with deep sequencing to capture intrahost diversity across the entire coding region of DENV-2. Using this approach, we sequenced DENV-2 genomes from the serum of 22 Nicaraguan individuals with secondary DENV infection and captured ∼75% of the DENV genome in each sample (range, 40 to 98%). We identified and quantified variants using a highly sensitive and specific method and determined that the extent of diversity was considerably lower than previous estimates. Significant differences in intrahost diversity were detected between genes and also between antigenically distinct domains of the Envelope gene. Interestingly, a strong association was discerned between the extent of intrahost diversity in a few genes and viral clade identity. Additionally, the abundance of viral variants within a host, as well as the impact of viral mutations on amino acid encoding and predicted protein function, determined whether intrahost variants were observed at the interhost level in circulating Nicaraguan DENV-2 populations, strongly suggestive of purifying selection across transmission events. Our data illustrate the value of high-coverage genome-wide analysis of intrahost diversity for high-resolution mapping of the relationship between intrahost diversity and clinical, epidemiological, and virological parameters of viral infection.

scholarly journals Genome-Wide Analysis of Estrogen Receptor α DNA Binding and Tethering Mechanisms Identifies Runx1 as a Novel Tethering Factor in Receptor-Mediated Transcriptional Activation

2010 ◽  
Vol 30 (16) ◽  
pp. 3943-3955 ◽  
Author(s):  
Joshua D. Stender ◽  
Kyuri Kim ◽  
Tze Howe Charn ◽  
Barry Komm ◽  
Ken C. N. Chang ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Estrogen Receptor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Estrogen Receptor Alpha ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Motif Analysis ◽  
Phenotypic Properties ◽  
Genome Wide

ABSTRACT Nuclear receptor estrogen receptor alpha (ERα) controls the expression of hundreds of genes responsible for target cell phenotypic properties, but the relative importance of direct versus tethering mechanisms of DNA binding has not been established. In this first report, we examine the genome-wide chromatin localization of an altered-specificity mutant ER with a DNA binding domain deficient in binding to estrogen response element (ERE)-containing DNA (DBDmut ER) versus wild-type ERα. Using high-throughput sequencing of ER chromatin immunoprecipitations (ChIP-Seq) and mRNA transcriptional profiling, we show that direct ERE binding is required for most of (75%) estrogen-dependent gene regulation and 90% of hormone-dependent recruitment of ER to genomic binding sites. De novo motif analysis of the chromatin binding regions in MDA-MB-231 human breast cancer cells defined unique transcription factor profiles responsible for genes regulated through tethering versus direct ERE binding, with Runx motifs enriched in ER-tethered sites. We confirmed a role for Runx1 in mediating ERα genomic recruitment and regulation of tethering genes. Our findings delineate the contributions of direct receptor ERE binding versus binding through response elements for other transcription factors in chromatin localization and ER-dependent gene regulation, paradigms likely to underlie the gene regulatory actions of other nuclear receptors as well.

scholarly journals Genome-wide profiling of heritable and de novo STR variations

2016 ◽  
Author(s):  
Thomas Willems ◽  
Dina Zielinski ◽  
Assaf Gordon ◽  
Melissa Gymrek ◽  
Yaniv Erlich
Keyword(s):  
Tandem Repeats ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Genetic Diseases ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Genome Wide ◽  
A Genome ◽  
Short Tandem

AbstractShort tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, STRs have proven problematic to genotype from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping, haplotyping, and phasing STRs from whole genome sequencing data and report a genome-wide analysis and validation of de novo STR mutations.

scholarly journals Six new reference-quality bat genomes illuminate the molecular basis and evolution of bat adaptations

2019 ◽  
Author(s):  
David Jebb ◽  
Zixia Huang ◽  
Martin Pippel ◽  
Graham M. Hughes ◽  
Ksenia Lavrichenko ◽  
...  
Keyword(s):  
De Novo ◽  
Phenotypic Diversity ◽  
Phylogenetic Analyses ◽  
Mammal Species ◽  
Protein Coding ◽  
Genome Wide ◽  
Long Read ◽  
Reference Quality ◽  
Transposon Activity

AbstractBats account for ~20% of all extant mammal species and are considered exceptional given their extraordinary adaptations, including biosonar, true flight, extreme longevity, and unparalleled immune systems. To understand these adaptations, we generated reference-quality genomes of six species representing the key divergent lineages. We assembled these genomes with a novel pipeline incorporating state-of-the-art long-read and long-range sequencing and assembly techniques. The genomes were annotated using a maximal evidence approach, de novo predictions, protein/mRNA alignments, Iso-seq long read and RNA-seq short read transcripts, and gene projections from our new TOGA pipeline, retrieving virtually all (>99%) mammalian BUSCO genes. Phylogenetic analyses of 12,931 protein coding-genes and 10,857 conserved non-coding elements identified across 48 mammalian genomes helped to resolve bats’ closest extant relatives within Laurasiatheria, supporting a basal position for bats within Scrotifera. Genome-wide screens along the bat ancestral branch revealed (a) selection on hearing-involved genes (e.g LRP2, SERPINB6, TJP2), which suggest that laryngeal echolocation is a shared ancestral trait of bats; (b) selection (e.g INAVA, CXCL13, NPSR1) and loss of immunity related proteins (e.g. LRRC70, IL36G), including pro-inflammatory NF-kB signalling; and (c) expansion of the APOBEC family, associated with restricting viral infection, transposon activity and interferon signalling. We also identified unique integrated viruses, indicating that bats have a history of tolerating viral pathogens, lethal to other mammal species. Non-coding RNA analyses identified variant and novel microRNAs, revealing regulatory relationships that may contribute to phenotypic diversity in bats. Together, our reference-quality genomes, high-quality annotations, genome-wide screens and in-vitro tests revealed previously unknown genomic adaptations in bats that may explain their extraordinary traits.

scholarly journals Altered Nucleoprotein Binding to Influenza Virus RNA Impacts Packaging Efficiency and Replication

2019 ◽  
Author(s):  
Valerie Le Sage ◽  
Jack P. Kanarek ◽  
Eric Nturibi ◽  
Adalena V. Nanni ◽  
Dan J. Snyder ◽  
...  
Keyword(s):  
Influenza A ◽  
High Throughput Sequencing ◽  
Particle Production ◽  
De Novo ◽  
Sequence Similarity ◽  
Independent Manner ◽  
Binding Profile ◽  
Genome Wide ◽  
Packaging Efficiency ◽  
Replication Fitness

AbstractThe genome of Influenza A viruses consists of eight negative-sense RNA segments that are bound by viral nucleoprotein (NP). We recently showed that NP binding is not uniform along the segments but exhibits regions of enrichment as well as depletion. Furthermore, genome-wide NP binding profiles are distinct even in strains with high sequence similarity, such as the two H1N1 strains A/WSN/1933 and A/California/07/2009. Here, we performed interstrain segment swapping experiments with segments of either high or low congruency in NP binding, which suggested that a segment with a similar overall NP binding profile preserved replication fitness of the resulting virus. Further sub-segmental swapping experiments demonstrated that NP binding is affected by changes to the underlying nucleotide sequence, as NP peaks can either become lost or appear de novo at mutated regions. Unexpectedly, these local nucleotide changes in one segment not only affect NP binding in cis, but also impact the genome-wide NP binding profile on other segments in a vRNA sequence-independent manner, suggesting that primary sequence alone is not the sole determinant for NP association to vRNA. Moreover, we observed that sub-segmental mutations that affect NP binding profiles can result in reduced replication fitness, which is caused by defects in vRNA packaging efficiency and an increase in semi-infectious particle production. Taken together, our results indicate that the pattern of NP binding to vRNA is important for efficient virus replication.Author SummaryEach viral RNA (vRNA) segment is bound by the polymerase complex at the 5′ and 3′ ends, while the remainder of the vRNA is coated non-uniformly and non-randomly by nucleoprotein (NP). To explore the constraints of NP binding to vRNA, we used high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) of mutant H1N1 strains with exchanged vRNA sequences and observed that NP binding can be changed based on vRNA sequence. The most striking observation of our study is that nucleotide changes in one segment can have genome-wide effects on the NP binding profile of other segments. We refer to this phenomenon as the ‘butterfly effect’ of influenza packaging. Our results provide an important context in which to consider future studies regarding influenza packaging and assembly.

scholarly journals First Report of Nasturtium as a Natural Host of Cherry leaf roll virus on Amsterdam Island

Plant Disease ◽  
2010 ◽  
Vol 94 (4) ◽  
pp. 477-477 ◽  
Author(s):  
A. Marais ◽  
C. Faure ◽  
T. Candresse ◽  
M. Hullé
Keyword(s):  
Natural Infection ◽  
Leaf Roll ◽  
Plant Viruses ◽  
Natural Host ◽  
Mechanical Transmission ◽  
Sequence Information ◽  
Coding Region ◽  
Rt Pcr ◽  
First Report ◽  
Cherry Leaf Roll Virus

Cherry leaf roll virus (CLRV) is a well-known virus belonging to the genus Nepovirus, but unlike most members of this genus, it is not known to be transmitted by nematodes but only through seeds and pollen. Since its first description in 1955 on Prunus avium L. in England (1), CLRV has been shown to have a worldwide distribution and a wide natural host range. During a survey of plant viruses in the French sub-Antarctic islands, samples from nasturtium plants (Tropaeolum majus), an introduced plant species, showing symptoms of leaf mosaic, deformation, and veinal necrosis were collected on Amsterdam Island. Upon mechanical transmission with sap extracts, necrotic ringspot and oak-leaf symptoms typical of Nepovirus infection were observed on the leaves of inoculated Nicotiana clevelandii and N. tabacum plants. Inoculation of healthy nasturtium plants resulted in mosaic and pin-point necrosis symptoms. Electron microscopy on negatively stained sap extracts revealed the presence of icosahedral virions, 28 to 30 nm in diameter, in the symptomatic Nicotiana leaves. Amplification by reverse transcription (RT)-PCR with a polyvalent test, which identifies viruses belonging to the family Comoviridae (2), yielded the expected 248-bp fragment. Sequencing of the cloned amplicon showed 80% nucleotide and 90% amino acid identity with a part of the RNA dependent RNA polymerase (RdRp) of CLRV (CAE83562). To confirm the presence of CLRV, an approximate 4.6-kbp cDNA fragment was PCR amplified from double-stranded RNAs purifed from infected Nicotiana plants using the sense primer 5′-GTGGGACTGCCATGCACCTACTC-3′ and an oligo-T25 as antisense primer. This PCR product (GenBank Accession No. GU167974) spans the region between the VPg gene and the polyA tail at the 3′ end of the genome and thus provides approximately 2.8 kb of new internal sequence information on RNA1 of CLRV. The presence of CLRV in the initial nasturtium samples was confirmed with a CLRV-specific RT-PCR assay that amplifies the 3′ non-coding region of the CLRV genome (3). Sequence of the amplified fragment showed it to be identical to the corresponding part of the 3′ non-coding region of 4.6-kbp clone obtained from the CLRV isolate mechanically transmitted to the N. tabacum and N. clevelandii plants. Experimental infection of nasturtium by CLRV has been reported (4), but to the best of our knowledge these results represent the first report of natural infection of T. majus by CLRV. Given its seed transmissible character in many hosts, CLRV likely was introduced in infected seeds of T. majus imported to the remote sub-Antarctic Amsterdam Island. References: (1) R. Cropley. Ann. Appl. Biol. 49:524, 1961. (2) V. Maliogka et al. J. Phytopathol. 152:404, 2004. (3) K. Rebenstorf et al. J. Virol. 80:2453, 2006. (4) K. Schmelzer. Phytopathol. Z. 55:317, 1966.

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