Interspecies Recombinants Research Articles

Fitness advantage of inter-species TYLCV recombinants induced by beneficial intra-genomic interactions rather than by specific mutations

Tomato yellow leaf curl virus (TYLCV) and its related viruses are prone to recombination. It was reported that random homologous recombination between 20% diverging TYLCV related species is rarely deleterious and may be associated with a fitness advantage. Indeed, TYLCV-IS76, a recombinant between the 20% divergent TYLCV and tomato yellow leaf curl Sardinia virus (TYLCSV), exhibited a higher fitness than that of parental viruses. As this typical fitness advantage was observed with TYLCV-IS76 representatives of different pedigrees, it was thought that it is induced by beneficial intra-genomic interactions rather than by specific mutations. This hypothesis was further supported with TYLCV-IS141, a TYLCV recombinant with a short TYLCSV inherited fragment of around 141 nts, slightly longer than that of TYLCV-IS76. Indeed, the typical fitness advantage was detected irrespective of the position of the recombination breakpoint (loci 76 or 141) and the sequences of the TYLCV and TYLCSV inherited fragments.

A complex evolutionary relationship between HHV-6A and HHV-6B.

Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6, iciHHV6). We reconstructed the population structure of HHV-6 and we show that HHV-6A genomes diverged less than HHV-6B genomes from the ancestral common HHV-6A/B population. Analysis of ancestry proportions indicated that HHV-6A exogenous viruses and iciHHV-6A derived most of their genomes from distinct ancestral sources. Conversely, exogenous viral and iciHHV-6B populations were similar in terms of ancestry components, with no evident geographic structuring. Most HHV-6B genomes sampled to date derive from viral populations that experienced considerable drift. However, a population of HHV-6 exogenous viruses, currently classified as HHV-6B and sampled in New York state, formed a separate cluster (NY cluster) and harbored a considerable portion of HHV-6A-like ancestry. Recombination detection methods identified these viruses as interspecies recombinants, but phylogenetic reconstruction indicated that the recombination signals are due to shared ancestry. In analogy to iciHHV-6A, NY cluster viruses have high nucleotide diversity and constant population size. We propose that HHV-6A sequences and the NY cluster population diverged from an ancestral HHV-6A-like population. A relatively recent bottleneck of the NY (or a related) population with subsequent expansion originated most HHV-6B genomes currently sampled. Our findings indicate that the distinction between HHV-6A and -6B is not as clear-cut as previously thought. More generally, epidemiological and clinical surveys would benefit from taking HHV-6 genetic diversity into account.

Retraction to: A complex evolutionary relationship between HHV-6A and HHV-6B.

[This retracts the article DOI: 10.1093/ve/vez043.].

Complexity and recombination analysis of novel begomovirus associated with Spinach yellow vein disease in India

Leaves with vein yellowing were observed on Spinach (Spinacia oleracea) in Rajasthan province of India. The plants were severely stunted in growth and exhibited symptoms typical of Begomovirus infection. Here we report a comprehensive study of complexity and recombination of novel begomovirus associated with spinach yellow vein disease. It is probably a perpetuation of Papaya leaf curl virus in absence of its main host and thus raises concern about its spread to other crops. Analysis of samples collected in the survey indicates that SYVD infected plants are associated with a begomoviruses (novel species showed <91% nucleotide sequence similarity) and its associated betasatellites. Interestingly, most of the begomoviruses were found to be inter-species recombinants and the betasatellites possess high nucleotide variability, due to recombination. This suggested the existence of a complex recombination pattern to form “gene pool” of the crop-infecting begomovirus–betasatellites complexes. The Nucleotide diversity (π) and nucleotide substitution rates were determined for the DNA-A of begomoviruses SYVSV is 0.10382 and 2.436×10−3substitutions site−1year−1 respectively. Thus mutation and recombination are driving forces for the emergence and evolution of new begomoviruses. This strengthens the hypothesis for increase of host range of begomovirus and indicates that the high evolutionary rate of the begomoviruses is primarily due to frequent recombination and mutation.

Worldwide circulation of HSV-2\u2009\xd7\u2009HSV-1 recombinant strains

Homo sapiens harbor two distinct, medically significant species of simplexviruses, herpes simplex virus (HSV)-1 and HSV-2, with estimated divergence 6–8 million years ago (MYA). Unexpectedly, we found that circulating HSV-2 strains can contain HSV-1 DNA segments in three distinct genes. Using over 150 genital swabs from North and South America and Africa, we detected recombinants worldwide. Common, widely distributed gene UL39 genotypes are parsimoniously explained by an initial >457 basepair (bp) HSV-1 × HSV-2 crossover followed by back-recombination to HSV-2. Blocks of >244 and >539 bp of HSV-1 DNA within genes UL29 and UL30, respectively, have reached near fixation, with a minority of strains retaining sequences we posit as ancestral HSV-2. Our data add to previous in vitro and animal work, implying that in vivo cellular co-infection with HSV-1 and HSV-2 yields viable interspecies recombinants in the natural human host.

Nucleolar dominance and maternal control of 45S rDNA expression.

Using a system of interspecies hybrids, trihybrids, and recombinants with varying proportions of genomes from three distinct Xenopus species, we provide evidence for de novo epigenetic silencing of paternal 45 S ribosomal ribonucleic acid (rRNA) genes and their species-dependent expression dominance that escapes transcriptional inactivation after homologous recombination. The same pattern of imprinting is maintained in the offspring from mothers being genetic males (ZZ) sex-reversed to females, indicating that maternal control of ribosomal deoxyribonucleic acid (rDNA) expression is not sex-chromosome linked. Nucleolar dominance (nucleolus underdevelopment) in Xenopus hybrids appears to be associated with a major non-Mendelian reduction in the number of 45 S rDNA gene copies rather than a specific pattern of their expression. The loss of rRNA gene copies in F1 hybrids was non-random with respect to the parental species, with the transcriptionally dominant variant preferentially removed from hybrid zygotes. This dramatic disruption in the structure and function of 45 S rDNA impacts transcriptome patterns of small nucleolar RNAs and messenger RNAs, with genes from the ribosome and oxidative stress pathways being among the most affected. Unorthodoxies of rDNA inheritance and expression may be interpreted as hallmarks of genetic conflicts between parental genomes, as well as defensive epigenetic mechanisms employed to restore genome integrity.

POLIO: OBSTACLES TO ERADICATION

Review is devoted to the situation of poliomyelitis in Ukraine and worldwide. For many years, the problem of polio remains relevant. Today circulation of «wild» strains of poliovirus continues in the three endemic countries in Asia and Africa. Thanks to the continuous growth of migration threatens to deliver «wild» polioviruses to the countries, free from virus circulation. It was demonstrated the low level of vaccination coverage of children in Ukraine, that leads to increased segment of the population susceptible to the disease. It was demonstrated the increase in the incidence of vaccine-associated paralytic poliomyelitis mainly in developed countries, due to the strengthening of epidemiological surveillance of poliomyelitis on the one hand, and the increasing number of persons with immunodeficiency states – on the other. It was reproduced the mechanism of viral revertants with the possible return of their entry neurovirulence properties and formation of virus interspecies recombinants. The review shows the main objectives of WHO, to combat polio, which ultimate goal is the complete eradication of the disease.

Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections

Human rhinoviruses (HRVs), in the Enterovirus genus within the family Picornaviridae, are a highly prevalent cause of acute respiratory infection (ARI). Enteroviruses are genetically highly variable, and recombination between serotypes is known to be a major contribution to their diversity. Recently it was reported that recombination events in HRVs cause the diversity of HRV-C. This study analyzed parts of the viral genes spanning the 5′ non- coding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. When analyzing parts of the 5′NCR and VP4/VP2 encoding sequences, we found intra- and interspecies recombinants in field strains of HRV-A and -C. Nineteen cases of recombination events (18.1%) were found among 105 field strains. For HRV-A, there were five cases (4.8%) of intraspecies recombination events and three cases (2.8%) of interspecies recombination events. For HRV-C, there were four cases (3.8%) of intraspecies recombination events and seven cases (6.7%) of interspecies recombination events. Recombination events were significantly more frequently observed in the ARINET samples (18 cases) than in the SLRI samples (1 case; P< 0.0001). The recombination breakpoints were located in nucleotides (nt) 472–554, which comprise stem-loop 5 in the internal ribosomal entry site (IRES), based on the HRV-B 35 sequence (accession no. FJ445187). Our findings regarding genomic recombination in circulating HRV-A and -C strains suggest that recombination might play a role in HRV fitness and could be a possible determinant of disease severity caused by various HRV infections in patients with ARI.

Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location.

The incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses.

Genetic structure and variability of virus populations in cross-protected grapevines superinfected by Grapevine fanleaf virus

Recombination was assessed in a vineyard site in which grapevines cross-protected with mild strains GHu of Grapevine fanleaf virus (GFLV) or Ta of Arabis mosaic virus (ArMV) were superinfected with GFLV field isolates following transmission by the nematode vector Xiphinema index. The genetic structure and variability within RNA2 of isolates from grapevines co-infected with GFLV field isolates and either GFLV-GHu or ArMV-Ta were characterized to identify intra- and interspecies recombinants. Sequence analysis and phylogenetic relationships inferred intraspecies recombination among GFLV field isolates but not between field isolates and GFLV-GHu. SISCAN analysis confirmed a mosaic structure for two GFLV field isolates for which recombination sites were located in the movement protein and coat protein genes. One of the recombinants was found in eight grapevines that were in close spatial proximity within the vineyard site, suggesting its transmission by X. index. No interspecies recombination was detected between GFLV field isolates and ArMV-Ta. Altogether, our findings suggest that mild protective strains GFLV-GHu and ArMV-Ta did not assist the emergence of viable recombinants to detectable level during a 12-year cross-protection trial. To our knowledge, this is the first extensive characterization of the genetic structure and variability of virus isolates in cross-protected plants.

A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression inSaccharomyces cerevisiae

A multispecies-based taxonomic microarray targeting coding sequences of diverged orthologous genes in Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, Saccharomyces bayanus, Saccharomyces kudriavzevii, Naumovia castellii, Lachancea kluyveri and Candida glabrata was designed to allow identification of isolates of these species and their interspecies hybrids. Analysis of isolates of several Saccharomyces species and interspecies hybrids demonstrated the ability of the microarray to differentiate these yeasts on the basis of their specific hybridization patterns. Subsequent analysis of 183 supposed S. cerevisiae isolates of various ecological and geographical backgrounds revealed one misclassified S. bayanus or Saccharomyces uvarum isolate and four aneuploid interspecies hybrids, one between S. cerevisiae and S. bayanus and three between S. cerevisiae and S. kudriavzevii. Furthermore, this microarray design allowed the detection of multiple introgressed S. paradoxus DNA fragments in the genomes of three different S. cerevisiae isolates. These results show the power of multispecies-based microarrays as taxonomic tools for the identification of species and interspecies hybrids, and their ability to provide a more detailed characterization of interspecies hybrids and recombinants.

Identification of interspecies recombination among hepadnaviruses infecting cross‐species hosts

Members of the family Hepadnaviridae are divided into two genera, Orthohepadnavirus (from mammalian) and Avihepadnavirus (from avian). Recombination had been found to occur among human hepatitis B virus (HBV) strains of different genotypes, or between hepadnavirus strains from human and nonhuman primate. To reach a comparatively complete inspection of interspecies recombination events among hepadnavirus strains from various hosts, 837 hepadnavirus complete genome sequences from human and 112 from animals were analyzed by using fragment typing to scan for potential interspecies recombinants. Further bootscanning and phylogenetic analyses of the potential recombinants revealed six genome sequences as interspecies recombinants. Interspecies recombination events were found to occur among HBV strains from human and nonhuman primates, from gibbons of different genera, from chimpanzee and an unknown host, and between two avian hepadnavirus strains from birds of different subfamilies, which was identified for the first time. HBV interspecies recombinants were found to have recombination hot spots similar to that of human HBV intergenotype recombinants, breakpoints frequently locating near gene boundaries. Interspecies recombination found in this study may alter current views on hepadnavirus host specificity.

Relationships between sexual processes and parasitic interactions in the host–pathogen systemAbsidia glauca–Parasitella parasitica

Parasitella parasitica is a facultative parasite of many Mucorales including Absidia glauca. The infection process includes the formation of a plasmatic continuum between host and parasite, which allows the invasion of the host by nuclei of the parasite. This process gives rise to interspecies recombinants. Auxotrophic A. glauca mutants are complemented by the transfer of genes from the parasite to the host. At the molecular level, we could show that plasmid-coded genes are also transferred. The successful formation of infection structures is mating-type dependent. Parasitella parasitica exclusively infects hosts belonging to the complementary mating type. The formation of infection structures is correlated with the ability to synthesise the sex pheromone trisporic acid, which is produced in mixed cultures by compatible combinations between host and parasite. Normally, trisporic acid is formed by a cooperative biosynthesis involving both mating types. Trisporic acid seems to be involved also in mediating the recognition between P. parasitica and A. glauca. To test the hypothesis of direct hormonal correlations between sex and parasitism, we have isolated one of the key enzymes for trisporic acid synthesis, dihydromethyltrisporic acid dehydrogenase, sequenced the N-termini of some proteolytic cleavage products, and have started to isolate the corresponding gene. Key words: mycoparasitism, zygomycetes, trisporic acid, Absidia glauca, Parasitella parasitica, Mucor.

The Subunits of Human Pituitary Thyroid-stimulating Hormone: ISOLATION, PROPERTIES, AND COMPOSITION

Abstract The subunits, α and β, of human thyroid-stimulating hormone (TSH) from the pituitary have been obtained by the same procedures utilized for the preparation of bovine TSH subunits, namely, dissociation in 1 m propionic acid and separation by gel filtration. The amino acid composition of human TSH-α indicates that this subunit is identical or nearly so with the α subunits of human luteinizing hormone and human chorionic gonadotropin. The NH2-terminal residue is valine and it appears that human TSH-α is shortened at its amino end by 7 residues relative to bovine TSH-α; a similar relationship has been shown by others for human LH-α relative to the ovine or bovine subunit. The β subunit of human TSH differs markedly in amino acid composition from those of the two human gonadotropins, particularly with respect to tyrosine, isoleucine, valine, proline, arginine, and lysine. The carbohydrate analyses for the 2 subunits are given. A major difference between human and bovine TSH is the presence of sialic acid in the former, nearly all in the α subunit. Immunological comparisons by double diffusion show that antisera to the intact hormone or its α subunit cross-react with homologous TSH and with the human gonadotropins but that the antiserum against the β subunit is specific for thyroid-stimulating hormone. The human subunits were shown, by gel electrophoresis and bioassay, to form intra- and interspecies recombinants with complementary subunits from other glycoprotein hormones.