Predictability and parallelism in the contemporary evolution of hybrid genomes

Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between two species pairs of swordtail fish: Xiphophorus birchmanni × X. cortezi and X. birchmanni × X. malinche. We find surprisingly high levels of repeatability in local ancestry across the two types of hybrid populations. This repeatability is attributable in part to the fact that the recombination landscape and locations of functionally important elements play a major role in driving variation in local ancestry in both types of hybrid populations. Beyond these broad scale patterns, we identify dozens of regions of the genome where minor parent ancestry is unusually low or high across species pairs. Analysis of these regions points to shared sites under selection across species pairs, and in some cases, shared mechanisms of selection. We show that one such region is a previously unknown hybrid incompatibility that is shared across X. birchmanni × X. cortezi and X. birchmanni × X. malinche hybrid populations.

Quadruple Recombination Events Discovered in Hepatitis E Virus

Hepatitis E virus (HEV) can infect humans, pigs, and many other animals, but the recombination of HEV has rarely been reported. In the present study, phylogenetic and recombination analyses were performed on 557 complete HEV genomes in GenBank. A potentially significant quadruple recombination event was identified by recombination detection analysis. The recombinant progeny virus HEV_32_Manchester_301214 was produced by recombination between the major parent HEPAC-44 and the minor parent HE-JA15-1335, thereby reflecting inter-genotype recombination. HEV_32_Manchester_301214 and HEPAC-44 belong to genotype 3, while HE-JA15-1335 belongs to genotype 1, and these three strains have all been separated from humans. Three breakpoints of the four recombination events occurred in the ORF2 region, while another occurred in the ORF1 region. This quadruple recombination event was confirmed by phylogenetic analysis. The genotype, host and the recombination regions of the three strains were analyzed. These results of the analyses provide valuable suggestions for future research on HEV diversity.

Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China

Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae. Typical viral symptoms of PeVYV including interveinal yellowing of leaves and upward leaf curling were observed in pod pepper plants (Capsicum frutescens) growing in Wenshan city, Yunnan province, China. The complete genome sequence of a virus from a sample of these plants was determined by next-generation sequencing and RT-PCR. Pod pepper vein yellows virus (PoPeVYV) (MT188667) has a genome of 6015 nucleotides, and the characteristic genome organization of a member of the genus Polerovirus. In the 5′ half of its genome (encoding P0 to P4), PoPeVYV is most similar (93.1% nt identity) to PeVYV-3 (Pepper vein yellows virus 3) (KP326573) but diverges greatly in the 3′-part encoding P5, where it is most similar (91.7% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event affecting nucleotide positions 4126 to 5192 nt, with PeVYV-3 as the major parent but with the region 4126–5192 nt derived from TVDV as the minor parent. A full-length clone of PoPeVYV was constructed and shown to be infectious in C. frutescens by RT-PCR and the presence of icosahedral viral particles.

Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China

Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae. Typical viral symptoms of PeVYV including interveinal yellowing of leaves and upward leaf curling were observed in pod pepper plants (Capsicum frutescens) growing in Wenshan city, Yunnan province, China. The complete genome sequence of a virus from a sample of these plants was determined by next-generation sequencing and RT-PCR. Pod pepper vein yellows virus (PoPeVYV) (MT188667) has a genome of 6015 nucleotides, and the characteristic genome organization of a member of the genus Polerovirus. In the 5’ half of its genome (encoding P0 to P4), PoPeVYV is most similar (93.1% nt identity) to PeVYV-3 (Pepper vein yellows virus 3) (KP326573) but diverges greatly in the 3’-part encoding P5, where it is most similar (91.7% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event affecting nucleotide positions 4126 to 5192 nt, with PeVYV-3 as the major parent but with the region 4126-5192 nt derived from TVDV as the minor parent. A full-length clone of PoPeVYV was constructed and shown to be infectious in C. frutescens by RT-PCR and the presence of icosahedral viral particles.

In silico Prediction and Designing of Potential siRNAs to be Used as Antivirals Against SARS-CoV-2

Background:: The unusual pneumonia outbreak that originated in the city of Wuhan, China in December 2019 was found to be caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19. Methods:: In this work, we have performed an in silico design and prediction of potential siRNAs based on genetic diversity and recombination patterns, targeting various genes of SARS-CoV-2 for antiviral therapeutics. We performed extensive sequence analysis to analyze the genetic diversity and phylogenetic relationships, and to identify the possible source of virus reservoirs and recombination patterns, and the evolution of the virus as well as we designed the siRNAs which can be used as antivirals against SARS-CoV-2. Results:: The sequence analysis and phylogenetic relationships indicated high sequence identity and closed clusters with many types of coronavirus. In our analysis, the full-genome of SARS-CoV-2 showed the highest sequence (nucleotide) identity with SARS-bat-ZC45 (87.7%). The overall sequence identity ranged from 74.3% to 87.7% with selected SARS viruses. The recombination analysis indicated the bat SARS virus is a potential recombinant and serves as a major and minor parent. We have predicted 442 siRNAs and finally selected only 19 functional, and potential siRNAs. Conclusions:: The siRNAs were predicted and selected based on their greater potency and specificity. The predicted siRNAs need to be validated experimentally for their effective binding and antiviral activity.

Legal Peculiarities of Child Custody of Minor Parents with an Incomplete Parental Status

Despite the existence of an article in modern Russian legislation on the legal status of minor parents, many legal issues related to the implementation and protection of the rights, duties, interests of a minor parent and his child remained outside family legal regulation, which exacerbates the already difficult problem of legal protection of early parenthood. Moreover, the provisions of Article 62 of the Family Code of the Russian Federation are very inharmoniously combined with the rules of guardianship of minors. The aim of the work is to analyze the legislation on the legal status of minor parents and guardians, to identify the legal characteristics of the care of a child of minor parents. The author concludes that the features of the care of a child of minor parents, in addition to the age of one or both parents, in the case of the appointment of a guardian include: a combination of parenthood and guardianship; unequal opportunities for the care of a child by a minor parent who is not able to independently provide care, and by the legal representative of the child of the minor parent; special (additional) grounds for terminating guardianship of a child of minor parents; the need for the guardian to live together not only with the child in care, but also with his parent. The norms of paragraph 2 of article 62 of the Family Code of the Russian Federation and paragraph 2 of article 29 of the Federal law «On Guardianship and Custodianship» should be adjusted. It is proposed to introduce special rules for the selection of the guardian of a child of a minor parent, which would properly ensure the right of the minor parent to live together with the child.

Naturally occurring recombinant isolate of Pea seed-borne mosaic virus – Short Communication

Whole genome sequences of three Czech Pea seed-borne mosaic virus isolates belonging to P1 pathotype and causing different symptom intensity were obtained. Using RDP4 analysis the natural recombinant isolate PSB204CZ bearing two breakpoints in nucleotide positions 4053 and 6080 was identified. The isolate was composed of fragment 2028 nt in length partially covering CI and 6K2 regions of the minor parent (PSB262CZ) incorporated into the major parent (PSB194CZ). The results suggest that the observed recombination in CI-6K2 region is responsible for severity of developed symptoms. This observation detected for the first time natural recombination within PSbMV isolates of an important pathogen of leguminous plants.

Treating the Infant of a Minor

TREATING A SICK NEWBORN IS challenging under any circumstances, but treating the infant of a minor parent can be doubly so because of the uncertain capacity of an immature parent to understand the condition and necessary care of the child. This situation could lead to potential challenges as to the validity of the minor’s consent and a possible claim in a lawsuit. In addition, the infant’s grandparents and parents may have differing opinions regarding care, leading to conflict between the decision makers. Therefore, having a working knowledge of your state’s laws and your facility’s policies regarding the authority or right of a minor to consent to treatment of the minor’s child is important when obtaining consent and a valuable tool in your arsenal against lawsuits.

A review of the genera comprising species of the genus Eurynogaster sensu Hardy & Kohn, 1964 in Hawai'i (Diptera: Dolichopodidae)

The generic limits are redefined for the endemic Hawaiian dolichopodid genera Eurynogaster Van Duzee, Sweziella Van Duzee, and Uropachys Parent, with the latter two resurrected from synonymy with Eurynogaster. Additionally, four new endemic Hawaiian genera are described: Arciellia, gen. n., Adachia, gen. n., Elmoia, gen. n., and Major, gen. n., to accommodate species previously placed in Eurynogaster. The related genus Sigmatineurum is redefined. Based on re-examination of male genitalic and other diagnostic characters and study of type material, a number of species previously placed in Eurynogaster are transferred to the other genera producing the following new combinations: Sweziella aeruginosa (Hardy & Kohn), comb. n., S. conspicua (Hardy & Kohn), comb. n., S. emarginata (Hardy & Kohn), comb. n., S. gracilipennata (Hardy & Kohn), comb. n.,S. pictilipenna (Tenorio), comb. n., S. tergoprolixa (Hardy & Kohn), comb. n., S. virida (Van Duzee), comb. n., Uropachys clavastylus (Hardy & Kohn), comb. n., U. crassicercus (Hardy & Kohn), comb. n., U. flavicrurus (Hardy & Kohn), comb. n., U. fusticercus (Hardy & Kohn), comb. n., U. palustricola (Hardy & Kohn), comb. n., U. pulvereus (Hardy & Kohn), comb. n., Arciellia dolichostoma (Hardy & Kohn), comb. n., A. flaviventer (Hardy & Kohn), comb. n., A. xanthopleura (Hardy & Kohn), comb. n., Adachia apicenigra (Van Duzee), comb. n., A. hispida (Hardy & Kohn), comb. n., A. nigripedis (Hardy & Kohn), comb. n., A. nudata (Hardy & Kohn), comb. n., A. williamsi (Hardy & Kohn), comb. n., Elmoia bullata (Hardy & Kohn), comb. n., E. exartema (Hardy & Kohn), comb. n., E. hamata (Hardy & Kohn), comb. n., E. lanceolata (Tenorio), comb. n., E. multispinosa (Hardy & Kohn), comb. n., E. nigrohalterata (Parent), comb. n., E. saxatilis (Grimshaw), comb. n., E. viridifacies (Parent), comb. n., and Major minor (Parent), comb. n. E urynogaster parenti Hardy & Kohn is synonymized with Pachyurus hawaiensis Parent, syn. n., which is removed from secondary homonymy with Eurynogaster hawaiiensis (Grimshaw) and returned to Uropachys, rev. stat. A key to the genus Eurynogaster and allies in the Hawaiian Islands is included.