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1.
Zootaxa ; 5016(4): 559-570, 2021 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-34810430

RESUMO

After morphological study and comparison with related material, the following synonymy is proposed: Pholeuonopsis Apfelbeck, 1901 (=Blattodromus Reitter, 1904 syn. nov.). Aredescription of the genus Pholeuonopsis Apfelbeck, 1901 is given.


Assuntos
Besouros , Animais , Península Balcânica , Besouros/genética , Recombinação Genética
2.
BMC Bioinformatics ; 22(1): 560, 2021 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-34809571

RESUMO

BACKGROUND: Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis. RESULTS: HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster. HaplotypeTools includes various utility scripts for downstream analysis including crossover detection and phylogenetic placement of haplotypes to other lineages or species. HaplotypeTools was assessed for accuracy against WhatsHap using simulated short and long reads, demonstrating higher accuracy, albeit with reduced haplotype length. HaplotypeTools was also tested on real Illumina data to determine the ancestry of hybrid fungal isolate Batrachochytrium dendrobatidis (Bd) SA-EC3, finding 80% of haplotypes across the genome phylogenetically cluster with parental lineages BdGPL (39%) and BdCAPE (41%), indicating those are the parental lineages. Finally, ~ 99% of phasing was conserved between overlapping phase groups between SA-EC3 and either parental lineage, indicating mitotic gene conversion/parasexuality as the mechanism of recombination for this hybrid isolate. HaplotypeTools is open source and freely available from https://github.com/rhysf/HaplotypeTools under the MIT License. CONCLUSIONS: HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and identifying parental ancestry for sub-genomic regions.


Assuntos
Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Algoritmos , Haplótipos , Filogenia , Polimorfismo de Nucleotídeo Único , Recombinação Genética , Análise de Sequência de DNA
4.
PLoS One ; 16(10): e0258298, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34637470

RESUMO

Papaya ringspot virus biotype-P is a detrimental pathogen of economically important papaya and cucurbits worldwide. The mutation prone feature of this virus perhaps accounts for its geographical dissemination. In this study, investigations of the atypical PRSV-P strain was conducted based on phylogenetic, recombination and genetic differentiation analyses considering of it's likely spread across India and Bangladesh. Full length genomic sequences of 38 PRSV isolates and 35 CP gene sequences were subjected to recombination analysis. A total of 61 recombination events were detected in aligned complete PRSV genome sequences. 3 events were detected in complete genome of PRSV strain PK whereas one was in its CP gene sequence. The PRSV-PK appeared to be recombinant of a major parent from Bangladesh. However, the genetic differentiation based on full length genomic sequences revealed less frequent gene flow between virus PRSV-PK and the population from America, India, Colombia, other Asian Countries and Australia. Whereas, frequent gene flow exists between Pakistan and Bangladesh virus populations. These results provided evidence correlating geographical position and genetic distances. We speculate that the genetic variations and evolutionary dynamics of this virus may challenge the resistance developed in papaya against PRSV and give rise to virus lineage because of its atypical emergence where geographic spread is already occurring.


Assuntos
Carica/genética , Carica/virologia , Evolução Molecular , Variação Genética , Doenças das Plantas/genética , Potyvirus/genética , Regiões 3' não Traduzidas/genética , Sequência de Bases , Fluxo Gênico , Genoma Viral , Funções Verossimilhança , Filogenia , Recombinação Genética , Estatística como Assunto
5.
Int J Mol Sci ; 22(19)2021 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-34638527

RESUMO

The ongoing pandemic coronavirus (CoV) disease 2019 (COVID-19) by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) has already caused substantial morbidity, mortality, and economic devastation. Reverse genetic approaches to generate recombinant viruses are a powerful tool to characterize and understand newly emerging viruses. To contribute to the global efforts for countermeasures to control the spread of SARS-CoV-2, we developed a passage-free SARS-CoV-2 clone based on a bacterial artificial chromosome (BAC). Moreover, using a Lambda-based Red recombination, we successfully generated different reporter and marker viruses, which replicated similar to a clinical isolate in a cell culture. Moreover, we designed a full-length reporter virus encoding an additional artificial open reading frame with wild-type-like replication features. The virus-encoded reporters were successfully applied to ease antiviral testing in cell culture models. Furthermore, we designed a new marker virus encoding 3xFLAG-tagged nucleocapsid that allows the detection of incoming viral particles and, in combination with bio-orthogonal labeling for the visualization of viral RNA synthesis via click chemistry, the spatiotemporal tracking of viral replication on the single-cell level. In summary, by applying BAC-based Red recombination, we developed a powerful, reliable, and convenient platform that will facilitate studies answering numerous questions concerning the biology of SARS-CoV-2.


Assuntos
COVID-19/virologia , Clonagem Molecular/métodos , Genoma Viral , SARS-CoV-2/genética , Animais , Chlorocebus aethiops , Células HEK293 , Humanos , Mutagênese , Plasmídeos/genética , Recombinação Genética , Células Vero
6.
Int J Mol Sci ; 22(19)2021 Oct 04.
Artigo em Inglês | MEDLINE | ID: mdl-34639080

RESUMO

The unconventional yeast Yarrowia lipolytica is extensively applied in bioproduction fields owing to its excellent metabolite and protein production ability. Nonetheless, utilization of this promising host is still restricted by the limited availability of precise and effective gene integration tools. In this study, a novel and efficient genetic tool was developed for targeted, repeated, and markerless gene integration based on Cre/lox site-specific recombination system. The developed tool required only a single selection marker and could completely excise the unnecessary sequences. A total of three plasmids were created and seven rounds of marker-free gene integration were examined in Y. lipolytica. All the integration efficiencies remained above 90%, and analysis of the protein production and growth characteristics of the engineered strains confirmed that genome modification via the novel genetic tool was feasible. Further work also confirmed that the genetic tool was effective for the integration of other genes, loci, and strains. Thus, this study significantly promotes the application of the Cre/lox system and presents a powerful tool for genome engineering in Y. lipolytica.


Assuntos
Proteínas Fúngicas/genética , Edição de Genes , Vetores Genéticos , Integrases/metabolismo , Plasmídeos/genética , Yarrowia/genética , Engenharia Genética , Integrases/genética , Recombinação Genética , Yarrowia/crescimento & desenvolvimento
7.
Nat Commun ; 12(1): 5876, 2021 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-34620865

RESUMO

Chromosomal recombinant gene expression offers a number of advantages over plasmid-based synthetic biology. However, the methods applied for bacterial genome engineering are still challenging and far from being standardized. Here, in an attempt to realize the simplest recombinant genome technology imaginable and facilitate the transition from recombinant plasmids to genomes, we create a simplistic methodology and a comprehensive strain collection called the Standardized Genome Architecture (SEGA). In its simplest form, SEGA enables genome engineering by combining only two reagents: a DNA fragment that can be ordered from a commercial vendor and a stock solution of bacterial cells followed by incubation on agar plates. Recombinant genomes are identified by visual inspection using green-white colony screening akin to classical blue-white screening for recombinant plasmids. The modular nature of SEGA allows precise multi-level control of transcriptional, translational, and post-translational regulation. The SEGA architecture simultaneously supports increased standardization of genetic designs and a broad application range by utilizing well-characterized parts optimized for robust performance in the context of the bacterial genome. Ultimately, its adaption and expansion by the scientific community should improve predictability and comparability of experimental outcomes across different laboratories.


Assuntos
Bactérias/genética , Engenharia Genética/métodos , Genoma Bacteriano , Biologia Sintética/métodos , Cromossomos , Escherichia coli/genética , Citometria de Fluxo/métodos , Regulação Bacteriana da Expressão Gênica , Vetores Genéticos , Plasmídeos , Regiões Promotoras Genéticas , Recombinação Genética , Padrões de Referência
8.
Int J Mol Sci ; 22(19)2021 Sep 29.
Artigo em Inglês | MEDLINE | ID: mdl-34638896

RESUMO

Human cytomegalovirus (HCMV) continues to be a major cause of morbidity in transplant patients and newborns. However, the functions of many of the more than 282 genes encoded in the HCMV genome remain unknown. The development of bacterial artificial chromosome (BAC) technology contributes to the genetic manipulation of several organisms including HCMV. The maintenance of the HCMV BAC in E. coli cells permits the rapid generation of recombinant viral genomes that can be used to produce viral progeny in cell cultures for the study of gene function. We optimized the Lambda-Red Recombination system to construct HCMV gene deletion mutants rapidly in the complete set of tested genes. This method constitutes a useful tool that allows for the quick generation of a high number of gene deletion mutants, allowing for the analysis of the whole genome to improve our understanding of HCMV gene function. This may also facilitate the development of novel vaccines and therapeutics.


Assuntos
Bacteriófago lambda/genética , Cromossomos Artificiais Bacterianos/genética , Citomegalovirus/genética , Escherichia coli/genética , Deleção de Genes , Recombinação Genética , Bacteriófago lambda/metabolismo , Linhagem Celular , Clonagem Molecular/métodos , Infecções por Citomegalovirus/virologia , Genoma Viral/genética , Células HEK293 , Humanos , Mutação , Plasmídeos/genética , Reprodutibilidade dos Testes
9.
Cells ; 10(9)2021 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-34571960

RESUMO

Meiosis involves a series of specific chromosome events, namely homologous synapsis, recombination, and segregation. Disruption of either recombination or synapsis in mammals results in the interruption of meiosis progression during the first meiotic prophase. This is usually accompanied by a defective transcriptional inactivation of the X and Y chromosomes, which triggers a meiosis breakdown in many mutant models. However, epigenetic changes and transcriptional regulation are also expected to affect autosomes. In this work, we studied the dynamics of epigenetic markers related to chromatin silencing, transcriptional regulation, and meiotic sex chromosome inactivation throughout meiosis in knockout mice for genes encoding for recombination proteins SPO11, DMC1, HOP2 and MLH1, and the synaptonemal complex proteins SYCP1 and SYCP3. These models are defective in recombination and/or synapsis and promote apoptosis at different stages of progression. Our results indicate that impairment of recombination and synapsis alter the dynamics and localization pattern of epigenetic marks, as well as the transcriptional regulation of both autosomes and sex chromosomes throughout prophase-I progression. We also observed that the morphological progression of spermatocytes throughout meiosis and the dynamics of epigenetic marks are processes that can be desynchronized upon synapsis or recombination alteration. Moreover, we detected an overlap of early and late epigenetic signatures in most mutants, indicating that the normal epigenetic transitions are disrupted. This can alter the transcriptional shift that occurs in spermatocytes in mid prophase-I and suggest that the epigenetic regulation of sex chromosomes, but also of autosomes, is an important factor in the impairment of meiosis progression in mammals.


Assuntos
Pareamento Cromossômico/genética , Epigênese Genética/genética , Mamíferos/genética , Meiose/genética , Proteínas Recombinantes/genética , Recombinação Genética/genética , Animais , Apoptose/genética , Marcadores Genéticos/genética , Masculino , Camundongos , Cromossomos Sexuais/genética , Espermatócitos/fisiologia , Transcrição Genética/genética
10.
Chem Rec ; 21(11): 2930-2957, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34472196

RESUMO

Glycals (carbohydrate enol-ethers) have enjoyed profound applications in organic synthesis for more than a century. They not only serve as versatile glycosyl donors or as substrates for Ferrier rearrangement, but also find extensive synthetic applications especially as a "chiral pool" for accomplishing the synthesis of a variety of natural and biologically important compounds. As cyclic enol ethers, they demonstrate high reactivity and are among the most and variously transformable monosaccharide derivatives. The uniqueness of the reactivity of glycals is that they can be synthetically tuned to get a library of derivatives through stereo- and regioselective introduction of a variety of functional groups at C1, C2, C3 as well as C4 carbons of the sugar. We have developed a practical approach for stereoselective mono- and diamination of glycals and over the years utilized these scaffolds for the synthesis of a variety of biologically important nitrogen heterocycles and carbocycles through a "Diversity Oriented Approach". Our synthetic strategy in this direction mainly relied on the cleavage of ring O-C bond of the sugar followed by an "intramolecular recombination" reaction. Utilizing this strategy, we have accomplished the synthesis of several biologically important natural products, their analogues and related unnatural derivatives. Examples of such compounds reported from our group include polyhydroxypyrrolidines, DMDP, anisomycin, steviamine, pochonicine, conduramines, bulgecinine, aminocyclitols, azepanes, 4-hydroxy-D-proline, azanucleosides and their analogues. A personal account highlighting these syntheses is presented here.


Assuntos
Produtos Biológicos , Nitrogênio , Técnicas de Química Sintética , Éteres , Recombinação Genética
11.
Cell ; 184(20): 5179-5188.e8, 2021 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-34499854

RESUMO

We present evidence for multiple independent origins of recombinant SARS-CoV-2 viruses sampled from late 2020 and early 2021 in the United Kingdom. Their genomes carry single-nucleotide polymorphisms and deletions that are characteristic of the B.1.1.7 variant of concern but lack the full complement of lineage-defining mutations. Instead, the remainder of their genomes share contiguous genetic variation with non-B.1.1.7 viruses circulating in the same geographic area at the same time as the recombinants. In four instances, there was evidence for onward transmission of a recombinant-origin virus, including one transmission cluster of 45 sequenced cases over the course of 2 months. The inferred genomic locations of recombination breakpoints suggest that every community-transmitted recombinant virus inherited its spike region from a B.1.1.7 parental virus, consistent with a transmission advantage for B.1.1.7's set of mutations.


Assuntos
COVID-19/epidemiologia , COVID-19/transmissão , Pandemias , Recombinação Genética , SARS-CoV-2/genética , Sequência de Bases/genética , COVID-19/virologia , Biologia Computacional/métodos , Frequência do Gene , Genoma Viral , Genótipo , Humanos , Mutação , Filogenia , Polimorfismo de Nucleotídeo Único , Reino Unido/epidemiologia , Sequenciamento Completo do Genoma/métodos
12.
Elife ; 102021 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-34581669

RESUMO

High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for next-generation sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called 'Tiled-ClickSeq', which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5'UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.


Assuntos
Sequência de Bases , Coronavirus/genética , Genoma Viral , RNA , SARS-CoV-2/genética , COVID-19/virologia , DNA Complementar , Biblioteca Gênica , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Nanoporos , Reação em Cadeia da Polimerase , RNA Mensageiro , RNA Viral/genética , Recombinação Genética , Sequenciamento Completo do Genoma
13.
PLoS Pathog ; 17(9): e1009814, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34473804

RESUMO

Many of us had refresher courses in virology, immunology, and epidemiology in 2020, and we were reminded of the fact that Homo sapiens, the wiliest predator on the planet, has been hunting everything that moves for millennia. These repeated interspecies contacts inherently lead to recurrent zoonosis (nonhuman to human) and anthroponosis (human to nonhuman). Given the accelerating changes in our ecosystems since the neolithic revolution, it was not surprising to see a virus that spreads via aerosolization and liquid droplets cause a pandemic in a few months. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic begs the question-which viruses could cause a global threat? In this Opinion, the characteristics that make adenoviruses a risk, which include efficient intra- and interspecies transmission, thermostable particles, persistent/latent infections in diverse hosts, and the ability to readily recombine and escape herd immunity, are discussed.


Assuntos
Infecções por Adenovirus Humanos/mortalidade , Pandemias/estatística & dados numéricos , Infecções por Adenovirus Humanos/epidemiologia , Animais , Interação Humano-Animal , Humanos , Recombinação Genética , Fatores de Risco , Especificidade da Espécie , Transcrição Genética
14.
Nat Commun ; 12(1): 5324, 2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34493730

RESUMO

Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary camels across the Middle East and Africa. Virus-induced pneumonia in humans results from animal contact, with a potential for limited onward transmission. Phenotypic changes have been suspected after a novel recombinant clade (lineage 5) caused large nosocomial outbreaks in Saudi Arabia and South Korea in 2016. However, there has been no functional assessment. Here we perform a comprehensive in vitro and ex vivo comparison of viruses from parental and recombinant virus lineages (lineage 3, n = 7; lineage 4, n = 8; lineage 5, n = 9 viruses) from Saudi Arabia, isolated immediately before and after the shift toward lineage 5. Replication of lineage 5 viruses is significantly increased. Transcriptional profiling finds reduced induction of immune genes IFNB1, CCL5, and IFNL1 in lung cells infected with lineage 5 strains. Phenotypic differences may be determined by IFN antagonism based on experiments using IFN receptor knock out and signaling inhibition. Additionally, lineage 5 is more resilient against IFN pre-treatment of Calu-3 cells (ca. 10-fold difference in replication). This phenotypic change associated with lineage 5 has remained undiscovered by viral sequence surveillance, but may be a relevant indicator of pandemic potential.


Assuntos
Infecções por Coronavirus/virologia , Coronavírus da Síndrome Respiratória do Oriente Médio/genética , Animais , Camelus , Células Cultivadas , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Genoma Viral , Humanos , Coronavírus da Síndrome Respiratória do Oriente Médio/isolamento & purificação , Coronavírus da Síndrome Respiratória do Oriente Médio/patogenicidade , Filogenia , Recombinação Genética , República da Coreia/epidemiologia , Arábia Saudita/epidemiologia , Replicação Viral
15.
BMC Genomics ; 22(1): 673, 2021 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-34536998

RESUMO

BACKGROUND: Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent a prominent case of adaptive evolution of recombination. However, our understanding of the relationship between social evolution and recombination rates is incomplete, partly due to lacking empirical data. Here, we present a linkage map of the monandrous, advanced eusocial Brazilian stingless bee, Frieseomelitta varia, providing the first recombination analysis in the diverse Meliponini (Hymenoptera, Apidae). RESULTS: Our linkage map includes 1417 markers in 19 linkage groups. This map spans approximately 2580 centimorgans, and comparisons to the physical genome assembly indicate that it covers more than 75 % of the 275 Megabasepairs (Mbp) F. varia genome. Thus, our study results in a genome-wide recombination rate estimate of 9.3-12.5 centimorgan per Mbp. This value is higher than estimates from nonsocial insects and comparable to other highly social species, although it does not support our prediction that monandry and strong queen-worker caste divergence of F. varia lead to even higher recombination rates than other advanced eusocial species. CONCLUSIONS: Our study expands the association between elevated recombination and sociality in the order Hymenoptera and strengthens the support for the hypothesis that advanced social evolution in hymenopteran insects invariably selects for high genomic recombination rates.


Assuntos
Himenópteros , Animais , Abelhas/genética , Ligação Genética , Genoma , Recombinação Genética , Comportamento Social
16.
Virologie (Montrouge) ; 25(4): 224-235, 2021 08 01.
Artigo em Francês | MEDLINE | ID: mdl-34468319

RESUMO

Genetic recombination is a major force driving the evolution of some species of positive sense RNA viruses. Recombination events occur when at least two viruses simultaneously infect the same cell, thereby giving rise to new genomes comprised of genetic sequences originating from the parental genomes. The main mechanism by which recombination occurs involves the viral polymerase that generates a chimera as it switches templates during viral replication. Various experimental systems have alluded to the existence of recombination events that are independent of viral polymerase activity. The origins and frequency of such events remain to be elucidated to this day. Furthermore, it is not known whether non-replicative recombination yields products that are different from recombinants generated by the viral polymerase. If this is the case, then non-replicative recombination may play a unique role in the evolution of positive sense RNA viruses. Finally, the sparse data available suggest that non-replicative recombination does not necessarily involve only virus-specific sequences. It is thus possible that the non-replicative recombination observed in virus-focused studies may in fact reveal a more generalized mechanism that is non-specific to virus RNAs.


Assuntos
Vírus de RNA de Cadeia Positiva , Recombinação Genética , Sequência de Bases , RNA Viral/genética , Recombinação Genética/genética , Replicação Viral/genética
17.
Virologie (Montrouge) ; 25(4): 62-73, 2021 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-34468320

RESUMO

Genetic recombination is a major force driving the evolution of some species of positive sense RNA viruses. Recombination events occur when at least two viruses simultaneously infect the same cell, thereby giving rise to new genomes comprised of genetic sequences originating from the parental genomes. The main mechanism by which recombination occurs involves the viral polymerase that generates a chimera as it switches templates during viral replication. Various experimental systems have alluded to the existence of recombination events that are independent of viral polymerase activity. The origins and the frequency of such events remain to be elucidated to this day. Furthermore, it is not known whether non-replicative recombination yields products that are different from recombinants generated by the viral polymerase. If this is the case, then non-replicative recombination may play a unique role in the evolution of positive sense RNA viruses. Finally, the sparse data available suggest that non-replicative recombination does not necessarily involve only virus-specific sequences. It is thus possible that the non-replicative recombination observed in virus-focused studies may in fact reveal a more generalized mechanism that is non-specific to virus RNAs.


Assuntos
Vírus de RNA de Cadeia Positiva , Recombinação Genética , Sequência de Bases , RNA Viral/genética , Recombinação Genética/genética , Replicação Viral/genética
18.
Cladistics ; 37(5): 461-488, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34570933

RESUMO

The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.


Assuntos
Quirópteros/virologia , Interações Hospedeiro-Patógeno/fisiologia , Coronavírus da Síndrome Respiratória do Oriente Médio/fisiologia , Filogenia , Vírus da SARS/fisiologia , SARS-CoV-2/fisiologia , Animais , Genoma Viral , Humanos , Funções Verossimilhança , Pangolins/virologia , Recombinação Genética/genética , Glicoproteína da Espícula de Coronavírus/metabolismo
19.
Int J Mol Sci ; 22(17)2021 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-34502253

RESUMO

In the past, major findings in meiosis have been achieved, but questions towards the global understanding of meiosis remain concealed. In plants, one of these questions covers the need for two diverse meiotic active SPO11 proteins. In Arabidopsis and other plants, both meiotic SPO11 are indispensable in a functional form for double strand break induction during meiotic prophase I. This stands in contrast to mammals and fungi, where a single SPO11 is present and sufficient. We aimed to investigate the specific function and evolution of both meiotic SPO11 paralogs in land plants. By performing immunostaining of both SPO11-1 and -2, an investigation of the spatiotemporal localization of each SPO11 during meiosis was achieved. We further exchanged SPO11-1 and -2 in Arabidopsis and could show a species-specific function of the respective SPO11. By additional changes of regions between SPO11-1 and -2, a sequence-specific function for both the SPO11 proteins was revealed. Furthermore, the previous findings about the aberrant splicing of each SPO11 were refined by narrowing them down to a specific developmental phase. These findings let us suggest that the function of both SPO11 paralogs is highly sequence specific and that the orthologs are species specific.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Endodesoxirribonucleases/genética , Splicing de RNA/genética , Arabidopsis/química , Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/fisiologia , Quebras de DNA de Cadeia Dupla , Proteínas de Ligação a DNA/metabolismo , Endodesoxirribonucleases/química , Endodesoxirribonucleases/metabolismo , Endodesoxirribonucleases/fisiologia , Meiose/fisiologia , Rad51 Recombinase/metabolismo , Recombinação Genética , Especificidade da Espécie
20.
G3 (Bethesda) ; 11(9)2021 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-34544126

RESUMO

Wolbachia is arguably one of the most ubiquitous heritable symbionts among insects and understanding its transmission dynamics is crucial for understanding why it is so common. While previous research has studied the transmission pathways of Wolbachia in several insect lineages including Lepidoptera, this study takes advantage of data collected from the lepidopteran tribe Aeromachini in an effort to assess patterns of transmission. Twenty-one of the 46 species of Aeromachini species were infected with Wolbachia. Overall, 25% (31/125) of Aeromachini specimens tested were Wolbachia positive. All Wolbachia strains were species-specific except for the wJho strain which appeared to be shared by three host species with a sympatric distribution based on a cophylogenetic comparison between Wolbachia and the Aeromachini species. Two tests of phylogenetic congruence did not find any evidence for cospeciation between Wolbachia strains and their butterfly hosts. The cophylogenetic comparison, divergence time estimation, and Wolbachia recombination analysis revealed that Wolbachia acquisition in Aeromachini appears to have mainly occurred mainly through horizontal transmission rather than codivergence.


Assuntos
Borboletas , Wolbachia , Animais , Borboletas/genética , Filogenia , Recombinação Genética , Especificidade da Espécie , Wolbachia/genética
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