Nejvíce citovaný článek - PubMed ID 22368248
Obligatory parthenogenesis in vertebrates is restricted to squamate reptiles and evolved through hybridisation. Parthenogens can hybridise with sexual species, resulting in individuals with increased ploidy levels. We describe two successive hybridisations of the parthenogenetic butterfly lizards (genus Leiolepis) in Vietnam with a parental sexual species. Contrary to previous proposals, we document that parthenogenetic L. guentherpetersi has mitochondrial DNA and two haploid sets from L. guttata and one from L. reevesii, suggesting that it is the result of a backcross of a parthenogenetic L. guttata × L. reevesii hybrid with a L. guttata male increasing ploidy from 2n to 3n. Within the range of L. guentherpetersi, we found an adult tetraploid male with three L. guttata and one L. reevesii haploid genomes. It probably originated from fertilisation of an unreduced triploid L. guentherpetersi egg by a L. guttata sperm. Although its external morphology resembles that of the maternal species, it possessed exceptionally large erythrocytes and was likely sterile. As increased ploidy level above triploidy or tetraploidy appears to be harmful for amniotes, all-female asexual lineages should evolve a strategy to prevent incorporation of other haploid genomes from a sexual species by avoiding fertilisation by sexual males.
- Klíčová slova
- Leiolepis, Hybridisation, Meiosis, Parthenogenesis, Tetraploidy, Vietnam,
- MeSH
- hybridizace genetická MeSH
- ještěři * genetika MeSH
- mitochondriální DNA genetika MeSH
- partenogeneze * genetika MeSH
- tetraploidie * MeSH
- triploidie * MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- mitochondriální DNA MeSH
In the rice agroecosystems of Southeast Asia, rice root knot nematode (Meloidogyne graminicola) significantly impairs yield, representing a major species within the 'graminis-group' known for its morphological similarities with other root knot nematodes (RKNs). This study delves into the variations in reproductive potential, morphology, morphometrics, and genetic diversity among thirty RKN populations in rice across three distinct agroecological zones in Jharkhand, India. Despite notable differences in reproductive potential among the populations, morphological and morphometric correlations to reproductive potential were inconclusive. However, male and juvenile morphometrics were crucial for identifying intraspecific variability. Genetic analysis utilizing five molecular markers (ITS, 18 S rRNA, D2-D3 of 28 S, COX-I, and COX-II) affirmed the populations as M. graminicola, with ITS marker revealing significant intraspecific variability. Phylogenetic analysis underscored the close relationship between M. oryzae and M. graminicola, distinct from other mitotic RKN species. Low genetic distance and nucleotide diversity, coupled with high haplotype diversity, negative Tajima's D, and Fu's Fs of haplotype network analysis, suggested that all M. graminicola populations are expanding. These findings highlight the urgent need for comprehensive management strategies against M. graminicola, providing valuable insights for growers, extension officials, and plant breeders to develop targeted management approaches and resistance breeding programs.
- Klíčová slova
- Meloidogyne graminicola, 18S rRNA, COX-I, COX-II, D2-D3, ITS, Multi-gene phylogeny,
- MeSH
- fylogeneze * MeSH
- genetická variace * MeSH
- haplotypy MeSH
- kořeny rostlin parazitologie MeSH
- nemoci rostlin * parazitologie MeSH
- rýže (rod) * parazitologie růst a vývoj genetika MeSH
- Tylenchoidea * genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Indie MeSH
Dothistroma septosporum and Dothistroma pini are severe foliar pathogens of conifers. They infect a broad spectrum of hosts (mainly Pinus spp.), causing chlorosis, defoliation of needles, and eventually the death of pine trees in extreme cases. Mycoviruses represent a novel and innovative avenue for controlling pathogens. To search for possible viruses hosted by Dothistroma spp. we screened a subset of isolates (20 strains of D. septosporum and one D. pini) originating from the Czech Republic, Slovenia, Italy, Austria and Ireland for viral dsRNA segments. Only five of them showed the presence of dsRNA segments. A total of 21 fungal isolates were prepared for total RNA extractions. RNA samples were pooled, and two separate RNA libraries were constructed for stranded total RNA sequencing. RNA-Seq data processing, pairwise sequence comparisons (PASC) and phylogenetic analyses revealed the presence of thirteen novel putative viruses with varying genome types: seven negative-sense single-stranded RNA viruses, including six bunya-like viruses and one new member of the order Mononegavirales; three positive-sense single-stranded RNA viruses, two of which are similar to those of the family Narnaviridae, while the genome of the third correspond to those of the family Gammaflexiviridae; and three double-stranded RNA viruses, comprising two novel members of the family Chrysoviridae and a potentially new species of gammapartitivirus. The results were confirmed with RT-PCR screening that the fungal pathogens hosted all the viruses and showed that particular fungal strains harbour multiple virus infections and that they are transmitted vertically. In this study, we described the narnavirus infecting D. pini. To our knowledge, this is the first virus discovered in D. pini.
- Klíčová slova
- Conifer pathogens, Dothistroma needle blight (DNB), High-throughput sequencing, Total RNA sequencing, Virus diversity,
- MeSH
- Ascomycota * virologie genetika MeSH
- borovice * mikrobiologie MeSH
- dvouvláknová RNA genetika MeSH
- fylogeneze * MeSH
- genom virový * MeSH
- mykoviry * genetika klasifikace izolace a purifikace MeSH
- nemoci rostlin * virologie mikrobiologie MeSH
- RNA virová * genetika MeSH
- RNA-viry genetika klasifikace izolace a purifikace MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
- Itálie MeSH
- Názvy látek
- dvouvláknová RNA MeSH
- RNA virová * MeSH
Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development and adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of the MSP cascade and cytokinin primary response genes, are thought to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, transcriptional data also suggest the involvement of RRA genes in stress-related responses. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRA genes, we identified five and 38 novel putative RRA genes in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassicaceae. We categorized RRA genes based on the kinetics of their cytokinin-mediated up-regulation and observed both similarities and specificities in this type of response across Brassicaceae species. Using bioinformatic analysis and experimental data demonstrating the cytokinin and abiotic stress responsiveness of the A. thaliana-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin- and stress-mediated up-regulation of RRA genes in B. rapa and B. napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus further demonstrating the role of cytokinin signaling in crop adaptive responses.
- Klíčová slova
- Arabidopsis thaliana, Brassica napus, Brassica oleracea, Brassica rapa, cytokinins, multistep phosphorelay, osmotic stress, salinity, two-component signaling, type-A response regulator,
- MeSH
- Arabidopsis genetika fyziologie metabolismus MeSH
- Brassica napus genetika fyziologie metabolismus MeSH
- Brassica * genetika fyziologie metabolismus MeSH
- cytokininy * metabolismus MeSH
- fylogeneze MeSH
- fyziologický stres * MeSH
- regulace genové exprese u rostlin MeSH
- regulátory růstu rostlin metabolismus MeSH
- rostlinné proteiny * genetika metabolismus MeSH
- signální transdukce MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- cytokininy * MeSH
- regulátory růstu rostlin MeSH
- rostlinné proteiny * MeSH
Castilleja tenuiflora is a native perennial plant used in traditional Mexican medicine. In June 2022, leaf blight symptoms were observed in a wild population of C. tenuiflora plants. Disease incidence was 80% and disease intensity reached up to 5% of the leaf area. Currently, there are no reports of pathogens causing leaf blight in this plant; therefore, this work aimed to identify the fungi responsible for the disease. The fungi recovered from the diseased tissue were characterized by means of pathogenicity tests and cultural, morphological, and molecular characterization. The information obtained revealed that Alternaria alternata and Alternaria gossypina are the pathogens responsible for the disease. This is the first report implicating species of Alternaria in causing leaf blight of C. tenuiflora in Mexico, as well as the first report of Alternaria gossypina also in Mexico. These pathogens may threaten the in situ conservation of native C. tenuiflora populations and limit their in vitro propagation. Future research lines should focus on determining the effect of these pathogens on metabolite production.
- Klíčová slova
- Alternaria, Mexican medicinal plants, Orobanchaceae, morphology, pathogenicity, phylogeny,
- Publikační typ
- časopisecké články MeSH
The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies and flowers in 13 different regions). Following sequencing, several polymorphisms and haplotypes were identified. Analysis of tRNAleu-cox2 sequences revealed three DraI haplotypes (C, A1, and A4). The tRNAleu-cox2 region yielded 10 C lineage haplotypes, one of which is a newly described variant. Three A lineage haplotypes were identified, two of which were novel. A similar analysis of cox1 sequences yielded 16 distinct haplotypes (7 new) within the population. The most prevalent tRNAleu-cox2 haplotype identified was C1a, followed by C2a, C2c, C2l, and C2d. For the cox1 locus, the most frequent haplotypes were HpB02, HpB01, HpB03, and HpB04. The haplotype and nucleotide diversity indices were high in both loci, in tRNAleu-cox2 with values of 0.682 and 0.00172, respectively, and in cox1 0.789 and 0.00203, respectively. The Tajima's D values were negative and lower in tRNAleu-cox2 than in cox1. The most frequent haplotypes were uniformly distributed across all regions of the Czech Republic. No haplotype of the indigenous M lineage was identified. High diversity and the occurrence of rare haplotypes indicate population expansion and continuous import of tribal material of the C lineage.
- Klíčová slova
- A lineage, Apis mellifera, cox1, introgression, mitochondrial DNA, population, tRNAleu-cox2,
- Publikační typ
- časopisecké články MeSH
Current methods of processing archaeological samples combined with advances in sequencing methods lead to disclosure of a large part of H. neanderthalensis and Denisovans genetic information. It is hardly surprising that the genome variability between modern humans, Denisovans and H. neanderthalensis is relatively limited. Genomic studies may provide insight on the metabolism of extinct human species or lineages. Detailed analysis of G-quadruplex sequences in H. neanderthalensis and Denisovans mitochondrial DNA showed us interesting features. Relatively similar patterns in mitochondrial DNA are found compared to modern humans, with one notable exception for H. neanderthalensis. An interesting difference between H. neanderthalensis and H. sapiens corresponds to a motif found in the D-loop region of mtDNA, which is responsible for mitochondrial DNA replication. This area is directly responsible for the number of mitochondria and consequently for the efficient energy metabolism of cell. H. neanderthalensis harbor a long uninterrupted run of guanines in this region, which may cause problems for replication, in contrast with H. sapiens, for which this run is generally shorter and interrupted. One may propose that the predominant H. sapiens motif provided a selective advantage for modern humans regarding mtDNA replication and function.
- Publikační typ
- časopisecké články MeSH
Hepatitis delta virus (HDV) is a highly unusual RNA satellite virus that depends on the presence of hepatitis B virus (HBV) to be infectious. Its compact and variable single-stranded RNA genome consists of eight major genotypes distributed unevenly across different continents. The significance of noncanonical secondary structures such as G-quadruplexes (G4s) is increasingly recognized at the DNA and RNA levels, particularly for transcription, replication, and translation. G4s are formed from guanine-rich sequences and have been identified in the vast majority of viral, eukaryotic, and prokaryotic genomes. In this study, we analyzed the G4 propensity of HDV genomes by using G4Hunter. Unlike HBV, which has a G4 density similar to that of the human genome, HDV displays a significantly higher number of potential quadruplex-forming sequences (PQS), with a density more than four times greater than that of the human genome. This finding suggests a critical role for G4s in HDV, especially given that the PQS regions are conserved across HDV genotypes. Furthermore, the prevalence of G4-forming sequences may represent a promising target for therapeutic interventions to control HDV replication.
- Publikační typ
- časopisecké články MeSH
Novel species of coagulase-negative staphylococci, which could serve as reservoirs of virulence and antimicrobial resistance factors for opportunistic pathogens from the genus Staphylococcus, are recognized in human and animal specimens due to advances in diagnostic techniques. Here, we used whole-genome sequencing, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize five coagulase-negative strains from the Staphylococcus haemolyticus phylogenetic clade obtained from human ear swabs, wounds, and bile. Based on the results of polyphasic taxonomy, we propose the species Staphylococcus brunensis sp. nov. (type strain NRL/St 16/872T = CCM 9024T = LMG 31872T = DSM 111349T). The genomic analysis revealed numerous variable genomic elements, including staphylococcal cassette chromosome (SCC), prophages, plasmids, and a unique 18.8 kb-long genomic island SbCIccrDE integrated into the ribosomal protein L7 serine acetyltransferase gene rimL. SbCIccrDE has a cassette chromosome recombinase (ccr) gene complex with a typical structure found in SCCs. Based on nucleotide and amino acid identity to other known ccr genes and the distinct integration site that differs from the canonical methyltransferase gene rlmH exploited by SCCs, we classified the ccr genes as novel variants, ccrDE. The comparative genomic analysis of SbCIccrDE with related islands shows that they can accumulate virulence and antimicrobial resistance factors creating novel resistance elements, which reflects the evolution of SCC. The spread of these resistance islands into established pathogens such as Staphylococcus aureus would pose a great threat to the healthcare system. IMPORTANCE The coagulase-negative staphylococci are important opportunistic human pathogens, which cause bloodstream and foreign body infections, mainly in immunocompromised patients. The mobile elements, primarily the staphylococcal cassette chromosome mec, which confers resistance to methicillin, are the key to the successful dissemination of staphylococci into healthcare and community settings. Here, we present a novel species of the Staphylococcus genus isolated from human clinical material. The detailed analysis of its genome revealed a previously undescribed genomic island, which is closely related to the staphylococcal cassette chromosome and has the potential to accumulate and spread virulence and resistance determinants. The island harbors a set of conserved genes required for its mobilization, which we recognized as novel cassette chromosome recombinase genes ccrDE. Similar islands were revealed not only in the genomes of coagulase-negative staphylococci but also in S. aureus. The comparative genomic study contributes substantially to the understanding of the evolution and pathogenesis of staphylococci.
Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of 'genetic camouflage' to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.
- MeSH
- biologická evoluce MeSH
- G-kvadruplexy * MeSH
- genom lidský MeSH
- genomika MeSH
- lidé MeSH
- paleontologie MeSH
- virus hepatitidy B * genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
