-
BioRxiv : the Preprint Server For... Apr 2024Viruses with double-stranded (ds) DNA genomes in the realm share a conserved structural gene module but show a broad range of variation in their repertoires of DNA...
Viruses with double-stranded (ds) DNA genomes in the realm share a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the order encode DNAPs of different families. Here we identify four additional groups of tailed phages in the class in which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs "in situ", without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage replication. We hypothesize that DNAP swapping is driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.
PubMed: 38903090
DOI: 10.1101/2024.04.26.591309 -
Nature Communications Jun 2024IS1111 and IS110 insertion sequence (IS) family members encode an unusual DEDD transposase type and exhibit specific target site selection. The IS1111 group include...
IS1111 and IS110 insertion sequence (IS) family members encode an unusual DEDD transposase type and exhibit specific target site selection. The IS1111 group include identifiable subterminal inverted repeats (sTIR) not found in the IS110 type. IS in both families include a noncoding region (NCR) of significant length and, as each individual IS or group of closely related IS selects a different site, we had previously proposed that an NCR-derived RNA was involved in target selection. Here, we find that the NCR is usually downstream of the transposase gene in IS1111 family IS and upstream in the IS110 type. Four IS1111 and one IS110 family members that target different sequences are used to demonstrate that the NCR determines a short seeker RNA (seekRNA) that co-purified with the transposase. The seekRNA is essential for transposition of the IS or a cargo flanked by IS ends from and to the preferred target. Short sequences matching both top and bottom strands of the target are present in the seekRNA but their order in IS1111 and IS110 family IS is reversed. Reprogramming the seekRNA and donor flank to target a different site is demonstrated, indicating future biotechnological potential for these systems.
Topics: Transposases; DNA Transposable Elements; RNA, Untranslated; Base Sequence
PubMed: 38898016
DOI: 10.1038/s41467-024-49474-9 -
Brazilian Journal of Biology = Revista... 2024The gall wasp, Leptocybe invasa, poses a significant global threat to Eucalyptus cultivation, by causing substantial economic losses. The objective of this study was to...
The gall wasp, Leptocybe invasa, poses a significant global threat to Eucalyptus cultivation, by causing substantial economic losses. The objective of this study was to differentiate between resistant and susceptible genotypes by morphological characteristics using image analysis based on the damage caused by the gall wasp. In addition, consensus sequences derived from transposable elements (TEs) and the genome of Eucalyptus spp. Were identified by in silico analysis. Furthermore, another objective was to discriminate Eucalyptus genotypes in response to Leptocybe invasa by conducting molecular analyses involving transposable elements and inter simple sequence markers. For image analysis, the GroundEye ® system was used to collect images of 60 leaves from six genotypes, three of which were resistant and three susceptible. Eucalyptus spp. sequences were obtained from the GenBank database by in silico analysis and pairwise alignments with TE sequences were conducted using BLASTN. Multiple sequence alignment was performed with Clustal Omega, followed by the identification of conserved regions in Jalview. A motif signature was generated using Weblogo. For molecular characterization using ISSR markers and TEs, samples of young leaves were obtained from a total of 80 Eucalyptus seedlings, of which 50 were classified as resistant and 30 as susceptible to L. invasa. It was possible to distinguish gall wasp susceptible and resistant genotypes by image analysis. In silico analysis enabled the identification of conserved regions in the Eucalyptus spp. genome, which were associated with proteins involved in secondary metabolite production, e.g., terpenes, which play a role in the response to L. invasa. The discrimination capacity of TEs and ISSR primers was demonstrated and bands were generated that could be used to identify resistant genotypes. However, increasing the number of markers required to discriminate genotypes in both cases is suggested.
Topics: Eucalyptus; Genotype; Phenotype; Animals; Wasps; Disease Resistance; Computer Simulation; Plant Diseases; DNA Transposable Elements
PubMed: 38896727
DOI: 10.1590/1519-6984.279850 -
International Journal of Molecular... May 2024Species of the genus have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are...
Species of the genus have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing females and males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, and , the functional RDC complex in hybrid ovaries was not assembled. However, the activity of the RDC complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, we found no evidence that their activity can be considered the main cause of hybrid sterility. We revealed a complicated pattern of Vasa protein expression in the hybrid germline, including partial piRNA targeting of the allele and a significant zygotic delay in expression. We arrived at the conclusion that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.
Topics: Animals; Female; Drosophila melanogaster; Male; Drosophila simulans; Drosophila Proteins; RNA, Small Interfering; DNA Transposable Elements; Ovary; Hybridization, Genetic; Oogenesis; Infertility; Crosses, Genetic; DEAD-box RNA Helicases
PubMed: 38891872
DOI: 10.3390/ijms25115681 -
International Journal of Molecular... May 2024(IIIb) is frequently isolated from reptiles and less frequently from birds and mammals. However, its isolation from invasive human infections has not been widely...
(IIIb) is frequently isolated from reptiles and less frequently from birds and mammals. However, its isolation from invasive human infections has not been widely reported. Migratory mallard ducks are excellent bioindicators of pathogen presence and pathogen antibiotic resistance (AMR). We present the first isolation from a mallard duck in central Europe of the antibiotic-resistant subsp. with the unique antigenic pattern 58:r:z and report its whole-genome sequencing, serosequencing, and genotyping, which enabled the prediction of its pathogenicity and comparison with phenotypic AMR. The isolated strain was highly similar to isolated from humans and food. Twenty-four AMR genes were detected, including those encoding aminoglycoside, fluoroquinolone, macrolide, carbapenem, tetracycline, cephalosporin, nitroimidazole, peptide antibiotic, and disinfecting agent/antiseptic resistance. Six pathogenicity islands were found (SPI-1, SPI-2, SPI-3, SPI-5, SPI-9, and SPI-13). An iron transport system was detected in SPI-1 centisome C63PI. Plasmid profile analyses showed three to be present. Sequence mutations in the and genes were noted, which truncated and elongated the proteins, respectively. The strain also harbored genes encoding type-III secretion-system effector proteins and many virulence factors found in associated with human infections. This study aims to elucidate the AMR and virulence genes in subsp. that may most seriously threaten human health.
Topics: Animals; Ducks; Humans; Salmonella; Whole Genome Sequencing; Genomic Islands; Salmonella Infections, Animal; Anti-Bacterial Agents; Salmonella enterica; Drug Resistance, Multiple, Bacterial; Genome, Bacterial; Phylogeny; Drug Resistance, Bacterial; Plasmids
PubMed: 38891852
DOI: 10.3390/ijms25115664 -
BMC Genomics Jun 2024To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon...
BACKGROUND
To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order.
RESULTS
We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group.
CONCLUSIONS
The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
Topics: Animals; Phylogeny; Cyprinodontiformes; Evolution, Molecular; Genome; DNA Transposable Elements; Genome Size
PubMed: 38890559
DOI: 10.1186/s12864-024-10416-w -
Methods in Molecular Biology (Clifton,... 2024Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved...
Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.
Topics: Salmonella; Humans; Genomics; Salmonella Infections; Phylogeny; Genome, Bacterial; Molecular Epidemiology; Virulence Factors; Disease Outbreaks; Drug Resistance, Bacterial; Interspersed Repetitive Sequences
PubMed: 38888768
DOI: 10.1007/978-1-0716-3890-3_2 -
BMC Microbiology Jun 2024Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this...
BACKGROUND
Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species.
RESULTS
In this study, we analyzed the morphological, physiological, and genomic characteristics of the newly identified B. porcorum sp. nov. strain QD2021 isolated from pigs. The complete genome sequence of the B. porcorum QD2021 strain consists of a single circular chromosome (2,271,736 bp, 38.51% G + C content), which encodes 2,578 genes. One plasmid with a size of 70,040 bp was detected. A total of 121 scattered repeat sequences, 319 tandem repeat sequences, 4 genomic islands, 5 prophages, 3 CRISPR sequences, and 51 ncRNAs were predicted. The coding genes of the B. porcorum genome were successfully annotated across eight databases (NR, GO, KEGG, COG, TCDB, Pfam, Swiss-Prot and CAZy) and four pathogenicity-related databases (PHI, CARD, VFDB and ARDB). In addition, a comparative genome analysis was performed to explore the evolutionary relationships of B. porcorum QD2021.
CONCLUSIONS
To our knowledge, this is the first study to provide fundamental phenotypic and whole-genome sequences for B. porcorum. Our results extensively expand the current knowledge and could serve as a valuable genomic resource for future research on B. porcorum.
Topics: Animals; China; Genome, Bacterial; Swine; Base Composition; Whole Genome Sequencing; Phylogeny; Flavobacteriaceae; Swine Diseases; DNA, Bacterial; Genomic Islands; Plasmids; Flavobacteriaceae Infections; Sequence Analysis, DNA; Molecular Sequence Annotation
PubMed: 38886642
DOI: 10.1186/s12866-024-03366-6 -
Methods in Molecular Biology (Clifton,... 2024Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance...
Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.
Topics: Conjugation, Genetic; Interspersed Repetitive Sequences; Gene Transfer, Horizontal; Streptococcus suis; Anti-Bacterial Agents; Drug Resistance, Bacterial; Polymerase Chain Reaction; Genes, Bacterial
PubMed: 38884912
DOI: 10.1007/978-1-0716-3898-9_7 -
ZooKeys 2024Three new species of the genera C. L. Koch, 1846 and Prószyński, 1979 are described and named as (♂♀), (♀) and (♂♀), from Hunan Province, China....
Three new species of the genera C. L. Koch, 1846 and Prószyński, 1979 are described and named as (♂♀), (♀) and (♂♀), from Hunan Province, China. Detailed descriptions, photos of somatic features and copulatory organs, as well as a distribution map are provided. Nucleotide data for the barcoding gene, cytochrome c oxidase subunit I (COI) of (♂♀) and (♀) are provided.
PubMed: 38882565
DOI: 10.3897/zookeys.1204.122887