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Journal articles on the topic 'Intragenomic rearrangement'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Leppik, Ludmila, Karin Gunst, Matti Lehtinen, Joakim Dillner, Karin Streker, and Ethel-Michele de Villiers. "In Vivo and In Vitro Intragenomic Rearrangement of TT Viruses." Journal of Virology 81, no. 17 (2007): 9346–56. http://dx.doi.org/10.1128/jvi.00781-07.

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ABSTRACT The in vitro replication of the Torque teno virus (TT virus) tth8 full-length genome and particle formation in a Hodgkin's lymphoma-derived cell line after transfection with cloned viral DNA were demonstrated. Analyses of the transcription patterns of tth8 and tth7 TT virus isolates in a number of lymphoma and T-cell leukemia cell lines indicated differential additional splicing events and intragenomic rearrangement generating open reading frames which could not be deducted from the genomic sequence. We also demonstrated the presence of rearranged TT virus genomes in vivo in sera take

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2

Pohl, Mary Ann, Sabine Kienesberger, and Martin J. Blaser. "Novel Functions for Glycosyltransferases Jhp0562 and GalT in Lewis Antigen Synthesis and Variation in Helicobacter pylori." Infection and Immunity 80, no. 4 (2012): 1593–605. http://dx.doi.org/10.1128/iai.00032-12.

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ABSTRACTLewis (Le) antigens are fucosylated oligosaccharides present in theHelicobacter pylorilipopolysaccharide. Expression of these antigens is believed to be important forH. pyloricolonization, since Le antigens also are expressed on the gastric epithelia in humans. A galactosyltransferase encoded by β-(1,3)galTis essential for production of type 1 (Leaand Leb) antigens. The upstream genejhp0562, which is present in many but not allH. pyloristrains, is homologous to β-(1,3)galTbut is of unknown function. BecauseH. pyloridemonstrates extensive intragenomic recombination, we hypothesized that

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3

Zattera, Michelle Louise, and Daniel Pacheco Bruschi. "Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome." Cells 11, no. 21 (2022): 3373. http://dx.doi.org/10.3390/cells11213373.

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The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host’s gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the eme

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4

Pfister, Thomas, Keith W. Jones, and Eckard Wimmer. "A Cysteine-Rich Motif in Poliovirus Protein 2CATPaseIs Involved in RNA Replication and Binds Zinc In Vitro." Journal of Virology 74, no. 1 (2000): 334–43. http://dx.doi.org/10.1128/jvi.74.1.334-343.2000.

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ABSTRACT Protein 2CATPase of picornaviruses is involved in the rearrangement of host cell organelles, viral RNA replication, and encapsidation. However, the biochemical and molecular mechanisms by which 2CATPase engages in these processes are not known. To characterize functional domains of 2CATPase, we have focused on a cysteine-rich motif near the carboxy terminus of poliovirus 2CATPase. This region, which is well conserved among enteroviruses and rhinoviruses displaying an amino acid arrangement resembling zinc finger motifs, was studied by genetic and biochemical analyses. A mutation that

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5

Faddeeva-Vakhrusheva, Anna, Ken Kraaijeveld, Martijn F. L. Derks, et al. "Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida." BMC Genomics 18, no. 1 (2017): 493. https://doi.org/10.1186/s12864-017-3852-x.

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<strong>Background: </strong> <i>Folsomia candida</i> is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of <i>Wolbachia</i>, and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.<strong>Results: </strong>We applied Pacific Bioscience sequencing and assembly to generate a reference genome for <i>F. candida</i> of 221.7 Mbp, comprising only 162 scaffolds. The c

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6

Eriksen, Kirsten T., Dorte Haubek, and Knud Poulsen. "Intragenomic recombination in the highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans." Microbiology 151, no. 10 (2005): 3371–79. http://dx.doi.org/10.1099/mic.0.28193-0.

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The highly leukotoxic JP2 clone of Actinobacillus actinomycetemcomitans is strongly associated with aggressive periodontitis in adolescents of African descent. DNA fingerprinting using the frequently cutting restriction enzyme MspI and multilocus sequence typing (MLST) showed that five strains of this clone were genetically virtually identical, although ribotyping of the six rrn genes and EcoRI RFLP analysis of the seven IS150-like elements revealed differences. PCR analyses demonstrated that these multi-copy sequences are subject to intragenomic homologous recombination, resulting in transloc

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7

Searle, Jeremy B., and Fernando Pardo-Manuel de Villena. "Meiotic Drive and Speciation." Annual Review of Genetics 58, no. 1 (2024): 341–63. http://dx.doi.org/10.1146/annurev-genet-111523-102603.

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Meiotic drive is the biased transmission of alleles from heterozygotes, contrary to Mendel's laws, and reflects intragenomic conflict rather than organism-level Darwinian selection. Theory has been developed as to how centromeric properties can promote female meiotic drive and how conflict between the X and Y chromosomes in males can promote male meiotic drive. There are empirical data that fit both the centromere drive and sex chromosome drive models. Sex chromosome drive may have relevance to speciation through the buildup of Dobzhansky-Muller incompatibilities involving drive and suppressor

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8

Kang, Josephine, and Martin J. Blaser. "UvrD Helicase Suppresses Recombination and DNA Damage-Induced Deletions." Journal of Bacteriology 188, no. 15 (2006): 5450–59. http://dx.doi.org/10.1128/jb.00275-06.

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ABSTRACT UvrD, a highly conserved helicase involved in mismatch repair, nucleotide excision repair (NER), and recombinational repair, plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species. In this report, we focus on the UvrD homolog in Helicobacter pylori, a genetically diverse organism that lacks many known DNA repair proteins, including those involved in mismatch repair and recombinational repair, and that is noted for high levels of inter- and intragenomic recombination and mutation. H. pylori contains numerous DNA repeats in

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9

Tomaszewska, Paulina, and Romuald Kosina. "Cytogenetic events in the endosperm of amphiploid Avena magna × A. longiglumis." Journal of Plant Research 134, no. 5 (2021): 1047–60. http://dx.doi.org/10.1007/s10265-021-01314-3.

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AbstractThis study analysed cytogenetic events occurring in the syncytial endosperm of the Avena magna H. C. Murphy & Terrell × Avena longiglumis Durieu amphiploid, which is a product of two wild species having different genomes. Selection through the elimination of chromosomes and their fragments, including those translocated, decreased the level of ploidy in the endosperm below the expected 3n, leading to the modal number close to 2n. During intergenomic translocations, fragments of the heterochromatin-rich C-genome were transferred to the D and Al genomes. Terminal and non-reciprocal ex

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10

Amosova, Alexandra V., Alexander A. Gnutikov, Alexander V. Rodionov, et al. "Genome Variability in Artificial Allopolyploid Hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu Based on Marker Sequences of Satellite DNA and the ITS1–5.8S rDNA Region." International Journal of Molecular Sciences 25, no. 10 (2024): 5534. http://dx.doi.org/10.3390/ijms25105534.

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Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S–ITS1–5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes

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11

Miller, William G., Emma Yee, and James L. Bono. "Complete Genome Sequencing of Four Arcobacter Species Reveals a Diverse Suite of Mobile Elements." Genome Biology and Evolution 12, no. 2 (2020): 3850–56. http://dx.doi.org/10.1093/gbe/evaa014.

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Abstract Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. por

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12

Kudryavtseva, Tamara Yu, and Alexander N. Mokrievich. "Strategies for tularemia pathogen survival, spread and virulence." Russian Journal of Infection and Immunity 14, no. 1 (2024): 9–23. http://dx.doi.org/10.15789/2220-7619-sft-17576.

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The bacterium Francisella tularensis is the etiological agent of tularemia, a natural focal, especially dangerous infection, which, “thanks to” its low infectious dose and ability to be transmitted to humans via all possible routes, is a potential bioterrorism agent. This pathogen has been known to mankind for over a hundred years, but it is still impossible to prevent massive human disease outbreaks and sporadic incidence cases, whereas tularemia diagnosis may be verified within several days-to-weeks. The basis for tularemia causative agent virulence is based on its ability to disrupt phagocy

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13

Tam, Yi Ling, Sarah Cameron, Andrew Preston, and Lauren Cowley. "GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events." Microbial Genomics 10, no. 7 (2024). http://dx.doi.org/10.1099/mgen.0.001268.

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The use of k-mers to capture genetic variation in bacterial genome-wide association studies (bGWAS) has demonstrated its effectiveness in overcoming the plasticity of bacterial genomes by providing a comprehensive array of genetic variants in a genome set that is not confined to a single reference genome. However, little attempt has been made to interpret k-mers in the context of genome rearrangements, partly due to challenges in the exhaustive and high-throughput identification of genome structure and individual rearrangement events. Here, we present GWarrange, a pre- and post-bGWAS processin

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14

Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, et al. "High Rates of Genome Rearrangements and Pathogenicity of Shigella spp." Frontiers in Microbiology 12 (April 12, 2021). http://dx.doi.org/10.3389/fmicb.2021.628622.

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Shigellaare pathogens originating within theEscherichialineage but frequently classified as a separate genus.Shigellagenomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes ofE. coliandShigellastrains to assess the contribution of genomic rearrangements toShigellaevolution. We found thatShigellaexperienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenicE. coli. The high rearr

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15

Li, Xiaolin, Lijiao Li, Zhijie Bao, et al. "The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement." Frontiers in Microbiology 11 (December 9, 2020). http://dx.doi.org/10.3389/fmicb.2020.591453.

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In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogen

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16

Patarca, Roberto, and William A. Haseltine. "Intragenomic rearrangements involving 5′-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses." Virology Journal 20, no. 1 (2023). http://dx.doi.org/10.1186/s12985-023-01998-0.

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Abstract Background Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5′-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted mo

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17

Liu, Yongbo, Yi Zhou, Feng Cheng, et al. "Chromosome‐level genome of putative autohexaploid Actinidia deliciosa provides insights into polyploidisation and evolution." Plant Journal, December 19, 2023. http://dx.doi.org/10.1111/tpj.16592.

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SUMMARYActinidia (‘Mihoutao’ in Chinese) includes species with complex ploidy, among which diploid Actinidia chinensis and hexaploid Actinidia deliciosa are economically and nutritionally important fruit crops. Actinidia deliciosa has been proposed to be an autohexaploid (2n = 174) with diploid A. chinensis (2n = 58) as the putative parent. A CCS‐based assembly anchored to a high‐resolution linkage map provided a chromosome‐resolved genome for hexaploid A. deliciosa yielded a 3.91‐Gb assembly of 174 pseudochromosomes comprising 29 homologous groups with 6 members each, which contain 39 854 gen

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18

Wang, Hanchen, Deyi Wang, Bingyi Shao, et al. "Unequally Abundant Chromosomes and Unusual Collections of Transferred Sequences Characterize Mitochondrial Genomes of Gastrodia (Orchidaceae), One of the Largest Mycoheterotrophic Plant Genera." Molecular Biology and Evolution, April 7, 2025. https://doi.org/10.1093/molbev/msaf082.

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Abstract The mystery of genomic alternations in heterotrophic plants is among the most intriguing in evolutionary biology. Compared to plastid genomes (plastomes) with parallel size reduction and gene loss, mitochondrial genome (mitogenome) variation in heterotrophic plants remains underexplored in many aspects. To further unravel evolutionary outcomes of heterotrophy, we present a comparative mitogenomic study with 13 de novo assemblies of Gastrodia (Orchidaceae), one of the largest fully mycoheterotrophic plant genera, and its relatives. Analyzed Gastrodia mitogenomes range from 0.56 to 2.1

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