Relevant bibliographies by topics / Gene order rearrangements

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters

Academic literature on the topic 'Gene order rearrangements'

Author: Grafiati
Published: 2 June 2025
Last updated: 31 July 2025

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Journal articles on the topic "Gene order rearrangements"

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Zheng, Chen-Guang, Zheng Liu, Yan-Min Zhao, et al. "First Report on Mitochondrial Gene Rearrangement in Non-Biting Midges, Revealing a Synapomorphy in Stenochironomus Kieffer (Diptera: Chironomidae)." Insects 13, no. 2 (2022): 115. http://dx.doi.org/10.3390/insects13020115.

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(1) Background: Gene rearrangement of mitochondrial genome, especially those with phylogenetic signals, has long fascinated evolutionary biologists. The synapomorphic gene rearrangements have been identified across multiple orders and at many different taxonomic levels, supporting the monophyletic or systematic relationships of related lineages. However, mitochondrial gene rearrangement has never been observed in the non-biting midges (Diptera: Chironomidae); (2) methods: in this study, the complete mitogenomes of seven Stenochironomus species were sequenced and analyzed for the first time; (3
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Yuan, Siqi, Yun Xia, Yuchi Zheng, and Xiaomao Zeng. "Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri." PeerJ 4 (December 15, 2016): e2786. http://dx.doi.org/10.7717/peerj.2786.

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Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order,Amolops chunganensisandQuasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced throug
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Piper, Hannah, Samuel Litwin, and Ramit Mehr. "Models for Antigen Receptor Gene Rearrangement. II. Multiple Rearrangement in the TCR: Allelic Exclusion or Inclusion?" Journal of Immunology 163, no. 4 (1999): 1799–808. http://dx.doi.org/10.4049/jimmunol.163.4.1799.

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Abstract This series of papers addresses the effects of continuous Ag receptor gene rearrangement in lymphocytes on allelic exclusion. The previous paper discussed light chain gene rearrangement and receptor editing in B cells, and showed that these processes are ordered on three different levels. This order, combined with the constraints imposed by a strong negative selection, was shown to lead to effective allelic exclusion. In the present paper, we discuss rearrangement of TCR genes. In the TCR α-chain, allelic inclusion may be the rule rather than the exception. Several previous models, wh
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Graninger, W. B., P. L. Goldman, C. C. Morton, S. J. O'Brien, and S. J. Korsmeyer. "The kappa-deleting element. Germline and rearranged, duplicated and dispersed forms." Journal of Experimental Medicine 167, no. 2 (1988): 488–501. http://dx.doi.org/10.1084/jem.167.2.488.

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Human light chain genes are used in a kappa before lambda order. Accompanying this hierarchy is the rearrangement of a kappa-deleting element (Kde) which eliminates the kappa locus before lambda gene rearrangement. In approximately 60% of rearrangements the Kde recombines at a conserved heptamer within the J kappa-C kappa intron. We demonstrated that aberrant V/J rearrangements possessing apparent "N" nucleotides existed 5' to the J kappa-Kde rearrangements. This suggests that the Kde may selectively eliminate nonfunctional V/J alleles. A kappa-producing cell that displayed the unusual finding
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Zhang, Yu, Lu Qi, Fengping Li, et al. "Mitogenomic Analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the Evolution of the Gene Rearrangements." Fishes 8, no. 10 (2023): 528. http://dx.doi.org/10.3390/fishes8100528.

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The complete mitogenomes of Pinctada albina and Pinctada margaritifera were sequenced in this study, with sizes of 23,841 bp and 15,556 bp, respectively. The mitochondrial genome analysis of eight Pterioidea species indicated the existence of gene rearrangements within the superfamily. The ATP8 gene was not detected in the two new mitogenomes, and rrnS was found to be duplicated in P. albina’s mitogenome. The reconstructed phylogeny based on mitogenomes strongly supported the monophyly of Pterioidea and provided robust statistical evidence of the phylogenetic relationships within Pteriomorphia
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Swenson, Krister M., and Mathieu Blanchette. "Large-scale mammalian genome rearrangements coincide with chromatin interactions." Bioinformatics 35, no. 14 (2019): i117—i126. http://dx.doi.org/10.1093/bioinformatics/btz343.

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Abstract Motivation Genome rearrangements drastically change gene order along great stretches of a chromosome. There has been initial evidence that these apparently non-local events in the 1D sense may have breakpoints that are close in the 3D sense. We harness the power of the Double Cut and Join model of genome rearrangement, along with Hi-C chromosome conformation capture data to test this hypothesis between human and mouse. Results We devise novel statistical tests that show that indeed, rearrangement scenarios that transform the human into the mouse gene order are enriched for pairs of br
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Cunha, Regina L., Katy R. Nicastro, Gerardo I. Zardi, et al. "Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus." PeerJ 10 (September 26, 2022): e13953. http://dx.doi.org/10.7717/peerj.13953.

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Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods To confirm the proposed gene rearrangements, we seque
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Xing, Zhi-Ping, Xin Liang, Xu Wang, Hao-Yuan Hu, and Yi-Xin Huang. "Novel gene rearrangement pattern in mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994: new gene order in Encyrtidae (Hymenoptera, Chalcidoidea)." ZooKeys 1124 (October 10, 2022): 1–21. https://doi.org/10.3897/zookeys.1124.83811.

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Studies of mitochondrial genomes have a wide range of applications in phylogeny, population genetics, and evolutionary biology. In this study, we sequenced and analyzed the mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994 (Hymenoptera, Encyrtidae). The nearly complete mitogenome of O. plautus was 15,730 bp in size, including 13 PCGs (protein-coding genes), 22 tRNAs, 2 rRNAs, and a nearly complete control region. The nucleotide composition was significantly biased toward adenine and thymine, with an A + T content of 84.6%. We used the reference sequence of Chouioia cunea and c
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Dowton, M., L. R. Castro, and A. D. Austin. "Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'." Invertebrate Systematics 16, no. 3 (2002): 345. http://dx.doi.org/10.1071/is02003.

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Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only
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Morley, Alexander A., Michael J. Brisco, Pamela J. Sykes, et al. "The Repertoire of Gene Rearrangements in Acute Lymphoblastic Leukemia." Blood 106, no. 11 (2005): 1464. http://dx.doi.org/10.1182/blood.v106.11.1464.1464.

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Abstract Rearrangements of the immunoglobulin and T-cell receptor genes provide molecular markers for clones in acute lymphoblastic leukemia (ALL). Determination of the repertoire of gene rearrangements in ALL aids in understanding the clonal biology of the disease and provides molecular markers which can be used to quantify minimal residual disease (MRD). We have developed a sensitive PCR-based method for analysing the repertoire of immunoglobulin heavy chain (IgH) rearrangements in ALL. Multiple parallel quantitative PCR’s are performed in microplates using different segment-specific primers
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Dissertations / Theses on the topic "Gene order rearrangements"

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Bernt, Matthias. "Gene order rearrangement methods for the reconstruction of phylogeny." Doctoral thesis, Universitätsbibliothek Leipzig, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-38666.

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The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explan
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Bernt, Matthias. "Gene order rearrangement methods for the reconstruction of phylogeny." Doctoral thesis, 2009. https://ul.qucosa.de/id/qucosa%3A11029.

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The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explan
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Bernt, Matthias [Verfasser]. "Gene order rearrangement methods for the reconstruction of phylogeny / vorgelegt von Matthias Bernt." 2010. http://d-nb.info/1006689540/34.

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Benzaid, Billel. "Évolution des génomes par mutations locales et globales : une approche d’alignement." Thèse, 2016. http://hdl.handle.net/1866/18470.

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Durant leur évolution, les génomes accumulent des mutations pouvant affecter d’un nucléotide à plusieurs gènes. Les modifications au niveau du nombre et de l’organisation des gènes dans les génomes sont dues à des mutations globales, telles que les duplications, les pertes et les réarrangements. En comparant les ordres de gènes des génomes, il est possible d’inférer les événements évolutifs les plus fréquents, le contenu en gènes des espèces ancestrales ainsi que les histoires évolutives ayant menées aux ordres observés. Dans cette thèse, nous nous intéressons au développement de nouvelles
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Book chapters on the topic "Gene order rearrangements"

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Fertin, Guillaume, Géraldine Jean, and Eric Tannier. "Genome Rearrangements on Both Gene Order and Intergenic Regions." In Lecture Notes in Computer Science. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-43681-4_13.

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Watson, Geoffrey Alan, Kirsty Taylor, and Lillian L. Siu. "Innovation and Advances in Precision Medicine in Head and Neck Cancer." In Critical Issues in Head and Neck Oncology. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-63234-2_24.

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AbstractThe clinical utility of precision medicine through molecular characterization of tumors has been demonstrated in some malignancies, especially in cases where oncogenic driver alterations are identified. Next generation sequencing data from thousands of patients with head and neck cancers have provided vast amounts of information about the genomic landscape of this disease. Thus far, only a limited number of genomic alterations have been druggable, such as NTRK gene rearrangements in salivary gland cancers (mainly mammary analogue secretory carcinoma), NOTCH mutations in adenoid cystic
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abrouk, Nadia El-M. "Genome Rearrangements with Gene Families." In Mathematics of Evolution and Phylogeny. Oxford University PressOxford, 2005. http://dx.doi.org/10.1093/oso/9780198566106.003.0011.

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Abstract The genome rearrangement approach to comparative genomics infers divergence history in terms of global genomic mutations. The major focus in the last decades has been to infer the most economical scenario of elementary operations transforming one linear order of genes into another. Implicit in most of these studies is that each gene has exactly one copy in each genome. This hypothesis is clearly unsuitable for divergent species containing several copies of highly analogous gene, for example, multigame families. In this chapter, we review the different algorithmic methods that have bee
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Sankoff, David. "Conserved Segment Statistics and Rearrangement Inferences in Comparative Genomics." In Mathematics of Evolution and Phylogeny. Oxford University PressOxford, 2005. http://dx.doi.org/10.1093/oso/9780198566106.003.0009.

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Abstract ‘l’he statistical treatment of chromosomal rearrangement has evolved along with the biological methods for producing pertinent data. We trace the development of conserved segment sta.tistics1 from the mouse linkage/human chromosome assignment data analysed by Nadeau and Taylor in 1984, through the comparative gene-order information on organelles (late 1980s) and prokaryotes (mid-1990s), to higher eukaryote genome sequences, whose rearrangements have been studied without prior gene identification. Each new type of data suggested new questions and led to new analyses. We focus on the pr
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White, P. Scott, Owatha L. Tatum, Hakan Tegelstrom, and Llewellyn D. Densmore III. "Mitochondrial DNA isolation, separation, and detection of fragments." In Molecular Genetic Analysis of Populations. Oxford University PressOxford, 1998. http://dx.doi.org/10.1093/oso/9780199636341.003.0003.

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Abstract The 'revolution' that began in the 1980s with the application of mitochondrial DNA (mtDNA) analyses to address questions of molecular evolutionary and population biology has now largely become the paradigm for such work (1). Studies ranging in scope from purely systematic problems to identification and recognition of species to documentation of genetic changes in populations that have occurred over a very short period of time, are based on both indirect or direct estimates of nucleic acid variation. While progress continues to be made in analysing coding regions of nuclear DNA, the se
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Tümmler, and Burkhard. "Long-range restriction mapping of genomic DNA." In Genome Mapping. Oxford University PressOxford, 1997. http://dx.doi.org/10.1093/oso/9780199636310.003.0012.

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Abstract Long-range restriction maps are important tools to determine the arrangement and distance of gene markers, and a prerequisite before committing oneself to costly and time-consuming cloning and sequencing projects in order to identify gene organization and rearrangements. For the construction of a low-resolution physical map of a genome or chromosomal region, the intact DNA is digested with a restriction endonuclease that cleaves infrequently and the fragments are separated by pulsed-field gel electrophoresis (PFGE) (1, 2). Restriction fragment patterns of small genomes, such as those
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"Molecular markers for cancer risk assessment, biodosimetry, and optimizing radiotherapy." In Book of Abstracts - RAD 2025 Conference. RAD Centre, Niš, Serbia, 2025. https://doi.org/10.21175/rad.abstr.book.2025.38.5.

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Our department elaborates effects of ionizing and non-ionizing radiations on genetic instability in human cells with focus on hematological stem cells. An effect of radiations on origination of leukemia, molecular mechanisms in etiology of leukemia and new approaches in prevention, treatments, and diagnostics of leukemia are being investigated. DNA damage response, circular and microRNA, gene and chromosome rearrangements, gene expression, and apoptosis are the main endpoints studied by the state-of-the-art techniques including automated fluorescent and imaging microscopy, DNA repair foci and
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Leach, David R. F. "Molecular processing of DNA folding anoinalies in Escherichia coli." In DNA Recombination and Repair. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780199637072.003.0001.

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Abstract For evolution to proceed, there must be a balance between genetic stability and rearrangement. Chromosomal arrangements that prove beneficial to an organism are expected to be maintained while retaining the potential to generate radically new organizations over an evolutionary time-scale. In order to maintain this balance, cells have evolved mechanisms to reduce the frequency of chromosomal rearrangements. An important threat to DNA stability comes from sequences that have the potential for unusual folding. Unusually folded DNAs also pose problems for DNA replication, which may be par
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Ferris, David. "Schumann’s Process of Composing a Cycle." In Echumann’s Eichendorff Liederkreil and the Genre of the Romantic Cycle. Oxford University PressNew York, NY, 2000. http://dx.doi.org/10.1093/oso/9780195124477.003.0007.

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Abstract The Eichendorff Liederlcrei.J provides us with an especially good opportunity to reevaluate the way in which we conceive Schumann’s song cycles, because there are two related circumstances concerning its genesis that have challenged our traditional assumptions about the genre. First, the poems that Schumann set were selected by Clara Wieck from Eichendorff’s collected edition and were never intended by the poet as a cycle. Second, the only complete set of manuscript sources that survives for the songs reveals that the order in which Schumann composed them bears virtually no relationsh
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