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Ustyantsev K, Biryukov M, Sukhikh I, Shatskaya NV, Fet V, Blinov A, Konopatskaia I. Diversity of <i>mariner</i>-like elements in Orthoptera. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mariner-like elements (MLEs) are among the most widespread DNA transposable elements in eukaryotes. Insects were the first organisms in which MLEs were identified, however the diversity of MLEs in the insect order Orthoptera has not yet been addressed. In the present study, we explore the diversity of MLEs elements in 16 species of Orthoptera belonging to three infraorders, Acridoidea (Caelifera), Grylloidea (Ensifera), and Tettigoniidea (Ensifera) by combining data mined from computational analysis of sequenced degenerative PCR MLE amplicons and available Orthoptera genomic scaffolds. In total, 75 MLE lineages (Ortmar) were identified in all the studied genomes. Automatic phylogeny-based classification suggested that the current known variability of MLEs can be assigned to seven statistically well-supported phylogenetic clusters (I–VII), and the identified Orthoptera lineages were distributed among all of them. The majority of the lineages (36 out of 75) belong to cluster I; 20 belong to cluster VI; and seven, six, four, one and one lineages belong to clusters II, IV, VII, III, and V, respectively. Two of the clusters (II and IV) were composed of a single Orthoptera MLE lineage each (Ortmar37 and Ortmar45, respectively) which were distributed in the vast majority of the studied Orthoptera genomes. Finally, for 16 Orthoptera MLE lineages, horizontal transfer from the distantly related taxa belonging to other insect orders may have occurred. We believe that our study can serve as a basis for future researches on the diversity, distribution, and evolution of MLEs in species of other taxa that are still lacking the sequenced genomes.
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Affiliation(s)
| | | | - I. Sukhikh
- Institute of Cytology and Genetics, SB RAS
| | | | | | - A. Blinov
- Institute of Cytology and Genetics, SB RAS; Institute of Molecular and Cellular Biology, SB RAS
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Wright K, Beck KM, Debnath S, Amini JM, Nam Y, Grzesiak N, Chen JS, Pisenti NC, Chmielewski M, Collins C, Hudek KM, Mizrahi J, Wong-Campos JD, Allen S, Apisdorf J, Solomon P, Williams M, Ducore AM, Blinov A, Kreikemeier SM, Chaplin V, Keesan M, Monroe C, Kim J. Benchmarking an 11-qubit quantum computer. Nat Commun 2019; 10:5464. [PMID: 31784527 PMCID: PMC6884641 DOI: 10.1038/s41467-019-13534-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/13/2019] [Indexed: 11/23/2022] Open
Abstract
The field of quantum computing has grown from concept to demonstration devices over the past 20 years. Universal quantum computing offers efficiency in approaching problems of scientific and commercial interest, such as factoring large numbers, searching databases, simulating intractable models from quantum physics, and optimizing complex cost functions. Here, we present an 11-qubit fully-connected, programmable quantum computer in a trapped ion system composed of 13 171Yb+ ions. We demonstrate average single-qubit gate fidelities of 99.5\documentclass[12pt]{minimal}
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\begin{document}$$\%$$\end{document}%. To illustrate the capabilities of this universal platform and provide a basis for comparison with similarly-sized devices, we compile the Bernstein-Vazirani and Hidden Shift algorithms into our native gates and execute them on the hardware with average success rates of 78\documentclass[12pt]{minimal}
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\begin{document}$$\%$$\end{document}%, respectively. These algorithms serve as excellent benchmarks for any type of quantum hardware, and show that our system outperforms all other currently available hardware. The growing complexity of quantum computing devices makes presents challenges for benchmarking their performance as previous, exhaustive approaches become infeasible. Here the authors characterise the quality of their 11-qubit device by successfully computing two quantum algorithms.
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Affiliation(s)
- K Wright
- IonQ, Inc., College Park, MD, 20740, USA.
| | - K M Beck
- IonQ, Inc., College Park, MD, 20740, USA
| | - S Debnath
- IonQ, Inc., College Park, MD, 20740, USA
| | - J M Amini
- IonQ, Inc., College Park, MD, 20740, USA
| | - Y Nam
- IonQ, Inc., College Park, MD, 20740, USA
| | - N Grzesiak
- IonQ, Inc., College Park, MD, 20740, USA
| | - J-S Chen
- IonQ, Inc., College Park, MD, 20740, USA
| | | | - M Chmielewski
- IonQ, Inc., College Park, MD, 20740, USA.,Joint Quantum Institute and Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - C Collins
- IonQ, Inc., College Park, MD, 20740, USA
| | - K M Hudek
- IonQ, Inc., College Park, MD, 20740, USA
| | - J Mizrahi
- IonQ, Inc., College Park, MD, 20740, USA
| | | | - S Allen
- IonQ, Inc., College Park, MD, 20740, USA
| | - J Apisdorf
- IonQ, Inc., College Park, MD, 20740, USA
| | - P Solomon
- IonQ, Inc., College Park, MD, 20740, USA
| | - M Williams
- IonQ, Inc., College Park, MD, 20740, USA
| | - A M Ducore
- IonQ, Inc., College Park, MD, 20740, USA
| | - A Blinov
- IonQ, Inc., College Park, MD, 20740, USA
| | | | - V Chaplin
- IonQ, Inc., College Park, MD, 20740, USA
| | - M Keesan
- IonQ, Inc., College Park, MD, 20740, USA
| | - C Monroe
- IonQ, Inc., College Park, MD, 20740, USA.,Joint Quantum Institute and Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - J Kim
- IonQ, Inc., College Park, MD, 20740, USA.,Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
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Guryev V, Makarevitch I, Blinov A, Martin J. Phylogeny of the genus Chironomus (Diptera) inferred from DNA sequences of mitochondrial cytochrome b and cytochrome oxidase I. Mol Phylogenet Evol 2001; 19:9-21. [PMID: 11286487 DOI: 10.1006/mpev.2001.0898] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two mitochondrial genes, Cytochrome b (Cytb) and Cytochrome c oxidase subunit I (COI), have been used as phylogenetic markers in Chironomids. The nucleotide sequences of 685 bp from Cytb and 596 bp from COI have been determined for 36 Chironomus species from the Palearctic, or Holarctic, and Australasia. The concatenated sequence of 1281 bp from both genes was used to investigate the phylogenetic relationships among these species. The nucleotide sequence alignments were used for construction of phylogenetic trees based on maximum-parsimony and neighbor-joining methods. Both techniques produced similar phylogenies. Monophyly of the genus Chironomus is supported by a bootstrap value of 100% at the basal branch. Six clusters of species have been revealed with high bootstrap values supporting both monophyly of each cluster and the validity of the branching order within each cluster. Four species, C. circumdatus, C. nepeanensis, C. dorsalis, and C. crassiforceps, cannot be placed into any cluster. Cytological phylogenies were constructed using the same set of species, except for C. biwaprimus. These trees showed many similarities to that obtained from the mitochondrial (mt) sequence analysis, but also a number of significant differences. When compared with the tree constructed from the sequence of 23 species available for one of the globin genes, globin 2b (gb2b), there was better support for the mt tree than for the cytological trees. An intron, which varies in its occurrence and position in gb2b, was also investigated and the distribution of the introns supports the phylogenetic history of the genus Chironomus obtained with mt data. The differences observed in the cytological trees seem to be attributable more to the retention of the same chromosome banding sequence across several species, rather than convergent evolutionary events. An important question is the determination of the position of the subgenus Camptochironomus in relation to the representatives of the nominal subgenus Chironomus, since it has been suggested that this is a separate genus. The Camptochironomus species are internal to the trees and have arisen more recently than some of the species of the subgenus Chironomus, indicating that they are not sufficiently differentiated to be considered more than a subgenus.
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Affiliation(s)
- V Guryev
- Laboratory of Cell Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
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Gruhl MC, Scherbik SV, Aimanova KG, Blinov A, Diez J, Bergtrom G. Insect globin gene polymorphisms: intronic minisatellites and a retroposon interrupting exon 1 of homologous globin genes in Chironomus (Diptera). Gene 2000; 251:153-63. [PMID: 10876092 DOI: 10.1016/s0378-1119(00)00197-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Exon 1 of globin gene ct-13RT in clone lambdagb2-1 from Chironomus thummi contains a 444nt SINE (CTRT1). Based on in situ hybridization to polytene salivary gland chromosomes, C. thummi (ct), C. piger (cp) and C. tentans (ctn) contain copies of CTRT1 at multiple chromosomal loci. Genomic PCR amplifications reveal interrupted (ct-13RT) and uninterrupted (ct-13) alleles of the globin gene in the German population of C. thummi maintained in our laboratory, and only uninterrupted alleles or their homologs in different populations of C. thummi, C. piger and C. tentans. PCR amplification did generate different length fragments from cp-13 gene homologs in natural and laboratory C. piger populations that were due to variation in the length of minisatellite expansions of the central introns of the genes rather than a CTRT1-like SINE. Within minisatellite arrays, aligned homologs were more similar than paralogs in a single population, indicating that a tandem cluster of these repeats predated separation of the C. piger populations. The ct-13 genes of several C. thummi populations lack the minisatellites, suggesting their origin in C. piger only after the thummi/piger split. CTRT1 transposition into a ct-13 allele is even more recent, occurring after separation of German and other European C. thummi populations. The nearly intact ct-13RT and comparison with its intact ct-13 allele support a very recent transposition of the CTRT1 SINE into one of at least two already diverged ct-13 globin gene alleles. PCR analysis of DNA from individual adults in C. thummi shows a 1:2:1 distribution of ct-13/ct-13:ct-13/ct-13RT:ct-13RT/ct-13RT genotypes, consistent with a neutral spread of the ct-13RT allele since transposition, and indicating that the hemoglobin encoded by ct-13 is not necessary for survival, at least in a laboratory population of C. thummi.
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Affiliation(s)
- M C Gruhl
- Department of Biological Sciences, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, WI 53201, USA
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