Double Copies Research Articles

Characterization of the complete chloroplast genome of Juniperus microsperma (Cupressaceae), a rare endemic from the Qinghai-Tibet Plateau

The complete chloroplast genome of Juniperus microsperma, a rare endemic conifer from the Qinghai-Tibet Plateau whose current status satisfies the IUCN Red List criteria of endangered species, was determined in this study. The genome size is 127,409 bp in length. The genome contained 119 genes, including 82 protein-coding genes, four ribosomal RNA genes and 33 transfer RNA genes. The most of genes occur as a single copy, while two genes occur in double copies (trnL-CAU and trnQ-UUG). In these genes, eight genes (atpF, ndhA, ndhB, rpoC1, petD, petB, rpl16 and rpl2) have a single intron, while two genes (rps12 and ycf3) harbor two introns. There are no inverted repeat sequences in this genome. The GC content of this cp genome is 35.0%. Phylogenomic analysis revealed a close relationship among J. microsperma, J. virginiana, J. scopulorum and J. bermudiana.

Complete chloroplast genome sequence of Rosa roxburghii and its phylogenetic analysis

Rosa roxburghii Tratt. is a famous Chinese traditional medicine with long history, here we characterized the whole chloroplast (cp) genome sequence of R. roxburghii by Illumina pair-end sequencing. The complete cp genome was 156,749 bp in length, containing a large single copy (LSC) region of 85,862 bp and a small single copy (SSC) region of 18,791 bp, which were separated by a pair of 26,053 bp inverted repeat regions (IRs). The genome contained 139 genes, including 88 protein-coding genes (82 PCG species), 39 tRNA genes (32 tRNA species), and eight ribosomal RNA genes (four rRNA species). Most of the gene species occur as a single copy, while 17 gene species occur in double copies. The overall AT content of R. roxburghii cp genome is 62.8%, while the corresponding values of the LSC, SSC, and IR regions are 64.8, 68.7, and 57.4%, respectively. Further, phylogenetic analysis suggested that R. roxburghii is closely related to R. odorata var. gigantea.

Two-exposure quasi-common-path point diffraction interferometric phase microscopy using a four-step algorithm

A two-exposure nearly common-path point diffraction interferometric phase microscopy (IPM) is presented using polarization modulation and one-step grating shifting to implement quantitative phase imaging. The IPM is constructed by an improved Michelson configuration with a reflective grating, and its frequency spectrum generated by a circularly polarized object beam makes double copies through a beam splitter. One copy is low-pass filtered and reflected by a reflective pinhole mirror to create a reference beam, and the other copy is converted by a polarizer and then reflected by a reflective grating to achieve a 45° linearly polarized object beam. By the combination of a polarizing cube beam splitter with 45° tilted angle and a translation of the reflective grating with a π phase shift, four interferograms with π/2 phase shift can be obtained in two exposures. The standard four-step algorithm can then be used to reconstruct the phase of the specimen. The utility of the proposed method was demonstrated with measurements on a phase plate, cells and an oil drop.

Scattering on plane waves and the double copy

Perturbatively around flat space, the scattering amplitudes of gravity are related to those of Yang–Mills by colour-kinematic duality, under which gravitational amplitudes are obtained as the ‘double copy’ of the corresponding gauge theory amplitudes. We consider the question of how to extend this relationship to curved scattering backgrounds, focusing on certain ‘sandwich’ plane waves. We calculate the 3-point amplitudes on these backgrounds and find that a notion of double copy remains in the presence of background curvature: graviton amplitudes on a gravitational plane wave are the double copy of gluon amplitudes on a gauge field plane wave. This is non-trivial in that it requires a non-local replacement rule for the background fields and the momenta and polarization vectors of the fields scattering on the backgrounds. It must also account for new ‘tail’ terms arising from scattering off the background. These encode a memory effect in the scattering amplitudes, which naturally double copies as well.

The Kerr-Schild double copy in curved spacetime

The double copy is a much-studied relationship between scattering amplitudes in gauge and gravity theories, that has subsequently been extended to classical field solutions. In nearly all previous examples, the graviton field is defined around Minkowski space. Recently, it has been suggested that one may set up a double copy for gravitons defined around a non-trivial background. We investigate this idea from the point of view of the classical double copy. First, we use Kerr-Schild spacetimes to construct graviton solutions in curved space, as double copies of gauge fields on non-zero gauge backgrounds. Next, we find that we can reinterpret such cases in terms of a graviton on a non-Minkowski background, whose single copy is a gauge field in the same background spacetime. The latter type of double copy persists even when the background is not of Kerr-Schild form, and we provide examples involving conformally flat metrics. Our results will be useful in extending the remit of the double copy, including to possible cosmological applications.

Genetic evaluation for birth and conformation traits in dual-purpose Belgian Blue cattle using a mixed inheritance model.

The segregation of the causal mutation () in the muscular hypertrophy gene in dual-purpose Belgian Blue (dpBB) cattle is considered to result in greater calving difficulty (dystocia). Establishing adapted genetic evaluations might overcome this situation through efficient selection. However, the heterogeneity of dpBB populations at the locus implies separating the major gene and other polygenic effects in complex modeling. The use of mixed inheritance models may be an interesting option because they simultaneously assume both influences. A genetic evaluation in dpBB based on a mixed inheritance model was developed for birth and conformation traits: gestation length (GL), calving difficulty (CD), birth weight (BiW), and body conformation score (BC). A total of 27,362 animals having records were used for analyses. The total number of animals in the pedigree used to build the numerator relationship matrix was 62,617. Genotypes at the locus were available for 2,671 animals. Missing records at this locus were replaced with genotype probabilities. A total of 13,221 (48.3%) were registered as dpBB, 1,287 (4.7%) as beef Belgian Blue, and 12,854 (47.0%) were unknown. From those 13,221 dpBB animals, 650, 849, and 534 had double or single copies or no copy, respectively, of the causal mutation () in the muscular hypertrophy gene, whereas 11,188 had missing genotypes. This heterogeneity at the locus may be the reason for high variability in the studied traits, that is, high heritability estimates of 0.33, 0.30, 0.38, and 0.43 for GL, CD, BiW, and BC, respectively. In general, additive ( < 0.05) and dominance ( < 0.001) allele substitution for calves and dams had significant impact for all traits. The moderate coefficient of genetic variation (27.80%) and high direct heritability (0.28) for CD suggested genetic variability in dpBB and possible genetic improvement through selection. This variability has allowed dpBB breeders to successfully apply mass selection in the past. Genetic trend means from 1988 to 2016 showed that sire selection for CD within genotype was progressively applied by breeders. The selection intensity was more important for CD in double-muscled lines than in segregated lines. Our study illustrated the possible confusion caused by the use of major genes in selection and the importance of fitting appropriate models such as mixed inheritance models that combine polygenic and gene content information.

The complete chloroplast genome sequence of an economic plant Coffea canephora

Coffea canephora is a paramount economic plant with great economic value. The complete chloroplast (cp) genome is 154,751 bp in length, including a large single copy (LSC) region of 84,850 bp, a small single copy (SSC) region of 18,131 bp and a pair of inverted repeats (IRs) of 25,885bp. This cp genome contains 131 genes, comprising of 86 protein-coding genes, 37 tRNAs and 8 rRNAs. The majority of these genes were single copy genes, while 18 genes existed as double copies, including 6 protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7 and ycf2), 8 tRNA genes (trnA-UGC, trnG-GCC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG and trnV-GAC) and 4 rRNA genes (rrn4.5, rrn5, rrn16 and rrn23). A neighbour-joining phylogenetic tree was reconstructed to indicate that Coffea canephora is evolutionarily close to Olea europaea within Asterids. The complete cp genome will provide intragenic information for molecular phylogeny and biological studies of the Rubiales.

Spontaneously broken Yang-Mills-Einstein supergravities as double copies

Color/kinematics duality and the double-copy construction have proved to be systematic tools for gaining new insight into gravitational theories. Extending our earlier work, in this paper we introduce new double-copy constructions for large classes of spontaneously-broken Yang-Mills-Einstein theories with adjoint Higgs fields. One gauge-theory copy entering the construction is a spontaneously-broken (super-)Yang-Mills theory, while the other copy is a bosonic Yang-Mills-scalar theory with trilinear scalar interactions that display an explicitly-broken global symmetry. We show that the kinematic numerators of these gauge theories can be made to obey color/kinematics duality by exhibiting particular additional Lie-algebraic relations. We discuss in detail explicit examples with mathcal{N}=2 supersymmetry, focusing on Yang-Mills-Einstein supergravity theories belonging to the generic Jordan family in four and five dimensions, and identify the map between the supergravity and double-copy fields and parameters. We also briefly discuss the application of our results to mathcal{N}=4 supergravity theories. The constructions are illustrated by explicit examples of tree-level and one-loop scattering amplitudes.

Characterization of the complete chloroplast genome of the invasive weed Galinsoga quadriradiata (Asterales: Asteraceae)

Galinsoga quadriradiata is an invasive weed in many parts of the world, and are causing serious damages to local biodiversity and agriculture. In this study, its complete chloroplast genome was assembled from the whole-genome Illumina sequencing data. The circular genome is 151,917 bp long, and comprises a pair of inverted repeat regions (IRs, 25,041 bp each), a large single-copy region (LSC, 83,620 bp) and a small single-copy region (SSC, 18,215 bp). It encodes a total of 111 gene species (80 protein-coding, 27 tRNA and four rRNA species), with 21 of them occurring in double copies. Introns were detected in ten PCG and six tRNA species. The nucleotide composition is asymmetric (31.07% A, 18.58% C, 19.08% G & 31.27% T) with an overall A + T content of 62.34%. Phylogenetic analysis challenged the traditional taxonomic framework of the family Asteraceae, and indicated that G. quadriradiata was relatively close to Guizotia abyssinica in phylogeny.

Gravity Amplitudes as Generalized Double Copies of Gauge-Theory Amplitudes.

Whenever the integrand of a gauge-theory loop amplitude can be arranged into a form where the Bern-Carrasco-Johansson duality between color and kinematics is manifest, a corresponding gravity integrand can be obtained simply via the double-copy procedure. However, finding such gauge-theory representations can be challenging, especially at high loop orders. Here, we show that we can, instead, start from generic gauge-theory integrands, where the duality is not manifest, and apply a modified double-copy procedure to obtain gravity integrands that include contact terms generated by violations of dual Jacobi identities. We illustrate this with three-, four- and five-loop examples in N=8 supergravity.

Characterization of the complete chloroplast genome of the Tertiary relict tree Phellodendron amurense (Sapindales: Rutaceae) using Illumina sequencing technology

The Amur cork tree (Phellodendron amurense) is an endangered deciduous tree species with high medicinal and economic values. In this study, its complete chloroplast genome was determined using high-throughput Illumina sequencing technology. The cp genome of P. amurense is 158,442 bp in length, and contains a pair of inverted repeat (IR) regions of 26,999 bp each, separated by a large single-copy (LSC) region of 86,160 bp and a small single-copy (SSC) region of 18,284 bp. It encodes 113 gene species (including 79 PCG, 30 tRNA and 4 rRNA species) with 21 of them occurring in double copies. The nucleotide composition is asymmetric (30.5% A, 19.6% C, 18.8% G & 31.1% T) with an overall A+T content of 61.6%. Phylogenetic analysis supports the morpho-taxonomy of the order Sapindales, and indicates that P. amurense is relatively closely related to the genus Zanthoxylum (as represented by Zanthoxylum bungeanum, Zanthoxylum piperitum and Zanthoxylum schinifolium).

Characterization of the complete chloroplast genome of the endangered Przewalskia tangutica Maxim

Przewalskia tangutica Maxim., an endangered medicinal species, is endemic to the Qinghai-Tibetan Plateau of China. In this study, we sequenced and characterized the chloroplast genome of P. tangutica for the first time. The P. tangutica chloroplast genome is 155,569 bp in length, exhibits a typical quadripartite structural organization, consisting of a LSC region of 86,707 bp, two IR regions of 25,287 bp and a SSC region of 18,288 bp. The genome contains 138 complete genes, including 85 protein-coding genes (85 PCG species), 44 tRNA genes (21 tRNA species) and eight rRNA genes (four rRNA species, rrn16S, rrn23S, rrn4.5 S, rrn5S). The most of gene species occur as a single copy, while 18 gene species occur in double copies including eight PCG species, six tRNA species (trnN, trnR, trnA, trnI, trnV, trnL) and all of rRNA species. Further, phylogenetic analysis indicated that P. tangutica clustered together with Scopolia parviflora, and formed a clade with Hyoscyamus niger in the Solanaceae. The whole chloroplast genome of P. tangutica not only provides important insight into conservation and restoration efforts for P. tangutica, but also plays a critical role in phylogenetic and evolution studies of the Solanaceae family. More importantly, it will contribute to the ongoing efforts for maintenance of existing genetic resource in the Qinghai-Tibet Plateau.

Characterization of the complete chloroplast genome of Camptotheca acuminata

The whole chloroplast (cp) genome sequence of Camptotheca acuminata has been characterized from Illumina pair-end sequencing. The complete cp genome was 162,382 bp in length, containing a large single copy region (LSC) of 89,493 bp and a small single copy region (SSC) of 16,540 bp, which were separated by two inverted repeat (IR) regions of 56,648 bp. The genome contained 129 genes, including 83 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall GC content of C. acuminata cp genome is 38%, while the corresponding values of the LSC, SSC and IR regions are 36.2, 32.7 and 42.3%, respectively. Further, phylogenetic analysis suggested that C. acuminata is closely related to the species of Davidia involucrata.

Characterization of the whole chloroplast genome of an endangered species Primula kwangtungensis (Primulaceae)

The complete chloroplast genome (plastome) of Primula kwangtungensis was characterized through Illumina paired-end sequencing. The plastome is circular and 153,757 bp in length, comprising a pair of 25,855 bp inverted repeat regions (IRs) which are separated by a large single copy region (LSC) of 84,479 bp and a small single copy region (SSC) of 17,568 bp. The plastome contains 130 genes, including 85 protein-coding genes (PCGs), 37 tRNA genes and eight ribosomal RNA genes. Of these, seven PCGs, seven tRNA genes and four rRNA genes occur in double copies. The overall AT content of the P. kwangtungensis plastome is 62.9 %, while the corresponding values of the LSC, SSC and IR regions are 65, 69.6 and 57.3 %, respectively. The phylogenetic analysis suggested that the sampled Primula species formed a monophyletic clade, and P. kwangtungensis is closely related to P. sinensis.

Characterization of the complete chloroplast genome of Cycas panzhihuaensis

The whole chloroplast (cp) genome sequence of Cycas panzhihuaensis has been characterized from Illumina pair-end sequencing. The complete cp genome was 162,470 bp in length, containing a large single copy region (LSC) of 88,932 bp and a small single copy region (SSC) of 23,448 bp, which were separated by a pair of 25,045 bp inverted repeat regions (IRs). The genome contained 156 genes, including 109 protein-coding genes (98 PCG species), 39 tRNA genes (32 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 22 gene species occur in double copies. The overall AT content of C. panzhihuaensis cp genome is 60.6 %, while the corresponding values of the LSC, SSC and IR regions are 61.3, 63.5 and 58.0 %, respectively. Further, phylogenetic analysis suggested that C. panzhihuaensis is closely related to the species of C. revoluta.

Complete Construction of Magical, Symmetric, and Homogeneous N=2 Supergravities as Double Copies of Gauge Theories.

We show that scattering amplitudes in magical, symmetric or homogeneous N=2 Maxwell-Einstein supergravities can be obtained as double copies of two gauge theories, using the framework of color-kinematics duality. The left-hand copy is N=2 super-Yang-Mills theory coupled to a hypermultiplet, whereas the right-hand copy is a nonsupersymmetric theory that can be identified as the dimensional reduction of a D-dimensional Yang-Mills theory coupled to P fermions. For generic D and P, the double copy gives homogeneous supergravities. For P=1 and D=7, 8, 10, 14, it gives the magical supergravities. We compute explicit amplitudes, discuss their soft limits, and study the UV behavior at one loop.

Characterization of the complete chloroplast genome of Populus ilicifolia

The whole chloroplast (cp) genome sequence of Populus ilicifolia has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,017 bp in length, containing a large single copy region (LSC) of 85,926 bp and a small single copy region (SSC) of 16,533 bp, which were separated by a pair of 27,780 and 27,778 bp inverted repeat regions (IRs). The genome contained 126 genes, including 82 protein-coding genes (75 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall AT content of P. ilicifolia cp genome is 63.5 %, while the corresponding values of the LSC, SSC and IR regions are 65.7, 69.4 and 58.2 %, respectively. Further, phylogenetic analysis suggested that P. ilicifolia is closely related to P. euphratica.

Characterization of the complete chloroplast genome of Idesia polycarpa

The whole chloroplast (cp) genome sequence of Idesia polycarpa has been characterized from Illumina pair-end sequencing. The complete cp genome was 157,017 bp in length, containing a large single copy region (LSC) of 84,787 bp and a small single copy region (SSC) of 16,512 bp, which were separated by a pair of 27,859 bp inverted repeat regions (IRs). The genome contained 130 genes, including 86 protein-coding genes (77 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 20 gene species occur in double copies. The overall AT content of I. polycarpa cp genome is 63.3 %, while the corresponding values of the LSC, SSC and IR regions are 65.5, 69.4 and 58.1 %, respectively. Further, phylogenetic analysis suggested that I. polycarpa is closely related to the genera of Salix and Populus.

The complete chloroplast genome of the dove tree Davidia involucrata (Nyssaceae), a relict species endemic to China

The dove tree, Davidia involucrate, with its distinguishing pair of white bracts, is endemic to China. Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. involucrata. The D. involucrata cp genome was 169,196 bp long, with 129 genes comprising 83 protein-coding genes (PCG), 40 tRNA genes, and six rRNA genes. The majority of the gene species occurred as a single-copy, while 18 gene species occurred in double copies, including six PCG species (ndhB, rpl2, rpl23, rps7, rps15, and ycf2), eight tRNA species (trnH-GTG, trnL-CAA, trnI-CAT, trnV-GAC, trnL-GAV, trnA-UGC, trnN-GTT, and trnR-ACG) and all four rRNA species (rrn4.5, rrn5, rrn16, and rrn23). A neighbor-joining (NJ) phylogenetic tree was reconstructed with sequences of complete cp, revealing that D. involucrata belongs to the asterids. The complete cp genome of D. involucrata will be useful for further investigations and the conservation of this endemic relict woody plant.

Characterization of the complete chloroplast genome of two sister species of Pugionium (Brassicaceae)

The complete chloroplast genomes from two sister species of Pugionium Gaertn are determined in this study. The genome sizes were 155,002 bp (Pugionium dolabratum) and 154,992 bp (Pugionium cornutum). Both genomes containing a large single copy region of 84 k bp and a small single copy region of 18 k bp, which were separated by a pair of 26,761 bp inverted repeat regions. The cpDNA contained 128 genes, including 83 protein-coding genes (76 PCG species), 37 tRNA genes (30 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. These complete chloroplast genomes can be subsequently used for population genomic studies of Pugionium, and provide valuable insight into conservation and restoration efforts for this endangered species.