Fourfold Sites Research Articles

Oxygen adsorption on spontaneously reconstructed Au(511)

The four-fold site on {100} facets, which are potential catalytic sites on high-curvature gold nanoparticles, is difficult to prepare on a gold single crystal due to surface reconstruction. Here, the Au(511) surface with a high density of step edges and a well-maintained {100} local structure was studied by scanning tunneling microscopy (STM), temperature programmed reaction spectroscopy (TPRS), and density functional theory (DFT) calculations. Annealing at 550 K and 870 K induces reconstruction on the Au(511) surface to a mixture of (311) and (711) micro-terraces. At room temperature and low oxygen coverage, oxygen adsorbs at both three- and four-fold sites on the surface, leading to a well-ordered zig-zag structure. Oxygen atoms cause significant orbital hybridization and a slight displacement of the gold atoms to which they bind. High oxygen coverages induce the formation of clusters, which are not active towards oxidation of isopropanol at room temperature and a pressure of 10−10 mbar. Oxygen adsorption saturates at 1 monolayer (ML), and two separate oxygen recombinative desorption peaks were observed at coverages above 0.11 ML. Our characterization of this surface and the O adsorption structure allows future studies of {100} micro-terraces for oxidation reactions, which contributes to studies on gold-based catalysts with an irregular shape.

Exonic splice regulation imposes strong selection at synonymous sites.

What proportion of coding sequence nucleotides have roles in splicing, and how strong is the selection that maintains them? Despite a large body of research into exonic splice regulatory signals, these questions have not been answered. This is because, to our knowledge, previous investigations have not explicitly disentangled the frequency of splice regulatory elements from the strength of the evolutionary constraint under which they evolve. Current data are consistent both with a scenario of weak and diffuse constraint, enveloping large swaths of sequence, as well as with well-defined pockets of strong purifying selection. In the former case, natural selection on exonic splice enhancers (ESEs) might primarily act as a slight modifier of codon usage bias. In the latter, mutations that disrupt ESEs are likely to have large fitness and, potentially, clinical effects. To distinguish between these scenarios, we used several different methods to determine the distribution of selection coefficients for new mutations within ESEs. The analyses converged to suggest that ∼15%–20% of fourfold degenerate sites are part of functional ESEs. Most of these sites are under strong evolutionary constraint. Therefore, exonic splice regulation does not simply impose a weak bias that gently nudges coding sequence evolution in a particular direction. Rather, the selection to preserve these motifs is a strong force that severely constrains the evolution of a substantial proportion of coding nucleotides. Thus synonymous mutations that disrupt ESEs should be considered as a potentially common cause of single-locus genetic disorders.

Fe incorporation into hydroxyapatite channels by Fe loading and post-annealing

Apatite-type solid solutions with the formula Ca10(PO4)6FexOyHz containing Fe atoms in the channel sites of Ca10(PO4)6(OH)2 were successfully synthesized by impregnation with aqueous solution of Fe, followed by heat treatment at 1150 °C in air and cooling to room temperature. The unit cell volume of Ca10(PO4)6FexOyHz increased with increasing Fe content. The results of structural refinement using powder X-ray diffraction data and Raman spectroscopy suggested that the incorporated Fe ions occupied four-fold sites, away from the center of the channel in the apatite lattice. This method may be useful for synthesizing novel apatite-type functional materials containing transition metals.

Electronic structure, pore size distribution, and sorption characterization of an unusual MOF, {[Ni(dpbz)][Ni(CN)4]}n, dpbz = 1,4-bis(4-pyridyl)benzene

The monoclinic (Ni(L)[Ni(CN)4] (L= 1,4-Bis(4-pyridyl) benzene) compound (defined as Ni-dpbz) is a flexible metal organic framework which assumes a pillared structure with layers defined by 2D Ni[Ni(CN)4]n nets and dpbz ligands as pillars. The structure features an entrapped dpbz ligand that links between the open ends of four-fold Ni sites from two neighboring chains. This arrangement results in an unusual 5-fold pseudo square-pyramid environment for Ni and a significantly long Ni-N distance of 2.369(4) Å. Using Density Functional Theory calculations, the different bonding characteristics between the 5-fold and 6-fold Ni's were determined. We found that there is weak covalent bonding between the 5-fold Ni and N in the entrapped ligand, and the 6-fold Ni-N bonds provide effective electronic conduction. The disordered dimethyl sulfoxide (DMSO) solvent molecules are not bonded to the framework. The material has a single pore with a diameter of 4.1 Å. This pore includes approximately 55% of the total free volume (based on a zero-diameter probe). The accessible pore surface area and pore volume were calculated to be 507 m2/g and 6.99 cm3/kg, respectively. The maximum amount of CO2 that can be accommodated in the pores after DMSO is removed was found to be 204 mg/g, agreeing with the results of adsorption/desorption experiments of about 220 mg/g.

Magnetocrystalline effects on the subsurface hydrogen diffusion in γ-Fe(0 0 1)

The effect of magnetism on hydrogen adsorption and subsurface diffusion through face-centred cubic (fcc) γ-Fe(0 0 1) was investigated using spin-polarised density functional theory (s-DFT). The non-magnetic (NM), ferromagnetic (FM), and antiferromagnetic single (AFM1) and double layer (AFMD) structures were considered. For each magnetic state, the hydrogen preferentially adsorbs at the fourfold site, with adsorption energies of 4.07, 4.12, 4.03 and 4.05 eV/H atom for the NM, FM, AFM1 and AFMD structures. A total barrier of 1.34, 0.90, 1.32 and 1.25 eV and a bulk-like diffusion barrier of 0.6, 0.2, 0.4 and 0.3 eV were calculated for the NM, FM, AFM1 and AFMD magnetic states. The Fe atoms nearest to the H atom exhibited a reduced magnetic moment, whereas the next-nearest neighbour Fe atoms exhibited a non-negligible local perturbation in the magnetic moment. The presence of magnetically ordered structures has a minimal influence on the minimum energy path for H diffusion through the lattice and on the adsorption of H atoms on the Fe(0 0 1) surface, but we computed a significant reduction of the bulk-like diffusion barriers with respect to the non-magnetic state of fcc γ-Fe.

Preventing carbon contamination of Ge (001) during atomic layer deposition with a barium-based Zintl layer

Carbon contamination of the clean Ge (001) 2 × 1 surface occurs during atomic layer deposition (ALD) of perovskite oxides and introduces impurities that can affect device performance. Zintl layers are formed by exposing a bare Ge (001) 2 × 1-reconstructed surface to 0.5-monolayers of elemental Ba, with the Ba atoms occupying the fourfold sites between Ge-dimer rows. The bare Ge (001) and Ba-Zintl layer surfaces feature a 2 × 1-reconstructed structure. Exposure of bare 2 × 1-reconstructed Ge (001) to 0.5 monolayers of elemental Sr leads to an 8 × 1- or 9 × 1-reconstructed Ge (001) surface. Bare Ge (001) and Ba-Zintl layer Ge (001), and 0.5-monolayer Sr-dosed Ge (001) surfaces were exposed to background molecules in the ALD chamber at 225 °C. Bare Ge (001) and Ba-Zintl layer Ge (001) were also exposed to barium bis(triisopropylcyclopentadienyl) at 225 °C and changes in the surface composition were monitored with x-ray photoelectron spectroscopy. The 2 × 1-reconstructed Ba-Zintl surface protects Ge (001) from carbon accumulation associated with ALD background molecules and cyclopentadienyl-based ligands originating from the ALD precursor. Surface structure is important in protecting Ge (001); the 8 × 1- or 9 × 1-reconstructed Ge (001) surface formed from 0.5-monolayers of Sr does not prevent carbon accumulation.

Evolutionary determinants of genome-wide nucleotide composition.

One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G+C vs. A+T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides, or a combination of the two. We demonstrate that although genomic G+C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G+C composition at four-fold redundant sites is consistently elevated above the neutral expectation, more so than for any other classes of sites.

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome.

Properly estimating genetic diversity in populations of nonmodel species requires a basic understanding of how diversity is distributed across the genome and among individuals. To this end, we analysed whole-genome resequencing data from 20 collared flycatchers (genome size ≈1.1Gb; 10.13 million single nucleotide polymorphisms detected). Genomewide nucleotide diversity was almost identical among individuals (mean=0.00394, range=0.00384-0.00401), but diversity levels varied extensively across the genome (95% confidence interval for 200-kb windows=0.0013-0.0053). Diversity was related to selective constraint such that in comparison with intergenic DNA, diversity at fourfold degenerate sites was reduced to 85%, 3' UTRs to 82%, 5' UTRs to 70% and nondegenerate sites to 12%. There was a strong positive correlation between diversity and chromosome size, probably driven by a higher density of targets for selection on smaller chromosomes increasing the diversity-reducing effect of linked selection. Simulations exploring the ability of sequence data from a small number of genetic markers to capture the observed diversity clearly demonstrated that diversity estimation from finite sampling of such data is bound to be associated with large confidence intervals. Nevertheless, we show that precision in diversity estimation in large outbred population benefits from increasing the number of loci rather than the number of individuals. Simulations mimicking RAD sequencing showed that this approach gives accurate estimates of genomewide diversity. Based on the patterns of observed diversity and the performed simulations, we provide broad recommendations for how genetic diversity should be estimated in natural populations.

The geographic distribution and complex evolutionary history of the NX-2 trichothecene chemotype from Fusarium graminearum

Fusarium graminearum and 21 related species comprising the F. sambucinum species complex lineage 1 (FSAMSC-1) are the most important Fusarium Head Blight pathogens of cereal crops world-wide. FSAMSC-1 species typically produce type B trichothecenes. However, some F. graminearum strains were recently found to produce a novel type A trichothecene (NX-2) resulting from functional variation in the trichothecene biosynthetic enzyme Tri1. We used a PCR-RFLP assay targeting the TRI1 gene to identify the NX-2 allele among a global collection of 2515 F. graminearum. NX-2 isolates were only found in southern Canada and the northern U.S., where they were observed at low frequency (1.8%), but over a broader geographic range and set of cereal hosts than previously recognized. Phylogenetic analyses of TRI1 and adjacent genes produced gene trees that were incongruent with the history of species divergence within FSAMSC-1, indicating trans-species evolution of ancestral polymorphism. In addition, placement of NX-2 strains in the TRI1 gene tree was influenced by the accumulation of nonsynonymous substitutions associated with the evolution of the NX-2 chemotype, and a significant (P<0.001) change in selection pressure was observed along the NX-2 branch (ω=1.16) in comparison to other branches (ω=0.17) in the TRI1 phylogeny. Parameter estimates were consistent with positive selection for specific amino-acid changes during the evolution of NX-2, but direct tests of positive selection were not significant. Phylogenetic analyses of fourfold degenerate sites and intron sequences in TRI1 indicated the NX-2 chemotype had a single evolutionary origin and evolved recently from a type B ancestor. Our results indicate the NX-2 chemotype may be indigenous, and possibly endemic, to southern Canada and the northern U.S. In addition, we demonstrate that the evolution of TRI1 within FSAMSC-1 has been complex, with evidence of trans-species evolution and chemotype-specific shifts in selective constraint.

Relaxation and diffusion barriers at step edges of Cu, Ag and Au homo- and heterogeneous systems: Case of (100) facet

Abstract Using molecular dynamics simulations based on the embedded atom method, we present the calculations of adsorption and activation energies for the diffusion of adatoms (Cu, Ag or Au) on Cu (100), Ag (100) or Au (100) surfaces with steps. We have also examined the relaxation trends and bond lengths of the adatoms for both fourfold and bridge sites. We note that the vertical distance of the adatom relaxation to the first nearest neighbors is the largest (1.56 %) for Ag on Cu (100) and the shortest (–14.58 %) for Cu on Au (100) as compared to other systems. On the other hand, for Cu on the Au (100) system, we find the adatom barrier for hopping along the step edges to be 0.44 eV, which is the highest for this process among the systems studied here, but the lowest barrier is found for Ag on Cu (100) compared to other systems and costs only 0.20 eV. Attention has also been focused on the evaluations of the adsorption and activation energies for the nine systems in the presence of step edges. The diffusion barriers over and along step edges are interpreted in terms of the cohesive energies of the adatoms and substrates. Moreover, these results can offer some basic rules for forecasting precise atomic surface morphologies in homo- and hetero-epitaxial growth.

Synthesis and structural characterization of a flexible metal organic framework {[Ni(dpbz)][Ni(CN)4]}n, dpbz = 1,4-bis(4-pyridyl)benzene) with an unusual Ni–N bond

The chartreuse monoclinic Ni-dpbz (Ni(L)[Ni(CN)4], (L = 1,4-Bis(4-pyridyl)benzene, or dpbz) crystal assumes a pillared structure with layers defined by 2-D Ni[Ni(CN)4]n nets and dpbz ligands as pillars, linking between coordinated Ni sites. In addition to the hysteretic adsorption/desorption feature of Ni-dpbz, in half of the parallelepiped-shape space enclosed by the pillars and nets, an additional dpbz ligand was found to link between the open ends of two four-fold Ni sites. This arrangement results in an unusual 5-fold pseudo square-pyramid environment for Ni and a significantly long Ni–N distance of 2.369(4) Å. The presence of disordered dimethyl sulfoxide (DMSO) solvent molecules give rise to the formula of Ni(dpbz)[Ni(CN)4]·½dpbz·0.44DMSO. Sorption isotherms showed flexible behavior during the adsorption and desorption of CO2.

Are Synonymous Sites in Primates and Rodents Functionally Constrained?

It has been claimed that synonymous sites in mammals are under selective constraint. Furthermore, in many studies the selective constraint at such sites in primates was claimed to be more stringent than that in rodents. Given the larger effective population sizes in rodents than in primates, the theoretical expectation is that selection in rodents would be more effective than that in primates. To resolve this contradiction between expectations and observations, we used processed pseudogenes as a model for strict neutral evolution, and estimated selective constraint on synonymous sites using the rate of substitution at pseudosynonymous and pseudononsynonymous sites in pseudogenes as the neutral expectation. After controlling for the effects of GC content, our results were similar to those from previous studies, i.e., synonymous sites in primates exhibited evidence for higher selective constraint that those in rodents. Specifically, our results indicated that in primates up to 24% of synonymous sites could be under purifying selection, while in rodents synonymous sites evolved neutrally. To further control for shifts in GC content, we estimated selective constraint at fourfold degenerate sites using a maximum parsimony approach. This allowed us to estimate selective constraint using mutational patterns that cause a shift in GC content (GT ↔ TG, CT ↔ TC, GA ↔ AG, and CA ↔ AC) and ones that do not (AT ↔ TA and CG ↔ GC). Using this approach, we found that synonymous sites evolve neutrally in both primates and rodents. Apparent deviations from neutrality were caused by a higher rate of C → A and C → T mutations in pseudogenes. Such differences are most likely caused by the shift in GC content experienced by pseudogenes. We conclude that previous estimates according to which 20-40% of synonymous sites in primates were under selective constraint were most likely artifacts of the biased pattern of mutation.

Rearrangement and evolution of mitochondrial genomes in parrots

Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated.

Molecular adsorption of NO on PdO(101)

We investigated the adsorption of NO on the PdO(101) surface using temperature programmed desorption (TPD), reflection absorption infrared spectroscopy (RAIRS) and density functional theory (DFT) calculations. From TPD, we find that NO reaches a saturation coverage of ~0.54 monolayer (ML) on PdO(101) at 90K, and that desorption from the saturated layer produces a complex TPD trace with five pronounced maxima between 100 and 550K. We observe negligible quantities of desorbing products other than NO during TPD, indicating that NO does not react on PdO(101) under the conditions studied. For low coverages, RAIR spectra reveal that NO adsorption at 90K produces both flat-lying and atop configurations of NO on the coordinatively unsaturated (cus) Pd atoms of PdO(101), but that these configurations are meta-stable and transform to bridge-NO species at higher temperature. RAIRS measurements further show that NO binding on atop-Pdcus sites becomes preferred with increasing coverage above ~25% of the Pdcus density, and provide evidence of a weakly-bound state at coverages above 100% (0.35 ML). Consistent with our experimental findings, DFT predicts that NO preferentially adsorbs on bridge-Pdcus sites at low coverage and that the site preference changes to atop-Pdcus sites with increasing NO coverage, resulting in mixtures of atop-bridge NO configurations as well as an all-atop configuration. DFT also predicts that NO can adopt a flat-lying configuration on the Pdcus row at low coverage, and can also achieve stable bonding on the fourfold Pd sites of PdO(101) at high NO coverages. Both the computational and experimental results show that NO binds on PdO(101) in multiple, local configurations even at low coverage.

Analysis of charge states in the mixed-valent ionic insulator AgO

The doubly ionized ${d}^{9}$ copper ion provides, originally in ${\mathrm{La}}_{2}{\mathrm{CuO}}_{4}$ and later in many more compounds, the platform for high temperature superconductivity when it is forced toward higher levels of oxidation. The nearest chemical equivalent is ${\mathrm{Ag}}^{2+}$, which is almost entirely avoided in nature. AgO is an illustrative example, being an unusual nonmagnetic insulating compound with an open $4d$ shell on one site. This compound has been interpreted in terms of one ${\mathrm{Ag}}^{3+}$ ion at the fourfold site and one ${\mathrm{Ag}}^{+}$ ion that is twofold coordinated. We analyze more aspects of this compound, finding that indeed the ${\mathrm{Ag}}^{3+}$ ion supports only four occupied $4d\ensuremath{-}\mathrm{based}$ Wannier functions per spin, while ${\mathrm{Ag}}^{+}$ supports five, yet their physical charges (as quantified by their spherical radial charge densities) are nearly equal. The oxygen $2p$ Wannier functions display two distinct types of behavior, one type of which includes conspicuous Ag $4d$ tails. Calculation of the Born effective charge tensor shows that the mean effective charges of the Ag ions differ by about a factor of 2, roughly consistent with the assigned formal charges. We analyze the $4d$ charge density and discuss it in terms of recent insights into charge states of insulating (and usually magnetic) transition-metal oxides. What might be expected in electron- and hole-doped AgO is discussed briefly.

Role of atomic radius andd-states hybridization in the stability of the crystal structure ofM2O3(M=Al, Ga, In) oxides

We study the stability of the corundum, gallia, and bixbyite structures of ${\mathrm{Al}}_{2}{\mathrm{O}}_{3},{\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$, and ${\mathrm{In}}_{2}{\mathrm{O}}_{3}$ with density functional theory calculations. To artificially control the relative position of the $d$ states within the band structure, we add a Hubbard-like on-site Coulomb interaction to the $d$ states. We quantitatively show that smaller (larger) atomic radii favor the corundum (bixbyte) structure, which supports empirical models based on the atomic radius ratio between the cation and anions and the spacing-filling condition. Thus, ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ and ${\mathrm{In}}_{2}{\mathrm{O}}_{3}$ crystallizes in the corundum and bixbyite structures, which is consistent with experimental observations. The empirical models based on atomic radius and space filling would predict a corundum or bixbyite structure for ${\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$. However, as expected from experimental observations, we find gallia to be the most stable structure for ${\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$. Our results explain why ${\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$ crystallizes in the gallia structures instead of the corundum or bixbyite as follows. The stability of gallia increases as the hybridization of the Ga $d$ states with the O $2s$ states grows and the $p\text{\ensuremath{-}}d$ splitting increases, which is maximized by the presence of fourfold cation sites. The presence of the fourfold cation sites in gallia is a key structural feature that increases its relative stability compared with the corundum and bixbyite structures for ${\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$, which contain only sixfold cation sites, so that the effect of the $d$ states is unimportant.

The inversion of the Control Region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication.

Mitochondrial genomes are known to have a strong strand-specific compositional bias that is more pronounced at fourfold redundant sites of mtDNA protein-coding genes. This observation suggests that strand asymmetries, to a large extent, are caused by mutational asymmetric mechanisms. In vertebrate mitogenomes, replication and not transcription seems to play a major role in shaping compositional bias. Hence, one can better understand how mtDNA is replicated – a debated issue – through a detailed picture of mitochondrial genome evolution. Here, we analyzed the compositional bias (AT and GC skews) in protein-coding genes of almost 2,500 complete vertebrate mitogenomes. We were able to identify three fish mitogenomes with inverted AT/GC skew coupled with an inversion of the Control Region. These findings suggest that the vertebrate mitochondrial replication mechanism is asymmetric and may invert its polarity, with the leading-strand becoming the lagging-strand and vice-versa, without compromising mtDNA maintenance and expression. The inversion of the strand-specific compositional bias through the inversion of the Control Region is in agreement with the strand-displacement model but it is also compatible with the RITOLS model of mtDNA replication.

Theoretical Study of Carbon Adsorption on Re Surfaces: Morphological Instability

We report results from new experiments on C/Re( $$11\bar{2}1$$ ) to identify threshold conditions for morphological instability of Re( $$11\bar{2}1$$ ). We have found that adsorption of carbon from 0.35 to 0.85 ML (0.3–6.0 L exposure of C2H2) at T ≥ 800 K leads to faceting of Re( $$11\bar{2}1$$ ) with formation of three-sided pyramids. Using density functional theory we have investigated binding sites and binding energies of C on planar and faceted Re surfaces as well as generated a surface phase diagram of C/Re to obtain an atomistic understanding of C-induced pyramidal faceting of Re( $$11\bar{2}1$$ ). The calculations reveal that at low to intermediate coverage, C atoms prefer binding at four-fold sites on the Re surfaces and formation of three-sided pyramids is thermodynamically favored. Using density functional theory and thermodynamic considerations as well as AES and LEED measurements we studied the structure of Re(11–21) surfaces in contact with C2H2. The experiments show that adsorption of carbon from 0.35 to 0.85 ML (0.3–6.0 L exposure of C2H2) at T ≥ 800 K leads to faceting of Re(11–21) with formation of three-sided pyramids. The calculations reveal that at low to intermediate coverage, C atoms prefer binding at four-fold sites on the Re surfaces and formation of three-sided pyramids is thermodynamically favored.

Nature of gap states in GeSbTe phase change memory materials

We have calculated the states associated with valence alternation pair defects in a Te-rich amorphous GeTe random network. Two-fold Te sites and four-fold Ge sites are found to introduce states that are resonant with the valence and conduction bands, respectively. The system has a band gap, but these defect states are in the same energy range as those found by modulated photocurrent experiments. The absence of electron spin resonance signals is still not explained.

The complete nucleotide sequence of the mitochondrial genome of Bactrocera minax (Diptera: Tephritidae).

The complete 16,043 bp mitochondrial genome (mitogenome) of Bactrocera minax (Diptera: Tephritidae) has been sequenced. The genome encodes 37 genes usually found in insect mitogenomes. The mitogenome information for B. minax was compared to the homologous sequences of Bactrocera oleae, Bactrocera tryoni, Bactrocera philippinensis, Bactrocera carambolae, Bactrocera papayae, Bactrocera dorsalis, Bactrocera correcta, Bactrocera cucurbitae and Ceratitis capitata. The analysis indicated the structure and organization are typical of, and similar to, the nine closely related species mentioned above, although it contains the lowest genome-wide A+T content (67.3%). Four short intergenic spacers with a high degree of conservation among the nine tephritid species mentioned above and B. minax were observed, which also have clear counterparts in the control regions (CRs). Correlation analysis among these ten tephritid species revealed close positive correlation between the A+T content of zero-fold degenerate sites (P0FD), the ratio of nucleotide substitution frequency at P0FD sites to all degenerate sites (zero-fold degenerate sites, two-fold degenerate sites and four-fold degenerate sites) and amino acid sequence distance (ASD) were found. Further, significant positive correlation was observed between the A+T content of four-fold degenerate sites (P4FD) and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites; however, we found significant negative correlation between ASD and the A+T content of P4FD, and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites. A higher nucleotide substitution frequency at non-synonymous sites compared to synonymous sites was observed in nad4, the first time that has been observed in an insect mitogenome. A poly(T) stretch at the 5′ end of the CR followed by a [TA(A)]n-like stretch was also found. In addition, a highly conserved G+A-rich sequence block was observed in front of the poly(T) stretch among the ten tephritid species and two tandem repeats were present in the CR.