The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria

Background

Period 10 dinucleotides are structurally and functionally validated factors that influence the ability of DNA to form nucleosomes, histone core octamers. Robust identification of periodic signals in DNA sequences is therefore required to understand nucleosome organisation in genomes. While various techniques for identifying periodic components in genomic sequences have been proposed or adopted, the requirements for such techniques have not been considered in detail and confirmatory testing for a priori specified periods has not been developed.

Results

We compared the estimation accuracy and suitability for confirmatory testing of autocorrelation, discrete Fourier transform (DFT), integer period discrete Fourier transform (IPDFT) and a previously proposed Hybrid measure. A number of different statistical significance procedures were evaluated but a blockwise bootstrap proved superior. When applied to synthetic data whose period-10 signal had been eroded, or for which the signal was approximately period-10, the Hybrid technique exhibited superior properties during exploratory period estimation. In contrast, confirmatory testing using the blockwise bootstrap procedure identified IPDFT as having the greatest statistical power. These properties were validated on yeast sequences defined from a ChIP-chip study where the Hybrid metric confirmed the expected dominance of period-10 in nucleosome associated DNA but IPDFT identified more significant occurrences of period-10. Application to the whole genomes of yeast and mouse identified ~ 21% and ~ 19% respectively of these genomes as spanned by period-10 nucleosome positioning sequences (NPS).

Conclusions

For estimating the dominant period, we find the Hybrid period estimation method empirically to be the most effective for both eroded and approximate periodicity. The blockwise bootstrap was found to be effective as a significance measure, performing particularly well in the problem of period detection in the presence of eroded periodicity. The autocorrelation method was identified as poorly suited for use with the blockwise bootstrap. Application of our methods to the genomes of two model organisms revealed a striking proportion of the yeast and mouse genomes are spanned by NPS. Despite their markedly different sizes, roughly equivalent proportions (19-21%) of the genomes lie within period-10 spans of the NPS dinucleotides {AA, TT, TA}. The biological significance of these regions remains to be demonstrated. To facilitate this, the genomic coordinates are available as Additional files 1, 2, and 3 in a format suitable for visualisation as tracks on popular genome browsers.

Reviewers

This article was reviewed by Prof Tomas Radivoyevitch, Dr Vsevolod Makeev (nominated by Dr Mikhail Gelfand), and Dr Rob D Knight.     

Quantitative genetic analysis of brain size variation in sticklebacks: support for the mosaic model of brain evolution

The mosaic model of brain evolution postulates that different brain regions are relatively free to evolve independently from each other. Such independent evolution is possible only if genetic correlations among the different brain regions are less than unity. We estimated heritabilities, evolvabilities and genetic correlations of relative size of the brain, and its different regions in the three-spined stickleback (Gasterosteus aculeatus). We found that heritabilities were low (average h² = 0.24), suggesting a large plastic component to brain architecture. However, evolvabilities of different brain parts were moderate, suggesting the presence of additive genetic variance to sustain a response to selection in the long term. Genetic correlations among different brain regions were low (average r_G = 0.40) and significantly less than unity. These results, along with those from analyses of phenotypic and genetic integration, indicate a high degree of independence between different brain regions, suggesting that responses to selection are unlikely to be severely constrained by genetic and phenotypic correlations. Hence, the results give strong support for the mosaic model of brain evolution. However, the genetic correlation between brain and body size was high (r_G = 0.89), suggesting a constraint for independent evolution of brain and body size in sticklebacks.     

Structure des caboxines: Alcaloïdes oxindoliques du Cabucala fasciculata

The structures of three new 11-monomethoxy pentacyclic oxindole alkaloids have been elucidated by chemical correlations with reserpinine: caboxine-A was assigned to the allo C₁₉-méthyl α series: 3S, 4R, 7S, 19S; isocaboxine-A and B to the epi-allo C₁₉-methyl α series and have, respectively, the following configurations 3R, 4S, 7S, 19S and 3R, 4S, 7R, 19S.     

Altered postural modulation of Hoffmann reflex in the soleus and fibularis longus associated with chronic ankle instability

Our purpose was to assess Hoffmann (H) reflex modulations of the soleus and fibularis longus in three body positions (prone, bipedal and unipedal stances) in subjects with and without chronic ankle instability (CAI). Sixteen subjects with unilateral CAI and 15 healthy controls participated. Maximum H-reflexes and motor (M) waves were recorded bilaterally from the soleus and fibularis longus while subjects lied prone and then stood in quiet bipedal and unipedal stances. Maximum H-reflexes were normalized to maximum M waves to obtain H_max:M_max ratios for the three positions. H-reflex modulations, for each muscle, were quantified as the percent change scores in H_max:M_max ratios between each pair of positions: prone to bipedal, bipedal to unipedal, and prone to unipedal. There were significant group by limb interactions found for all three modulations (P < 0.05) for the soleus. In the CAI group, soleus modulations in involved limbs were significantly lower than in uninvolved limbs and both limbs in the controls. For the fibularis longus, similar results were found for the bipedal to unipedal and prone to unipedal modulations. Constrained ability of the sensorimotor system to down regulate H-reflex in more demanding postures may represent a potential mechanism of postural control deficits associated with CAI.     

Genetic parameters for carcass weight,conformation and fat in five beef cattle breeds

Profitability of beef production can be increased by genetically improving carcass traits. To construct breeding value evaluations for carcass traits, breed-specific genetic parameters were estimated for carcass weight, carcass conformation and carcass fat in five beef cattle breeds in Finland (Hereford, Aberdeen Angus, Simmental, Charolais and Limousin). Conformation and fat were visually scored using the EUROP carcass classification. Each breed was separately analyzed using a multitrait animal model. A total of 6879–19 539 animals per breed had phenotypes. For the five breeds, heritabilities were moderate for carcass weight (h²=0.39 to 0.48, s.e.=0.02 to 0.04) and slightly lower for conformation (h²=0.30 to 0.44, s.e.=0.02 to 0.04) and carcass fat (h²=0.29 to 0.44, s.e.=0.02 to 0.04). The genetic correlation between carcass weight and conformation was favorable in all breeds (r_G=0.37 to 0.53, s.e.=0.04 to 0.05), heavy carcasses being genetically more conformed. The phenotypic correlation between carcass weight and carcass fat was moderately positive in all breeds (r_P=0.21 to 0.32), implying that increasing carcass weight was related to increasing fat levels. The respective genetic correlation was the strongest in Hereford (r_G=0.28, s.e.=0.05) and Angus (r_G=0.15, s.e.=0.05), the two small body-sized British breeds with the lowest conformation and the highest fat level. The correlation was weaker in the other breeds (r_G=0.08 to 0.14). For Hereford, Angus and Simmental, more conformed carcasses were phenotypically fatter (r_P=0.11 to 0.15), but the respective genetic correlations were close to zero (r_G=−0.05 to 0.04). In contrast, in the two large body-sized and muscular French breeds, the genetic correlation between conformation and fat was negative and the phenotypic correlation was close to zero or negative (Charolais: r_G=−0.18, s.e.=0.06, r_P=0.02; Limousin: r_G=−0.56, s.e.=0.04, r_P=−0.13). The results indicate genetic variation for the genetic improvement of the carcass traits, favorable correlations for the simultaneous improvement of carcass weight and conformation in all breeds, and breed differences in the correlations of carcass fat.     

CD correlation of C-2′substituted monocyclic carotenoids

The scope and limitation of circular dichroism (CD) correlations of several C-2′ substituted monocyclic monochiral, homodichiral and heterodichiral carotenoids have been investigated, aiming at the assignment of absolute configuration at C-2′ by using the diester and 2′-β-d-tetraacetylglucosyl derivative of (2′R)-plectaniaxanthin and a synthetic chiral C₄₅-carotene as key references. The correlations are based on the additivity hypothesis, the conformational rule and a comparison of CD spectra, preferably conservative ones. Quantitative aspects of the conformational rule are considered. Substituent effects at C-2′ and C-1′ have been studied. Absolute configurations are suggested for (2′)-phleixanthophyll (3S,2′S)-2′-hydroxyflexixanthin, (3R,2′S)-myxoxanthophyll, (3S,2′S-4-ketomyxoxanthophyll (3R,2′S)-myxol-2′-O-methyl methylpentoside and (2R,2′S)-Cp. 473 from relevant CD correlations. The chiralities of (2′S)-4-ketophleixanthophyll and (2R,6R,2′S)-A.g. 471 are suggested from biogenetic considerations. A chemosystematic consideration of chirality and source is included.     

Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection

Reliable selection criteria are required for young riding horses to increase genetic gain by increasing accuracy of selection and decreasing generation intervals. In this study, selection strategies incorporating genomic breeding values (GEBVs) were evaluated. Relevant stages of selection in sport horse breeding programs were analyzed by applying selection index theory. Results in terms of accuracies of indices (r_TI) and relative selection response indicated that information on single nucleotide polymorphism (SNP) genotypes considerably increases the accuracy of breeding values estimated for young horses without own or progeny performance. In a first scenario, the correlation between the breeding value estimated from the SNP genotype and the true breeding value (= accuracy of GEBV) was fixed to a relatively low value of r_mg = 0.5. For a low heritability trait (h² = 0.15), and an index for a young horse based only on information from both parents, additional genomic information doubles r_TI from 0.27 to 0.54. Including the conventional information source ‘own performance’ into the before mentioned index, additional SNP information increases r_TI by 40%. Thus, particularly with regard to traits of low heritability, genomic information can provide a tool for well-founded selection decisions early in life. In a further approach, different sources of breeding values (e.g. GEBV and estimated breeding values (EBVs) from different countries) were combined into an overall index when altering accuracies of EBVs and correlations between traits. In summary, we showed that genomic selection strategies have the potential to contribute to a substantial reduction in generation intervals in horse breeding programs.     

Thermoluminescence study of charge recombination in Photosystem II at low temperatures. II. Oscillatory properties of the Zv and A thermoluminescence bands in chloroplasts dark-adapted for various time periods

The oscillations of the Z_V and A thermoluminescence bands were investigated in spinach chloroplasts which had been dark-adapted for various time periods and subjected to a series of flashes at +2°C before continuous illumination at various low temperatures. When excited with continuous light below −65°C, the Z_V band exhibited period-4 oscillation, with maxima on preflashes 0, 4 and 8. Above −65°C, the oscillation pattern depended greatly on the dark-adaptation period of the chloroplasts. In preilluminated samples (15 s light followed by 3 min dark), when the Q_B pool is half oxidized, the oscillation of the thermoluminescence intensity measured at −50°C was similar to that observed below −65°C. However, after the thorough dark-adaptation of the chloroplasts (6 h), when the major fraction of the Q_B pool is assumed to be oxidized, a binary oscillation appeared in the oscillation pattern, with maxima at odd flash numbers. Below −65°C, period-2 oscillation of the Z_V band could not be induced by the dark-adaptation of the chloroplasts, suggesting an inhibition of electron exchange between Q_A and Q_B. Upon excitation of the chloroplasts with continuous light at −30°C, the A band oscillated with a periodicity of 4 with maxima at preflash numbers 2 and 6. At pH 7.5, the period-4 oscillation was converted into a period-2 oscillation by thorough dark-adaptation of the chloroplasts (24 h). Model calculations of the oscillatory patterns suggest that the period-4 oscillations of the Z_V and A bands are determined by the concentrations [S₀] + [S₁] and [S₂] + [S₃], respectively, which are present after the preflashes prior to the low-temperature continuous illumination. The period-2 oscillations in the amplitudes of the Z_V and A bands reflect the changes occurring in the redox state of the Q_B pool in a sequence of flashes. The possible relationship between the characteristics of the Z_V and A bands and the temperature-dependence of the S state transitions was investigated. Comparison of the amplitudal changes of the B (S₂Q⁻_B and S₃Q⁻_B recombination) and Q (S₂Q⁻_A recombination) thermoluminescence bands as a function of the excitation temperature suggests that the S₂ → S₃ and S₃ → S₄ transitions are blocked at about −65 and −40°C, respectively. It is also concluded that the thermoluminescence intensity emitted by the reaction center is about twice as high in the S₃ state as in the S₂ state.     

在种与属两个级别评价太子河硅藻群落与环境因子的关系

2009年8—9月,对辽宁省太子河流域67个点位进行采样调查,以硅藻群落为研究对象,比较硅藻属级水平与种级水平相对多度、物种丰富度以及生物多样性指数间的相关性,并比较硅藻属级与种级属性与环境因子的相关性。实验结果表明,太子河流域硅藻属级水平的相对多度、丰富度和多样性指数与硅藻种级水平都极显著相关。Pearson相关性分析表明,硅藻属级水平的丰富度与环境显著相关的因子与种级水平丰富度与环境显著相关的因子相一致。Mantel-Test相关性分析表明,硅藻属级水平的相对多度与环境因子的相关性弱于种级水平与环境因子相关性。典范对应分析结果显示,影响硅藻属级和种级群落结构分布的主要环境因子均为悬浮物。基于硅藻生物评价指数的流域健康评价结果表明,应用硅藻属级和种级属性对太子河流域进行健康评价,其评价结果相一致。     

Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation

We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3′-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3′-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3′-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences.     

Did Genetic Drift Drive Increases in Genome Complexity?

Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious. Effective population size (N_e) has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large (but not small) N_e. Strong support for this model was claimed from a comparative analysis of N_eu and genome size for ≈30 phylogenetically diverse species ranging from bacteria to vertebrates, but analyses at that scale have so far failed to account for phylogenetic nonindependence of species. In our reanalysis, accounting for phylogenetic history substantially altered the perceived strength of the relationship between N_eu and genomic attributes: there were no statistically significant associations between N_eu and gene number, intron size, intron number, the half-life of gene duplicates, transposon number, transposons as a fraction of the genome, or overall genome size. We conclude that current datasets do not support the hypothesis of a mechanistic connection between N_e and these genomic attributes, and we suggest that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables.     

Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

Genetic correlations between quantitative traits measured in many breeding programs are pervasive. These correlations indicate that measurements of one trait carry information on other traits. Current single-trait (univariate) genomic selection does not take advantage of this information. Multivariate genomic selection on multiple traits could accomplish this but has been little explored and tested in practical breeding programs. In this study, three multivariate linear models (i.e., GBLUP, BayesA, and BayesCπ) were presented and compared to univariate models using simulated and real quantitative traits controlled by different genetic architectures. We also extended BayesA with fixed hyperparameters to a full hierarchical model that estimated hyperparameters and BayesCπ to impute missing phenotypes. We found that optimal marker-effect variance priors depended on the genetic architecture of the trait so that estimating them was beneficial. We showed that the prediction accuracy for a low-heritability trait could be significantly increased by multivariate genomic selection when a correlated high-heritability trait was available. Further, multiple-trait genomic selection had higher prediction accuracy than single-trait genomic selection when phenotypes are not available on all individuals and traits. Additional factors affecting the performance of multiple-trait genomic selection were explored.     

Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Key message

“To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.”

Abstract

Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F_3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.     

Relative impact of earlier diagnosis and improved treatment on survival for colorectal cancer: A US database study among elderly patients

PurposesTo estimate what proportion of improvement in relative survival was attributable to smaller stage/size due to early detection and what proportion was attributable to cancer chemotherapy in patients with colorectal cancer (CRC).MethodsWe studied 69,718 patients with CRC aged ≥66 years in 1992–2009 from Surveillance, Epidemiology, and End Results registries. Study periods were categorized into three periods according to the major changes or advances in screening and chemotherapy regimens: (1) Period-1 (1992–1995), during which there was no evidence-based recommendation for routine CRC screening and 5-fluorouracil was the mainstay for chemotherapy; (2) Period-2 (1996–2000), during which evidences and guidelines supported the use of fecal occult blood test (FOBT) and sigmoidoscopy for routine CRC screening; and (3) Period-3 (2001–2009), during which Medicare Program added the full coverage for colonoscopy screening to average-risk individuals, and several newly developed chemotherapy regimens were approved. Outcome variables included the likelihood of being diagnosed at an early stage or with a small tumor size, and improvement in relative survival.ResultsCompared to period-1, likelihood of being diagnosed with early stage CRC increased by 20% in period-2 (odds ratio = 1.2, 95%CI: 1.1–1.2) and 30% in period-3 (1.3, 1.2–1.4); and likelihood of being diagnosed with small-size CRC increased by 60% in period-2 and 110% in period-3. Similarly, 5-year overall relative survival increased from 51% in period-1 to 56% in period-2 and 60% in period-3. Increase in survival attributable to migration in stage/size was 9% in period-2 and 20% in period-3, while the remaining survival improvement during period-2 and period-3 were largely attributable to more effective chemotherapy regimens (≥71.6%) and other treatment factors (≤25%).ConclusionsImprovements in CRC screening resulted in a migration of CRC toward earlier tumor stage and smaller size, which contributed to ≤20% of survival increase. Survival improvement over the past 2 decades was largely explained by more effective chemotherapy regimens (≥71.6%).     

Novel Apolar Plasmonic Nanostructures with Extended Optical Tunability for Sensing Applications

This paper outlines the design of complex nanostructures with apolar behavior which pave the way to a wider range of plasmon resonance tuning and applications requiring higher enhancement. These new nanostructure families are simply defined by symmetry considerations. An irreducible decomposition of optical response tensor demonstrates that nanoparticles which belong to C _n , with n?≥?3, symmetry point group for at least one scale have an optical response insensitive on the light polarization. This is experimentally confirmed by extinction and surface-enhanced Raman-scattering measurements.     

Simultaneous [18F]FDG-PET/MRI: Correlation of Apparent Diffusion Coefficient (ADC) and Standardized Uptake Value (SUV) in Primary and Recurrent Cervical Cancer

Objectives

Previous non–simultaneous PET/MR studies have shown heterogeneous results about the correlation between standardized uptake values (SUVs) and apparent diffusion coefficients (ADCs). The aim of this study was to investigate correlations in patients with primary and recurrent tumors using a simultaneous PET/MRI system which could lead to a better understanding of tumor biology and might play a role in early response assessment.

Methods

We included 31 patients with histologically confirmed primary (n = 14) or recurrent cervical cancer (n = 17) who underwent simultaneous whole-body ¹⁸F-FDG-PET/MRI comprising DWI. Image analysis was performed by a radiologist and a nuclear physician who identified tumor margins and quantified ADC and SUV. Pearson correlations were calculated to investigate the association between ADC and SUV.

Results

92 lesions were detected. We found a significant inverse correlation between SUV_max and ADC_min (r = -0.532, p = 0.05) in primary tumors as well as in primary metastases (r = -0.362, p = 0.05) and between SUV_mean and ADC_min (r = -0.403, p = 0.03). In recurrent local tumors we found correlations for SUV_max and ADC_min (r = -0.747, p = 0.002) and SUV_mean and ADC_min (r = -0.773, p = 0.001). Associations for recurrent metastases were not significant (p>0.05).

Conclusions

Our study demonstrates the feasibility of fast and reliable measurement of SUV and ADC with simultaneous PET/MRI. In patients with cervical cancer we found significant inverse correlations for SUV and ADC which could play a major role for further tumor characterization and therapy decisions.

Key Point 1

This study investigates the correlation of functional parameters in a simultaneous PET/MRI.

Key Point 2

We found significant inverse correlations between ADC and SUV in cervical carcinoma which could increase knowledge about tumor biology.     

The Correlation between Rates of Cancer and Autism: An Exploratory Ecological Investigation

Background

Autism is associated with high rates of genomic aberrations, including chromosomal rearrangements and de novo copy-number variations. These observations are reminiscent of cancer, a disease where genomic rearrangements also play a role. We undertook a correlative epidemiological study to explore the possibility that shared risk factors might exist for autism and specific types of cancer.

Methodology/Principal Findings

To determine if significant correlations exist between the prevalence of autism and the incidence of cancer, we obtained and analyzed state-wide data reported by age and gender throughout the United States. Autism data were obtained from the U.S. Department of Education via the Individuals with Disabilities Education Act (IDEA) (2000–2007, reported annually by age group) and cancer incidence data were obtained from the Centers for Disease Control and Prevention (CDC) (1999–2005). IDEA data were further subdivided depending on the method used to diagnose autism (DSM IV or the Code of Federal Regulations, using strict or expanded criteria). Spearman rank correlations were calculated for all possible pairwise combinations of annual autism rates and the incidence of specific cancers. Following this, Bonferroni''s correction was applied to significance values. Two independent methods for determining an overall combined p-value based on dependent correlations were obtained for each set of calculations. High correlations were found between autism rates and the incidence of in situ breast cancer (p≤10⁻¹⁰, modified inverse chi square, n = 16) using data from states that adhere strictly to the Code of Federal Regulations for diagnosing autism. By contrast, few significant correlations were observed between autism prevalence and the incidence of 23 other female and 22 male cancers.

Conclusions

These findings suggest that there may be an association between autism and specific forms of cancer.     

Genomic imbalance determines positive and negative modulation of gene expression in diploid maize

Genomic imbalance caused by changing the dosage of individual chromosomes (aneuploidy) has a more detrimental effect than varying the dosage of complete sets of chromosomes (ploidy). We examined the impact of both increased and decreased dosage of 15 distal and 1 interstitial chromosomal regions via RNA-seq of maize (Zea mays) mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated toward the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which the expression of many genes under genome imbalance are modulated toward the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.

Genomic imbalance caused by the addition or subtraction of chromosomal segments leads to modulations of gene expression inversely or directly related to chromosomal dosage but also to nonlinear responses.     

The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization

Background

Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience adaptive or purifying selection, yet the role that selection plays on genomic reorganization remains unclear. We sequence the mitogenomes of three species of Glandirana and hot spots of gene rearrangements of 20 frog species to investigate the diversity of mitogenomic reorganization in the Neobatrachia. By combing these data with other mitogenomes in GenBank, we evaluate if selective pressures or functional constraints act on mitogenomic reorganization in the Neobatrachia. We also look for correlations between tRNA positions and codon usage.

Results

Gene organization in Glandirana was typical of neobatrachian mitogenomes except for the presence of pseudogene trnS (AGY). Surveyed ranids largely exhibited gene arrangements typical of neobatrachian mtDNA although some gene rearrangements occurred. The correlation between codon usage and tRNA positions in neobatrachians was weak, and did not increase after identifying recurrent rearrangements as revealed by basal neobatrachians. Codon usage and tRNA positions were not significantly correlated when considering tRNA gene duplications or losses. Change in number of tRNA gene copies, which was driven by genomic reorganization, did not influence codon usage bias. Nucleotide substitution rates and d_N/d_S ratios were higher in neobatrachian mitogenomes than in archaeobatrachians, but the rates of mitogenomic reorganization and mt nucleotide diversity were not significantly correlated.

Conclusions

No evidence suggests that adaptive selection drove the reorganization of neobatrachian mitogenomes. In contrast, protein-coding genes that function in metabolism showed evidence for purifying selection, and some functional constraints appear to act on the organization of rRNA and tRNA genes. As important nonadaptive forces, genetic drift and mutation pressure may drive the fixation and evolution of mitogenomic reorganizations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-691) contains supplementary material, which is available to authorized users.