Structural Divergence Research Articles

About the Genetic Divergence of Populations Coupled by Migrations: Modern Modeling Based on Experimental Results of Yu.P. Altukhov and Coauthors

The existence possibility of stable differences in a selection-homogeneous range looks somewhat paradoxical from the population genetics point of view, but it is disruptive selection that can give such a divergence. Examples of population systems with stable divergence of the genetic structures of subpopulations living in a homogeneous area occur in nature and experimental systems. Comparison of these observations and modeling results allow us to explain the persistence of the stability of natural genetic divergence by the mechanism of interaction between disruptive selection (in the form of reduced fitness of hybrid forms) and a weak migration process. The results of experiments performed by Yu.P. Altukhov et al. with box populations of Drosophila melanogaster, in which the primary divergence of the genetic structures of the subpopulation at the α-GDH locus appeared, are in good agreement with this statement. One can assume the disruptive selection, in this case, the reduced fitness of heterozygotes in α-HDG, played the significant role in maintaining this divergence. An alternative hypothesis is genetic drift that fixed the differences. To identify and substantiate the possibility of the presence of this factor in a given system, and to assess the significant role that disruptive selection plays in maintaining the stability of primary genetic divergence, we analyzed mathematical models of the allele frequencies’ dynamics in a large panmictic population and in a system of 30 local migration coupled populations. Comparison of the simulation results with those of the experiment allows us to conclude with a high probability, in the considered experimental population system, there was a disruptive selection at the α‑GDH locus that facilitated the primary genetic divergence.

Identification of a covert evolutionary pathway between two protein folds

Although homologous protein sequences are expected to adopt similar structures, some amino acid substitutions can interconvert α-helices and β-sheets. Such fold switching may have occurred over evolutionary history, but supporting evidence has been limited by the: (1) abundance and diversity of sequenced genes, (2) quantity of experimentally determined protein structures, and (3) assumptions underlying the statistical methods used to infer homology. Here, we overcome these barriers by applying multiple statistical methods to a family of ~600,000 bacterial response regulator proteins. We find that their homologous DNA-binding subunits assume divergent structures: helix-turn-helix versus α-helix + β-sheet (winged helix). Phylogenetic analyses, ancestral sequence reconstruction, and AlphaFold2 models indicate that amino acid substitutions facilitated a switch from helix-turn-helix into winged helix. This structural transformation likely expanded DNA-binding specificity. Our approach uncovers an evolutionary pathway between two protein folds and provides a methodology to identify secondary structure switching in other protein families.

ANALYSIS OF WAGE LEVELS DYNAMICS IN UKRAINE AND THE EU COUNTRIES AS A COMPONENT RESEARCH OF THE LABOUR MARKET CONDITIONS

At the present stage of deepening the processes of Ukraine's European integration, studies of the state and prospects of development of the labour markets of Ukraine and the European Union countries are becoming increasingly relevant, since in recent years, according to some indicators of the labour market functioning, there has been a process of their separation (structural divergence), which has disintegration potential. In particular, one of the structural factors of their divergence is the imbalance in the field of remuneration.The article is devoted to the study and analysis of the dynamics of wages in Ukraine and the European Union as one of the components of the labour market research process. To achieve this goal, the author used a number of general scientific andspecial research methods interrelated and consistently applied in the work: the method of abstraction, theoretical generalisation, analysis and synthesis, induction, graphical and analytical method (graphs of dynamic changes in indicators).Based on a review of the minimum wages in the European Union, it is determined that in 2022 the EU countries will be divided into three groups: with a national minimum wage of more than EUR 1,500 per month; with a national minimum wage above EUR 1,000 but below EUR 1,500 per month; and with a national minimum wage below EUR 1,000 per month.It is established that the EU labour market has gender and cross-country imbalances in remuneration, while the Ukrainian labour market has gender and regional imbalances. It is determined that there are a number of global problems in the labour market. In the area of remuneration, these include low levels of minimum and average wages, excessive differentiation in remuneration in different regions and sectors of the economy, high and growing wage arrears, lack of connection between wages and the level of employee's qualifications and performance, and the existence of shadow remuneration schemes. The labour market conditions in Ukraine are of a falling type, as they are characterised by an excess of demand over supply (a decrease in vacancies and an increase in the number of unemployed) and a decrease in market prices (the real wage index)

Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture

Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.

Historical contingency in parasite community assembly: Community divergence results from early host exposure to symbionts and ecological drift.

Host individuals are commonly coinfected with multiple parasite species that may interact to shape within-host parasite community structure. In addition to within-host species interactions, parasite communities may also be structured by other processes like dispersal and ecological drift. The timing of dispersal (in particular, the temporal sequence in which parasite species infect a host individual) can alter within-host species interactions, setting the stage for historical contingency by priority effects, but how persistently such effects drive the trajectory of parasite community assembly is unclear, particularly under continued dispersal and ecological drift. We tested the role of species interactions under continued dispersal and ecological drift by simultaneously inoculating individual plants of tall fescue with a factorial combination of three symbionts (two foliar fungal parasites and a mutualistic endophyte), then deploying the plants in the field and tracking parasite communities as they assembled within host individuals. In the field, hosts were exposed to continued dispersal from a common pool of parasites, which should promote convergence in the structure of within-host parasite communities. Yet, analysis of parasite community trajectories found no signal of convergence. Instead, parasite community trajectories generally diverged from each other, and the magnitude of divergence depended on the initial composition of symbionts within each host, indicating historical contingency. Early in assembly, parasite communities also showed evidence of drift, revealing another source of among-host divergence in parasite community structure. Overall, these results show that both historical contingency and ecological drift contributed to divergence in parasite community assembly within hosts.

Mutations in asparaginase II from E. coli and implications for inactivation and PEGylation

All clinically-used asparaginases convert L-asparagine (L-Asn) to l-aspartate (L-Asp) and l-glutamine (L-Gln) to L-glutamate (L-Glu), which has been useful in reducing bioavailable asparagine and glutamine in patients under treatment for acute lymphoblastic leukemia. The E. coli type 2 L-asparaginase (EcA2) can present different sequences among varying bacterial strains, which we hypothesized that might affect their biological function, stability and interchangeability. Here we report the analysis of two EcA2 provided by the public health system of a middle-income country. These enzymes were reported to have similar specific activity in vitro, whereas they differ in vivo. Protein sequencing by LC-MS-MS and peptide mapping by MALDI-ToF-MS of their tryptic digests revealed that Aginasa™ share similar sequence to EcA2 from E. coli strain BL21(DE3), while Leuginase™ has sequence equivalent to EcA2 from E. coli strain AS1.357. The two amino acid differences between Aginasa™ (64D and 252 T) and Leuginase™ (64 N and 252S) resulted in structural divergences in solution as accessed by small-angle X-ray scattering and molecular dynamics simulation trajectories. The conformational variability further results in dissimilar surface accessibility with major consequences for PEGylation, as well as different susceptibility to degradation by limited proteolysis. The present results reveal that the sequence variations between these two EcA2 variants results in conformational changes associated with differential conformational plasticity, potentially affecting physico-chemical and biological properties, including proteolytic and immunogenic silent inactivation.

Philo-Semitic Civilisationism or Anti-Semitic Nationalism? The Ambivalent Stance of the Alternative for Germany Towards Judaism, Jews, and Israel

ABSTRACT This article follows up on assumptions of Rogers Brubaker and Benjamin Moffitt, according to whom, some Western and Northern European right-wing populist parties use ‘civilisationist’ and liberal-illiberal narratives that are, for instance, characterised by a ‘philo-Semitic stance’. The paper analyses to what extent the German right-wing populist party Alternative for Germany (AfD) fits into this concept, considering the party’s ambivalent attitude towards Judaism, Jews, and Israel. Using qualitative content analysis, the study is based on an examination of AfD electoral manifestos and parliamentary documents from the federal level as well as from states such as Berlin, Baden-Württemberg, and Thuringia between 2014 and 2019. Our results reveal differences that range from open anti-Semitic statements to self-definitions as a ‘pro-Jewish’ party. We argue that different positions can be explained by regionally divergent discursive opportunity structures as well as personnel heterogeneity across the party sections under study. Furthermore, we reason that a combination of anti-Semitic and pro-Jewish/Israeli statements fits into the AfD’s strategy of addressing both voters from the radical right with anti-Semitic prejudices and more moderate, conservative voters that reject open hostility towards Jews and Israel. We conclude that the AfD fulfils Brubaker’s and Moffitt’s concepts only to a rather limited extent.

The Lesson Learned from the Unique Evolutionary Story of Avirulence Gene AvrPii of Magnaporthe oryzae.

Blast, caused by Magnaporthe oryzae, is one of the most destructive diseases affecting rice production. Understanding population dynamics of the pathogen's avirulence genes is pre-required for breeding and then deploying new cultivars carrying promising resistance genes. The divergence and population structure of AvrPii was dissected in the populations of southern (Guangdong, Hunan, and Guizhou) and northern (Jilin, Liaoning, and Heilongjiang) China, via population genetic and evolutionary approaches. The evolutionary divergence between a known haplotype AvrPii-J and a novel one AvrPii-C was demonstrated by haplotype-specific amplicon-based sequencing and genetic transformation. The different avirulent performances of a set of seven haplotype-chimeric mutants suggested that the integrity of the full-length gene structures is crucial to express functionality of individual haplotypes. All the four combinations of phenotypes/genotypes were detected in the three southern populations, and only two in the northern three, suggesting that genic diversity in the southern region was higher than those in the northern one. The population structure of the AvrPii family was shaped by balancing, purifying, and positive selection pressures in the Chinese populations. The AvrPii-J was recognized as the wild type that emerged before rice domestication. Considering higher frequencies of avirulent isolates were detected in Hunan, Guizhou, and Liaoning, the cognate resistance gene Pii could be continuously used as a basic and critical resistance resource in such regions. The unique population structures of the AvrPii family found in China have significant implications for understanding how the AvrPii family has kept an artful balance and purity among its members (haplotypes) those keenly interact with Pii under gene-for-gene relationships. The lesson learned from case studies on the AvrPii family is that much attention should be paid to haplotype divergence of target gene.

Genetic Divergence and Population Structure of Xanthomonas albilineans Strains Infecting Saccharum spp. Hybrid and Saccharum officinarum.

Leaf scald caused by Xanthomonas albilineans (Xa) is a major bacterial disease in sugarcane that represents a threat to the global sugar industry. Little is known about the population structure and genetic evolution of this pathogen. In this study, 39 Xa strains were collected from 6 provinces in China. Of these strains, 15 and 24 were isolated from Saccharum spp. hybrid and S. officinarum plants, respectively. Based on multilocus sequence analysis (MLSA), with five housekeeping genes, these strains were clustered into two distinct phylogenetic groups (I and II). Group I included 26 strains from 2 host plants, Saccharum spp. hybrid and S. officinarum collected from 6 provinces, while Group II consisted of 13 strains from S. officinarum plants in the Zhejiang province. Among the 39 Xa strains, nucleotide sequence identities from 5 housekeeping genes were: ABC (99.6-100%), gyrB (99.3-100%), rpoD (98.4-100%), atpD (97.0-100%), and glnA (97.6-100%). These strains were clustered into six groups (A-F), based on the rep-PCR fingerprinting, using primers for ERIC2, BOX A1R, and (GTG)5. UPGMA and PCoA analyses revealed that group A had the most strains (24), followed by group C with 11 strains, while there was 1 strain each in groups B and D-F. Neutral tests showed that the Xa population in S. officinarum had a trend toward population expansion. Selection pressure analysis showed purification selection on five concatenated housekeeping genes from all tested strains. Significant genetic differentiation and infrequent gene flow were found between two Xa populations hosted in Saccharum spp. hybrids and S. officinarum. Altogether, these results provide evidence of obvious genetic divergence and population structures among Xa strains from China.

Description of the Wild Strain Rhizobium rosettiformans DSM26376, Reclassified under Peteryoungia rosettiformans comb.nov., for Producing Glucuronan.

Glucuronan is a polysaccharide composed of β-(1,4)-linked d-glucuronic acids having intrinsic properties and biological activities recoverable in many fields of application. Currently, the description of Sinorhyzobium meliloti M5N1CS mutant bacterial strain as the sole source of glucuronan makes it relevant to the exploration of new microorganisms producing glucuronan. In this study, the Peteryoungia rosettifformans strain (Rhizobia), was identified as a wild producer of an exopolysaccharide (RhrBR46) related to glucuronan. Structural and biochemical features, using colorimetric assays, Fourier infrared spectroscopy, nuclear magnetic resonance, high pressure size exclusion chromatography coupled to multi-angle light laser scattering, and enzymatic assays allowed the characterization of a polyglucuronic acid, having a molecular mass (Mw¯) of 1.85 × 105 Da, and being partially O-acetylated at C-2 and/or C-3 positions. The concentration of Mg2+ ions in the cultivation medium has been shown to impact the structure of RhrBR46, by reducing drastically its Mw¯ (73%) and increasing its DA (10%). Comparative structural analyses between RhrBR46 and the glucuronan from Sinorhyzobium meliloti M5N1CS strain revealed differences in terms of molecular weight, degree of acetylation (DA), and the distribution of acetylation pattern. These structural divergences of RhrBR46 might contribute to singular properties or biological activities of RhrBR46, offering new perspectives of application.

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context.

Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

Investigating the Psychometric Properties of Sex Addiction Screening Test-revised for Persian Population

Introduction: Sexual addiction is known as a disorder that afflicts a person with difficulty in controlling or delaying sexual behaviors. To prevent social, physical, and psychological consequences, validated screening tests are needed to diagnose this disorder. One of these tests is established by Carnes with the name of sexual addiction screening test-revised (SAST-R). In this study, SAST-R has been translated and verified in the Persian language. Methods: The original screening test was translated into the Persian language and also back-translated for matching by two separate expert teams. The data was collected through an online survey of 1268 participants who were in the age range of 18 to 65 years (Mean±SD 29.44±6.90), and 56.1% and 43.9% of the population were women and men, respectively. Three questionnaires, including the SAST-R, the hypersexual behavior consequences scale, and the Connor-Davidson resilience scale as the principal, convergent, and divergent tests were administered to the participants. Results: The reliability of the test’s internal consistency (Cronbach α=0.883), split-half (Cronbach α=0.779), and Guttman (lambda coefficients were between 0.773 to 0.883) tests were used. In addition, 4 methods of content validity (sexual hyperactivity specialist approved), convergent structure validity (P<0.001, R=0.731), the validity of divergent structure (P<0.09, R=-0.132), and factor validity (comparative fit index=0.884, goodness of fit index=0.873, root mean square error of approximation=0.047) were measured and confirmed the validity of the test. Conclusion: The Persian version of SAST-R is a reliable preclinical tool to assess the severity of sexual desire in patients.

Strong selection is poorly aligned with genetic variation in Ipomoea hederacea: implications for divergence and constraint.

The multivariate evolution of populations is the result of the interactions between natural selection, drift, and the underlying genetic structure of the traits involved. Covariances among traits bias responses to selection, and the multivariate axis which describes the greatest genetic variation is expected to be aligned with patterns of divergence across populations. An exception to this expectation is when selection acts on trait combinations lacking genetic variance, which limits evolutionary change. Here we used a common garden field experiment of individuals from 57 populations of Ipomoea hederacea to characterize linear and nonlinear selection on 5 quantitative traits in the field. We then formally compare patterns of selection to previous estimates of within population genetic covariance structure (the G-matrix) and population divergence in these traits. We found that selection is poorly aligned with previous estimates of genetic covariance structure and population divergence. In addition, the trait combinations favored by selection were generally lacking genetic variation, possessing approximately 15%-30% as much genetic variation as the most variable combination of traits. Our results suggest that patterns of population divergence are likely the result of the interplay between adaptive responses, correlated responses, and selection favoring traits lacking genetic variation.

De Quervain's Disease: A Discourse on Etiology, Diagnosis, and Treatment.

Since Fritz De Quervain first postulated stenosing tenosynovitis within the radial dorsum of the wrist, much research has been conducted to provide further insights. De Quervain's Disease (DQD) is a condition that affects the tendons that control the movement of the thumb, specifically the abductor pollicis longus and extensor pollicis brevis. Numerous studies have shown that structural divergence from normal anatomy is partly related to contingency for developing DQD. Even though this condition was discovered many years ago, its exact etiology remains a subject of debate. Two schools of thought exist, one that contends an inflammatory-mediated pathway and the other degenerative changes. Substantial evidence exists for both theories, thus necessitating further studies into the etiology of DQD. Classically, Finkelstein's and Eichhoff's tests have been used as the physical examinations of choice for clinically diagnosing this condition. However, these tests have been shown to have low specificity, hence, the emergence of the wrist hyperflexion and abduction of the thumb test. Evidence also suggests that ultrasonography may become a critical diagnostic tool, especially to identify anatomical variations before invasive treatment, reducing the risk of further complications. The management of DQD is typically conservative, with escalation to steroid injections before surgery is indicated. Future research into this disease should focus on establishing a clearer picture of how anatomical variations and other pathological and occupational factors may interplay to bring about this condition. While current research has suggested possible novel approaches for diagnosing and treating DQD, more studies are required to gain greater insights into the effectiveness of these interventions.

Determining decidability: How issue salience divergence structures party systems and affects citizens

AbstractThis paper argues that issue salience divergence – the extent to which parties in a party system diverge in their allocation of salience across issues – is a key characteristic of party system decidability. Elections do not only matter in that politicians and parties with different policy positions may come to power. They can also matter if competing elites emphasize different issues. Using data from the MARPOR project and the Comparative Study of Electoral Systems, I demonstrate that voters perceive greater differences between parties when parties propose agendas that diverge with respect to issue salience. Furthermore, I demonstrate that perceptions of differences between parties mediate the effect of issue salience divergence on respondents’ satisfaction with democracy and self‐reported voter turnout. These findings indicate that salience‐based differentiation influences the quality of party systems alongside the traditional party system characteristics with important implications for public opinion and political behavior.

The persistent homology of mitochondrial ATP synthases

Relatively little is known about ATP synthase structure in protists, and the investigated ones exhibit divergent structures distinct from yeast or animals. To clarify the subunit composition of ATP synthases across all eukaryotic lineages, we used homology detection techniques and molecular modeling tools to identify an ancestral set of 17 ATP synthase subunits. Most eukaryotes possess an ATP synthase comparable to those of animals and fungi, while some have undergone drastic divergence (e.g., ciliates, myzozoans, euglenozoans). Additionally, a ∼1 billion-year-old gene fusion between ATP synthase stator subunits was identified as a synapomorphy of the SAR (Stramenopila, Alveolata, Rhizaria) supergroup (stramenopile, alveolate, rhizaria). Our comparative approach highlights the persistence of ancestral subunits even amidst major structural changes. We conclude by urging that more ATP synthase structures (e.g., from jakobids, heteroloboseans, stramenopiles, rhizarians) are needed to provide a complete picture of the evolution of the structural diversity of this ancient and essential complex.

Species boundaries within the recently diverged South American monocot‐like Eryngium (Apiaceae, Saniculoideae) based on biogeographic, climatic, morphological, and molecular data: E. cerradense, a new species from Paraguay

AbstractThe species of Eryngium with a monocot‐like habit are among the most taxonomically complex. They show low phenotypic and molecular differentiation due to their recent, rapid, and reticulate speciation during the Quaternary period. In this study, we evaluate the boundaries of the monocot‐like Eryngium regnellii and a closely related entity from the grasslands in the Cerrado of Paraguay. We integrated evidence from multiple data sources to test species delimitation: we estimated the phylogenetic position of both entities within Eryngium based on ITS nrDNA and cpDNA sequences; we carried out univariate and multivariate morphometric analyses to test statistically significant differences and to recognize morphological diagnostic characters; we also analyzed geographic distribution, habitat, and bioclimatic variables to evaluate divergence in environmental niche, and finally, we used Bayesian coalescent‐based delimitation approaches to test genetic structure. Divergence in morphology, environmental niche, and genetic structure between E. regnellii and the lineage from Paraguay support the hypothesis of evolutionary independence among these two lineages. Therefore, based on an integrative approach, we recognize and describe a new species from Paraguay: Eryngium cerradense.

Citizen Science and Natural Resource Management: A Social Network Analysis of Two Community-Based Water Monitoring Programs

In natural resource management contexts, citizen science programs often involve a diversity of actors collaborating in broad social networks. However, the characteristics and functioning of these networks has received limited attention. In this article, we demonstrate the benefits of applying social network research to citizen science practice. Through a mixed methods approach, we compare data sharing and collaboration networks of two community-based water monitoring programs in Australia. The quantitative component revealed that despite similarities in actor diversity and activities, both programs have created divergent network structures (centralized vs decentralized) corresponding to their scale of influence in environmental decision-making (regional vs local impacts). The qualitative component showed how individuals navigated their relationships and managed key tensions inherent to network functioning. This study provides new insights on the role of social networks in citizen science and concludes by recommending program leaders adopt a “networking mindset” to maximize their sphere of influence.

Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences

BackgroundPlant organelle genomes are a valuable resource for evolutionary biology research, yet their genome architectures, evolutionary patterns and environmental adaptations are poorly understood in many lineages. Rhodiola species is a type of flora mainly distributed in highland habitats, with high medicinal value. Here, we assembled the organelle genomes of three Rhodiola species (R. wallichiana, R. crenulata and R. sacra) collected from the Qinghai-Tibet plateau (QTP), and compared their genome structure, gene content, structural rearrangements, sequence transfer and sequence evolution rates.ResultsThe results demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes in three Rhodiola species, with the former possessing more conserved genome structure but faster evolutionary rates of sequence, while the latter exhibiting structural diversity but slower rates of sequence evolution. Some lineage-specific features were observed in Rhodiola mitogenomes, including chromosome fission, gene loss and structural rearrangement. Repeat element analysis shows that the repeats occurring between the two chromosomes may mediate the formation of multichromosomal structure in the mitogenomes of Rhodiola, and this multichromosomal structure may have recently formed. The identification of homologous sequences between plastomes and mitogenomes reveals several unidirectional protein-coding gene transfer events from chloroplasts to mitochondria. Moreover, we found that their organelle genomes contained multiple fragments of nuclear transposable elements (TEs) and exhibited different preferences for TEs insertion type. Genome-wide scans of positive selection identified one gene matR from the mitogenome. Since the matR is crucial for plant growth and development, as well as for respiration and stress responses, our findings suggest that matR may participate in the adaptive response of Rhodiola species to environmental stress of QTP.ConclusionThe study analyzed the organelle genomes of three Rhodiola species and demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes. Signals of positive selection were detected in the matR gene of Rhodiola mitogenomes, suggesting the potential role of this gene in Rhodiola adaptation to QTP. Together, the study is expected to enrich the genomic resources and provide valuable insights into the structural dynamics and sequence divergences of Rhodiola species.

Domain shuffling of a highly mutable ligand-binding fold drives adhesin generation across the bacterial kingdom.

Bacterial fibrillar adhesins are specialized extracellular polypeptides that promote the attachment of bacteria to the surfaces of other cells or materials. Adhesin-mediated interactions are critical for the establishment and persistence of stable bacterial populations within diverse environmental niches and are important determinants of virulence. The fibronectin (Fn)-binding fibrillar adhesin CshA, and its paralogue CshB, play important roles in host colonization by the oral commensal and opportunistic pathogen Streptococcus gordonii. As paralogues are often catalysts for functional diversification, we have probed the early stages of structural and functional divergence in Csh proteins by determining the X-ray crystal structure of the CshB adhesive domain NR2 and characterizing its Fn-binding properties in vitro. Despite sharing a common fold, CshB_NR2 displays an ~1.7-fold reduction in Fn-binding affinity relative to CshA_NR2. This correlates with reduced electrostatic charge in the Fn-binding cleft. Complementary bioinformatic studies reveal that homologues of CshA/B_NR2 domains are widely distributed in both Gram-positive and Gram-negative bacteria, where they are found housed within functionally cryptic multi-domain polypeptides. Our findings are consistent with the classification of Csh adhesins and their relatives as members of the recently defined polymer adhesin domain (PAD) family of bacterial proteins.