Divergent Regions Research Articles

A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube.

Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.

Deciphering functional roles and interplay between Beclin1 and Beclin2 in autophagosome formation and mitophagy.

The degradation of macromolecules and organelles by the process of autophagy is critical for cellular homeostasis and is often compromised during aging and disease. Beclin1 and Beclin2 are implicated in autophagy induction, and these homologs share a high degree of amino acid sequence similarity but have divergent N-terminal regions. Here, we investigated the functions of the Beclin homologs in regulating autophagy and mitophagy, a specialized form of autophagy that targets mitochondria. Both Beclin homologs contributed to autophagosome formation, but a mechanism of autophagosome formation independent of either Beclin homolog occurred in response to starvation or mitochondrial damage. Mitophagy was compromised only in Beclin1-deficient HeLa cells and mouse embryonic fibroblasts because of defective autophagosomal engulfment of mitochondria, and the function of Beclin1 in mitophagy required the phosphorylation of the conserved Ser15 residue by the kinase Ulk1. Mitochondria-ER-associated membranes (MAMs) are important sites of autophagosome formation during mitophagy, and Beclin1, but not Beclin2 or a Beclin1 mutant that could not be phosphorylated at Ser15, localized to MAMs during mitophagy. Our findings establish a regulatory role for Beclin1 in selective mitophagy by initiating autophagosome formation adjacent to mitochondria, a function facilitated by Ulk1-mediated phosphorylation of Ser15 in its distinct N-terminal region.

Inversions maintain differences between migratory phenotypes of a songbird

Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4–13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.

Application of Interpolating Matrix Method to Study Dynamics of Axially Moving Beams Made of Functionally Graded Materials

In this paper, the divergent instability and coupled flutter characteristics of axially moving beams made of functionally graded materials (FGM) are studied using the interpolation matrix method. The material property of the beam is designed to change smoothly and continuously along the thickness direction. In considering the Euler-Bernoulli beam theory, Hamilton’s principle is used to derive the differential equation of the transverse vibration kinematics of axially moving FGM beams. In addition, the calculation model for solving the complex frequency of the beam based on the interpolation matrix method has been established. The presented solutions are compared with those in the literature to illustrate the effectiveness of the interpolation matrix method. The results show that the divergence and flutter velocities of axially moving FGM beams tend to decrease with the increase of the material gradient index, and there is a very narrow stability region between the first static instability region (divergence) and the first dynamic instability region (first- and second-order coupled flutter).

The Import of Differential Traditional Mode of Dressing in Campaign Poster Designs as Leverages to Gain Electioneering Advantages by Political Parties in Nigeria

In Graphics design production, there are established modes of practices which have been established over the years, be it a simple hand stenciled banner, to the creation of crests on fabrics by screen printing or by the new, more sophisticated, method of printing by direct imaging, designers have always focused on the adoption of elements and principles of design as the basis to put the design rubrics together. But more than that, the entire breadth of design creation is often taken beyond the mundane of the simple rudiments. This paper, therefore, focused on a new phenomenon of personality induced impetus which became a noticeable trend on the production of political campaign posters in Nigeria. The paper delved into the historical appearance of campaign posters in Nigeria across the major political epochs, it was found out that the Nation’s political imbalance from divergent tribal regions was a primary flare which festered the personality induced visuals on posters in order to douse political tensions. Three major presidential candidates’ campaign posters were purposively selected for scrutiny from the 2023 Nigeria’s General election and the Art historical method of visual art criticism was adopted to appraise the posters and the practice of the Graphics designers. The paper concluded by ideating the inseparability of the role of art from the dictates of the society.

Transformation and differentiation of spatial development of Belgorod, Voronezh and Kursk regions

The purpose of the work is to analyze the transformation, differentiation of spatial socio–economic development of the regions bordering Ukraine as part of the Central Chernozem region and their regional metropolises. The results of the study confirmed two types of structures of regional settlement systems of the CCR border regions: Belgorod dual-core and monocentric Voronezh and Kursk with established features of non-metropolitan reduction trends and different vectors of development of border settlement. Dynamics of economic development of the regions since 2010 it indicates a significant transformation and differentiation, a change of leader, a stable nature of the processes of divergence of regions in the levels of development. It is revealed that in 2020 the highest indicators of economic development were achieved by the Voronezh region, the first signs of stagnation of the economic development of the Belgorod region were established, in which a reduction in investment, a change in the geopolitical situation in 2022, the border situation can lead to a decrease in the investment attractiveness of large businesses, a further drop in the pace of economic development, the emergence of instability. The reduction of the share of metropolises in the socio-economic development of the regions, the formation of a new trend – "de-monocentricity" has been established. A retrospective analysis of the population growth/loss ratio revealed a persistent trend of population concentration in suburban metropolitan areas against the background of a continuing decline in the population of the deep regions of the regions. The territories bordering Ukraine are characterized by different vectors of economic and demographic development. The conducted research allowed us to establish the trends of uneven spatial development; the polarization of the development of regional metropolises, non-metropolitan and border areas; the tightening of the population in the regional capitals-metropolises and suburban areas. The methodology of studying the spatial development of regions, regional metropolises provides an opportunity to monitor their levels of development, identify priority problems, and make effective management decisions.

Comparative genomics of widespread and narrow-range white-bellied rats in the Niviventer niviventer species complex sheds light on invasive rodent success.

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation, thus enabling range expansion. In contrast, narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions, thus limiting their ability to expand into novel environments. However, the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood. The Niviventer niviventer species complex (NNSC), consisting of highly abundant wild rats in Southeast Asia and China, offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related. In the present study, we combined ecological niche modeling with phylogenetic analysis, which suggested that sister species cannot be both widespread and dominant within the same geographical region. Moreover, by assessing heterozygosity, linkage disequilibrium decay, and Tajima's D analysis, we found that widespread species exhibited higher genetic diversity than narrow-range species. In addition, by exploring the "genomic islands of speciation", we identified 13 genes in highly divergent regions that were shared by the two widespread species, distinguishing them from their narrow-range counterparts. Functional annotation analysis indicated that these genes are involved in nervous system development and regulation. The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.

Heterogeneity of Research and Development Expenditure: A Convergence Analysis for the Spanish Regions

In the present study, we investigate the convergence of research and development (R&D) expenditure, a relevant factor in competitiveness, across Spanish regions through a club convergence analysis for the period 2000 to 2017. The results show large regional disparities in R&D expenditure in Spain. We have identified four clusters, plus a divergent region: the Basque Country. The results are similar for the two perspectives considered: percentage of GDP and per capita. We discuss these results taking into account the effects of the Great Recession and compare the outcomes with those for a club convergence of regional GDP per capita. Finally, we carry out an ordered logit model to analyse the factors behind the clusters, with human capital and economic openness being significant.

KARYOTYPAL VARIABILITY OF UKRAINIAN BROWN DAIRY BREED COWS

KARYOTYPAL VARIABILITY OF UKRAINIAN BROWN DAIRY BREED COWS

The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species.

Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.

Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species.

Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria-Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus.

Characterization of the Complete Chloroplast Genome and Phylogenetic Implications of Euonymus microcarpus (Oliv.) Sprague

Euonymus microcarpus (Oliv.) Sprague, is a species of evergreen shrub of the genus Euonymus, family Celastraceae. Here, we extracted the genomic DNA from the leaves of E. microcarpus and constructed a paired-end library. The chloroplast genome of E. microcarpus was generated with the high-throughput sequencing by the illumina Hiseq X Ten platform and de novo assembly. The chloroplast genome had a quadripartite structure, containing a long single copy region with a size of 85,386 bp and a short single copy region with a size of 18,456 bp, separated by two inverted repeat regions of 26,850 bp. The chloroplast genome contained 133 genes identified in total, including 87 potential protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. A total of 282 simple sequence repeats and 63 long repeats were found. Furthermore, the phylogenetic relationships inferred that E. microcarpus is sister to E. japonicus and E. schensianus. A comparison of the structure of the chloroplast genomes of eight Euonymus species suggests a nucleotide variability of the junction sites and a higher divergence of non-coding regions, compared to the coding regions. The original findings of the study serves as a good reference for chloroplast genome assembly and a valuable foundation for the genetic diversity and evolution of E. microcarpus.

A numerical rotating water tank can reproduce the Coriolis effect on the urban heat dome flow

Urban heat dome flow forms under calm background conditions, which has large impacts on urban ventilation, building energy consumption and pollutants dispersion. With ongoing rapid and intense urbanisation, an increasing number of megacities have emerged. The hydraulic diameter of megacities can reach beyond than 20 km, leading to the Coriolis force playing an important role in urban heat dome flow over high-latitude cities. In this study, based on the Rossby number similarity criterion, a numerical rotating tank model (length scale of 0.5 m) was designed and compared with the real atmospheric scale (length scale of 20 km) large eddy simulation (LES) models. The reduced-scale model reproduced the deflection behaviour of the urban heat dome flow compared with those of the atmospheric cases at the same Ro number. To quantify the magnitude of deflection, an outflow angle γ in the upper-level divergent outflow region was defined. The outflow angle of the reduced-scale cases agrees well with those of the corresponding atmospheric cases. The velocity fields, temperature fields, vorticity fields, and dome structures were also analysed in both reduced scale numerical reduced-scale cases and real atmospheric scale cases. The computational time in reduced-scale cases can be reduced significantly with acceptable accuracy. These findings suggest that a rotating tank can be used to study the effect of the Coriolis force.

Russo-Chinese Energy Collaboration and Divergence in the Arctic Ocean Region: from Yamal LNG to Arctic LNG 2

The paper investigates mainly the financial aspects of the Arctic energy projects, as well as the strategic analysis of Russo-Chinese interest in the region. Therefore, the main purpose of this paper is to review the increasing interdependence of the relevant policies of the two countries and the growing Chinese involvement in Russian LNG megaprojects. China-Russia economic and political relationships have many facets, and collaboration in the LNG area is a vivid example of how cooperation between the two nations is built. While Beijing was interested in supplies from the northern neighbor for decades, the economic relationship strengthened when China included Russian LNG projects in the BRI. The project finance framework was chosen to analyze the ongoing Sino-Russian efforts to deliver Yamal LNG and Arctic LNG 2 integrated plants. According to the framework, four areas, namely equity, debt, contracts, and offtakes, are shaped by the efforts of China and Russia. While cooperation in some areas is seamless and mutually beneficial, the results in other ones are less straightforward.

Candidate pigmentation genes related to feather color variation in an indigenous chicken breed revealed by whole genome data.

Chicken plumage color is an inheritable phenotype that was naturally and artificially selected for during domestication. The Baicheng You chicken is an indigenous Chinese chicken breed presenting three main feather colors, lavender, black, and yellow plumages. To explore the genetic mechanisms underlying the pigmentation in Baicheng You chickens, we re-sequenced the whole genome of Baicheng You chicken with the three plumage colors. By analyzing the divergent regions of the genome among the chickens with different feather colors, we identified some candidate genomic regions associated with the feather colors in Baicheng You chickens. We found that EGR1, MLPH, RAB17, SOX5, and GRM5 genes were the potential genes for black, lavender, and yellow feathers. MLPH, GRM5, and SOX5 genes have been found to be related to plumage colors in birds. Our results showed that EGR1 is a most plausible candidate gene for black plumage, RAB17, MLPH, and SOX5 for lavender plumage, and GRM5 for yellow plumage in Baicheng You chicken.

Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication.

The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F ST analysis based on SVs (SV-F ST) while not by F ST analysis based on SNPs (SNP-F ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.

Machine learning assisted dynamic phenotypes and genomic variants help understand the ecotype divergence in rapeseed.

Three ecotypes of rapeseed, winter, spring, and semi-winter, have been formed to enable the plant to adapt to different geographic areas. Although several major loci had been found to contribute to the flowering divergence, the genomic footprints and associated dynamic plant architecture in the vegetative growth stage underlying the ecotype divergence remain largely unknown in rapeseed. Here, a set of 41 dynamic i-traits and 30 growth-related traits were obtained by high-throughput phenotyping of 171 diverse rapeseed accessions. Large phenotypic variation and high broad-sense heritability were observed for these i-traits across all developmental stages. Of these, 19 i-traits were identified to contribute to the divergence of three ecotypes using random forest model of machine learning approach, and could serve as biomarkers to predict the ecotype. Furthermore, we analyzed genomic variations of the population, QTL information of all dynamic i-traits, and genomic basis of the ecotype differentiation. It was found that 213, 237, and 184 QTLs responsible for the differentiated i-traits overlapped with the signals of ecotype divergence between winter and spring, winter and semi-winter, and spring and semi-winter, respectively. Of which, there were four common divergent regions between winter and spring/semi-winter and the strongest divergent regions between spring and semi-winter were found to overlap with the dynamic QTLs responsible for the differentiated i-traits at multiple growth stages. Our study provides important insights into the divergence of plant architecture in the vegetative growth stage among the three ecotypes, which was contributed to by the genetic differentiation, and might contribute to environmental adaption and yield improvement.

Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7.

Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.

The complete chloroplast genome of two Firmiana species and comparative analysis with other related species.

Firmiana is a small genus within the subfamily Sterculioideae of the Malvaceae. There are nine Firmiana species distributed in South and South-west China, most of which are endangered. Due to the shortage of plastid genomes data, the phylogenetic relationships and the evolutionary history of this genus remain unclear. Therefore, the complete chloroplast genomes of F. calcarean and F. hainanensis were sequenced using high-throughput sequencing and then compared with the chloroplast genomes of other reported Firmiana species. The genome size of F. calcarean and F. hainanensis is 161,263 and 160,031bp long, respectively, containing a total of 131 genes (including 85 protein coding genes, 37 tRNAs, 8 rRNAs, and one pseudogene). Comparative analysis revealed that the genome structure, GC content, gene content and order, as well as the RNA editing sites within the chloroplast genomes of F. calcarean and F. hainanensis were similar to previously reported Firmiana species. ML phylogenetic analysis revealed that F. danxiaensis, F. hainanensis, F. calcarean, F. simplex, and F. major form a sister group to F. colorata, F. pulcherrima, and F. kwangsiensis. The SSRs, long repeats, and 21 highly divergent regions (Pi > 0.01) identified in this study might provide potential DNA markers for further population genetics and phylogenetic studies of Firmiana. Our findings can help design new species-specific molecular markers and the general framework to further explore the evolutionary history of Firmiana and to address their conservation challenges.

Comparative chloroplast genome analysis of 10 Ilex species and the development of species-specific identification markers

The genus Ilex L. (Aquifoliaceae) includes economically important species of ornamental and medicinal value. However, germplasm identification and phylogenetic analysis of Ilex are limited due to morphological similarities and insufficient genomic resources. In this study, the complete chloroplast genome sequences of I. intermedia, I. dabieshanensis 2, and I. vomitoria were described, and along with seven published chloroplast genomes of Ilex—all of which are widely used in mid-southern China—for comparative genomics analysis. The 10 chloroplast genomes were 157,216–157,988 bp in length and displayed a typical quadripartite structure. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Genome structure, gene content, and genome arrangement were conserved, with some variations in the IR/SC (inverted repeats/single-copy) boundary regions and divergent hotspot regions. Phylogenetic analysis among 39 genus members clarified evolutionary relationships within Ilex based on complete chloroplast genome sequences. I. intermedia, I. dabieshanensis 2, and I. vomitoria were clustered in section Aquifolium in clade C. This study also developed 11 molecular markers as DNA barcodes for discriminating among the 10 Ilex species based on hypervariable regions and validated successfully. This study provides resources for further investigations on the identification, genetic engineering, evolution, and phylogeny of Ilex species.