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Betaine aldehyde dehydrogenase (BADH), mitogen-activated protein kinase (MAPK) and sodium/hydrogen exchanger (NHX) play important roles in the response to salt stress. This is the first study to identify the BADH and NHX genes in maize (Zea mays) via genome-wide analysis. The qRT‒PCR results indicated that ZmNHX was upregulated by 4.38-fold, while a significant difference was not observed in ZmBADH or ZmMAPK, with fold changes of 0.96 and 1.06, respectively, under salinity stress. Genome-wide analysis revealed 8 ZmBADH, 19 ZmMAPK and 11 ZmNHX proteins in Z. mays. Domain analysis confirmed the presence of the aldehyde dehydrogenase superfamily (ALDH-SF), protein kinase and Na_H_Exchanger domains in the ZmBADH, ZmMAPK and ZmNHX proteins, respectively. Motif analysis indicated that the phylogenetic relationships were similar to the conserved motif distributions within the clade. The Ka/Ks ratio indicated that the ZmBADH, ZmMAPK and ZmNHX genes were influenced primarily by purifying selection. This study provides comprehensive identification, characterization, and evolutionary analysis for a better understanding of the ZmBADH, ZmMAPK and ZmNHX genes in maize. [ABSTRACT FROM AUTHOR]

Paenibacillus polymyxa, a Gram-positive bacterium commonly found in soil and plant roots, plays an important role in the environment due to its nitrogen-fixing ability and is renowned for producing antibiotics like polymyxin. In this study, we present a robust framework for investigating the evolutionary and taxonomic connections of strains belonging to P. polymyxa available at the National Center for Biotechnology Information, as well as five new additional strains isolated at the University of Camerino (Italy), through pangenome analysis. These strains can produce secondary metabolites active against Staphylococcus aureus and Klebsiella pneumoniae. Employing techniques such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) estimation, OrthoFinder, and ribosomal multilocus sequence typing, we consistently divided these P. polymyxa strains into four clusters, which differ significantly in terms of ANI and dDDH percentages, both considered as reference indices for separating bacterial species. Moreover, the strains of Cluster 2 were re-classified as belonging to the Paenibacillus ottowii species. By comparing the pangenomes, we identified the core genes of each cluster and analyzed them to recognize distinctive features in terms of biosynthetic/metabolic potential. The comparison of pangenomes also allowed us to pinpoint differences between clusters in terms of genetic variability and the percentage of the genome dedicated to core and accessory genes. In conclusion, the data obtained from our analyses of strains belonging to the P. polymyxa species converge toward a necessary reclassification, which will require a fundamental contribution from microbiologists in the near future. IMPORTANCE The development of sequencing technologies has led to an exponential increase in microbial sequencing data. Accurately identifying bacterial species remains a challenge because of extensive intra-species variability, the need for multiple identification methods, and the rapid rate of taxonomic changes. A substantial contribution to elucidating the relationships among related bacterial strains comes from comparing their genomic sequences. This comparison also allows for the identification of the “pangenome,” which is the set of genes shared by all individuals of a species, as well as the set of genes that are unique to subpopulations. Here, we applied this approach to Paenibacillus polymyxa, a species studied for its potential as a biofertilizer and biocontrol agent and known as an antibiotic producer. Our work highlights the need for a more efficient classification of this bacterial species and provides a better delineation of strains with different properties. [ABSTRACT FROM AUTHOR]

This paper mainly establishes the network-based evolution model for a class of hybrid dynamic games (HDG) systems by considering the fixed event-triggering mechanism. First, a general state-space model for HDG is introduced, and a seven-tuple representation for its normal form is established. Then we establish the directed network models, which include a tree network structure form and a multi-layer temporal model. Such network models present the advantages of evolution analysis on HDG. Finally, we use HDG example with the Lanchester equation to demonstrate the feasibility of the model and the reliability of its evolutionary process. [ABSTRACT FROM AUTHOR]

ObjectiveTo analyze the hemagglutinin variation and the genetic evolution of A(H1N1)pdm09 influenza virus in Huzhou City, 2023.MethodsRespiratory tract specimens from two influenza monitoring hospitals were collected for the isolation of A(H1N1)pdm09 influenza virus and HA genome sequencing. MEGA 7.0 and BioAider were utilized to analyze genetic similarity, genetic evolution, antigen mutation sites, receptor binding sites, pathogenicity, and potential glycosylation sites of the influenza virus sequencing results.ResultsThe nucleotide and amino acid similarities between the 25 A(H1N1)pdm09 strains and the vaccine strain A/Wisconsin/67/2022 were 98.41% to 99.22% and 98.41% to 99.36%, respectively. These strains belonged to the 6B.1A.5a.2a evolutionary lineage. Notably, there were 19 amino acid variations in the HA protein, including substitutions of S137P and R142K in the epitope Ca2 cluster. Additionally, seven potential glycosylation sites were found in the HA protein, and no new or missing sites were observed in the 25 A(H1N1)pdm09 influenza virus isolates compared to the vaccine strains. Furthermore, no multiple continuous alkaline amino acids were detected in the HA cleavage site of the 25 isolates.ConclusionThe A(H1N1)pdm09 pandemic strain in 2023 closely matches the vaccine strain, indicating good protection against the currently circulating A(H1N1)pdm09 influenza virus. The circulating A(H1N1)pdm09 strain in Huzhou is characterized as a low-pathogenic influenza virus.

Abstract To reveal the molecular function of elongation family of very long chain fatty acids(ELO) protein in Cyrtotrachelus buqueti, we have identified 15 ELO proteins from C.buqueti genome. 15 CbuELO proteins were located on four chromosomes. Their isoelectric points ranged from 9.22 to 9.68, and they were alkaline. These CbuELO proteins were stable and hydrophobic. CbuELO proteins had transmembrane movement, and had multiple phosphorylation sites. The secondary structure of CbuELO proteins was mainly α-helix. A total of 10 conserved motifs were identified in CbuELO protein family. Phylogenetic analysis showed that molecular evolutionary relationships of ELO protein family between C. buqueti and Tribolium castaneum was the closest. Developmental transcriptome analysis indicated that CbuELO10, CbuELO13 and CbuELO02 genes were key enzyme genes that determine the synthesis of very long chain fatty acids in pupae and eggs, CbuELO6 and CbuELO7 were that in the male, and CbuELO8 and CbuELO11 were that in the larva. Transcriptome analysis under different temperature conditions indicated that CbuELO1, CbuELO5, CbuELO12 and CbuELO14 participated in regulating temperature stress responses. Transcriptome analysis at different feeding times showed CbuELO12 gene expression level in all feeding time periods was significant downregulation. The qRT-PCR experiment verified expression level changes of CbuELO gene family under different temperature and feeding time conditions. Protein-protein interaction analysis showed that 9 CbuELO proteins were related to each other, CbuELO1, CbuELO4 and CbuELO12 had more than one interaction relationship. These results lay a theoretical foundation for further studying its molecular function during growth and development of C. buqueti.

The R2R3-MYB gene family represents a widely distributed class of plant transcription factors. This gene family plays an important role in many aspects of plant growth and development. However, the characterization of R2R3-MYB genes present in the genome of Coptis teeta has not been reported. Here, we describe the bioinformatic identification and characterization of 88 R2R3-MYB genes in this species, and the identification of members of the R2R3-MYB gene family in species within the order Ranales most closely related to Coptis teeta. The CteR2R3-MYB genes were shown to exhibit a higher degree of conservation compared to those of A. thaliana, as evidenced by phylogeny, conserved motifs, gene structure, and replication event analyses. Cis-acting element analysis confirmed the involvement of CteR2R3-MYB genes in a variety of developmental processes, including growth, cell differentiation, and reproduction mediated by hormone synthesis. In addition, through homology comparisons with the equivalent gene family in A. thaliana, protein regulatory network prediction and transcriptome data analysis of floral organs across three time periods of flower development, 17 candidate genes were shown to exhibit biased expression in two floral phenotypes of C. teeta. This suggests their potential involvement in floral development (anther development) in this species. [ABSTRACT FROM AUTHOR]

Whirly transcription factors are unique to plants, playing pivotal roles in managing leaf senescence and DNA repair. While present in various species, their identification in Brassica napus L. (B. napus) and their differences during hybridization and polyploidy has been elusive. Addressing this, our study delves into the functional and evolutionary aspects of the Whirly gene family during the emergence of B. napus, applying bioinformatics and comparative genomics. We identified six Whirly genes in B. napus. In Brassica rapa L. (B. rapa), three Whirly genes were identified, while four were found in Brassica oleracea L. (B. oleracea). The results show that the identified Whirly genes not only have homology but also share the same chromosomal positions. Phylogenetic analysis indicates that Whirly genes in monocots and dicots exhibit high conservation. In the evolutionary process, the Whirly gene family in B. napus experienced events of intron/exon loss. Collinearity insights point to intense purifying selection post-duplication. Promoter regions housed diverse cis-acting elements linked to photoresponse, anaerobic initiation, and methyl jasmonate responsiveness. Notably, elements tied to abscisic acid signaling and meristem expression were prominent in diploid ancestors but subdued in tetraploid B. napus. Tissue-specific expression unveiled analogous patterns within subfamily genes. Subsequent qRT-PCR analysis spotlighted BnAWHY1b's potential significance in abiotic stress response, particularly drought. These findings can be used as theoretical foundations to understand the functions and effects of the Whirly gene family in B. napus, providing references for the molecular mechanism of gene evolution between this species and its diploid ancestors. [ABSTRACT FROM AUTHOR]

To reveal the molecular function of elongation family of very long chain fatty acids(ELO) protein in Cyrtotrachelus buqueti, we have identified 15 ELO proteins from C.buqueti genome. 15 CbuELO proteins were located on four chromosomes. Their isoelectric points ranged from 9.22 to 9.68, and they were alkaline. These CbuELO proteins were stable and hydrophobic. CbuELO proteins had transmembrane movement, and had multiple phosphorylation sites. The secondary structure of CbuELO proteins was mainly α-helix. A total of 10 conserved motifs were identified in CbuELO protein family. Phylogenetic analysis showed that molecular evolutionary relationships of ELO protein family between C. buqueti and Tribolium castaneum was the closest. Developmental transcriptome analysis indicated that CbuELO10, CbuELO13 and CbuELO02 genes were key enzyme genes that determine the synthesis of very long chain fatty acids in pupae and eggs, CbuELO6 and CbuELO7 were that in the male, and CbuELO8 and CbuELO11 were that in the larva. Transcriptome analysis under different temperature conditions indicated that CbuELO1, CbuELO5, CbuELO12 and CbuELO14 participated in regulating temperature stress responses. Transcriptome analysis at different feeding times showed CbuELO12 gene expression level in all feeding time periods was significant downregulation. The qRT-PCR experiment verified expression level changes of CbuELO gene family under different temperature and feeding time conditions. Protein-protein interaction analysis showed that 9 CbuELO proteins were related to each other, CbuELO1, CbuELO4 and CbuELO12 had more than one interaction relationship. These results lay a theoretical foundation for further studying its molecular function during growth and development of C. buqueti. [ABSTRACT FROM AUTHOR]

The mitochondrial cytochrome c oxidase subunit I (COI) genes of six endangered goose breeds (Xupu, Yangjiang, Yan, Wuzong, Baizi, and Lingxian) were sequenced and compared to assess the genetic diversity of endangered goose breeds. By constructing phylogenetic trees and evolutionary maps of genetic relationships, the affinities and degrees of genetic variations among the six different breeds were revealed. A total of 92 polymorphic sites were detected in the 741 bp sequence of the mtDNA COI gene after shear correction, and the GC content of the processed sequence (51.11%) was higher than that of the AT content (48.89%). The polymorphic loci within the populations of five of the six breeds (Xupu, Yangjiang, Yan, Baizi, and Lingxian) were more than 10, the haplotype diversity > 0.5, and the nucleotide diversity (Pi) > 0.005, with the Baizi geese being the exception. A total of 35 haplotypes were detected based on nucleotide variation among sequences, and the goose breed haplotypes showed a central star-shaped dispersion; the FST values were −0.03781 to 0.02645, The greatest genetic differentiation (FST = 0.02645) was observed in Yan and Wuzong breeds. The most frequent genetic exchange (Nm > 15.00) was between the Wuzong and Yangjiang geese. An analysis of molecular variance showed that the population genetic variation mainly came from within the population; the base mismatch differential distribution analysis of the goose breeds and the Tajima's D and Fu's Fs neutral detection of the historical occurrence dynamics of their populations were negative (p > 0.10). The distribution curve of the base mismatches showed a multimodal peak, which indicated that the population tended to be stabilised. These results provide important genetic information for the conservation and management of endangered goose breeds and a scientific basis for the development of effective conservation strategies. [ABSTRACT FROM AUTHOR]

Plant sterols are known to be involved in plant growth and development and also in plants' response to stress conditions. Squalene synthase (SQS) is an important enzyme for the biosynthesis of sterols and triterpenoids. Owing to their crucial role in plants, SQS genes have been identified and characterized in several plants, however not much is known about their cis-regulatory regions. In our previous study, we identified Brassicaceae specific duplications of the gene, providing an ideal opportunity to explore the diversification of the regulatory regions across the gene copies. In this study, we identified 49 SQS genes from 12 species of Brassicaceae and analyzed their genomic distribution, physicochemical properties, subcellular localization, cis-regulatory element (CRE) landscape and sequence evolution (Ka/Ks ratios). The SQS proteins were predicted to be highly stable, dominated by aliphatic amino acids, hydrophilic in nature and localized within the endoplasmic reticulum. In-silico promoter analysis identified 50 types of CREs with the predominance of light-responsive (22), followed by hormone-responsive (9), stress-responsive (7) and plant growth and development (9) elements. We identified differences both in the type and distribution of CREs across the SQS duplicates suggestive of regulatory divergence of the paralogs. The Ka/Ks analysis depicted that all the SQS genes are under purifying selection pressure. The information generated in this study would provide a useful resource for further investigations in SQS genes in Brassicaceae. [ABSTRACT FROM AUTHOR]

Ancient Chinese murals have a splendid history in ancient times, experiencing thousands of years and countless dynasties. There have been artistic classics such as Dunhuang murals that are still applauded, and the murals of Goguryeo in Ji'an are also impressive. Through systematically combing and analyzing the lotus pattern in the Goguryeo murals in Ji'an, this paper reveals the artistic expression, style changes, and cultural factors behind the lotus pattern in different historical periods. It is found that the lotus pattern in the Goguryeo period not only showed an evolution trend from simplicity to complexity and from realism to abstraction in form but also reflected the profound transformation from nature worship to Buddhist belief to royal power symbolism in meaning. However, due to the age of the murals and the interference of natural climate and artificial damage, most of the murals have been damaged, falling off, cracks, and other pathological problems, which need to be protected urgently. Therefore, the combination of mural restoration and computer technology, the use of digital technology, vision and pattern recognition technology, the restoration of mural images for automated pattern recognition and analysis of mural paintings to assist in virtual restoration, not only for artificial restoration to provide an important and practical significance of the value of the reference, but also after the restoration of the mural paintings for the digitization of longterm preservation. [ABSTRACT FROM AUTHOR]

Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribution of the SAP gene family to salt tolerance and drought resistance in sunflower. [ABSTRACT FROM AUTHOR]

The spread of digitalisation has led to the global penetration of digital finance in all sectors of the economy. The high relevance of the problem of digital finance necessitates deepening research in this area, in particular by carrying out a comprehensive analysis of the accumulated knowledge in it. The aim of the present research is to reveal the main trends and determinants of the evolution of scientific investigations in the field of digital finance by means of a bibliometric analysis of publications in the journals indexed by the Scopus scientometric database. This study was carried out in accordance with the traditional approach to bibliometric analysis and is aimed at the following objectives: determining the features of the scientific landscape in the field of digital finance by carrying out an evolutionary analysis of publication activity; identification of the main determinants for the development of research by mapping and clustering the existing array of publications using VOSviewer software. The time frame of the study was set as 2008 - 1st quarter of 2024. The results showed that the term «digital finance» is of an interdisciplinary nature. It is found that China is leading in the number of publications in this area, followed by the United States, Great Britain, and India by a notable margin. 8 clusters have been selected that characterise the key research areas. The results of the bibliometric analysis showed that the most significant development of research in the field of digital finance was in 2021-2023, with an emphasis on the development of fintech, banking services and cryptocurrencies. In 2023, it was found that the number of studies on the following issues increased: the Green Deal, COVID-19, ecosystem formation, and green energy. They are considered to be research areas that require further development in the near future. [ABSTRACT FROM AUTHOR]

ABSTRACT4-coumaric acid coenzyme A ligase (4CL) plays an important role in plant growth, development and resistance. Based on the Musa acuminata (A genome) genome database, we performed genome-wide identification and evolutionary analysis of the 4CL gene family.The results showed that there were 20 members of 4CL, and the amino acids encoded ranged from 160 to 700, all of which were hydrophobic proteins. All the members of the 4CL gene family had no signal peptide, and phosphorylation sites ranged from 10 to 60. The 4CL genes were uniformly distributed and disordered in the chromosomes. All protein members can interact with each other.Transcriptome expression analysis showed that Ma4CL3-2 expression was down-regulated and Ma4CL11-1 expression was up-regulated. Musa acuminata genomics has 22 and 19 pairs of co-linear members with Musa balbisiana and Musa itinerans genomics, respectively.The above results provide a good foundation for further research on the function of the 4CL genes and resistance breeding.Highlights Twenty 4CL gene family members were found in banana (Musa acuminata) genomes.Banana 4CLs were expressed in response to low temperature stress.The members of the banana 4CL gene family were found to be relatively structurally diverse, and it was further hypothesised that 4CL may be involved in plant lignin synthesis and closely related to the process of plant differentiation into monocotyledons and dicotyledons, based on the hypothesis of Huang et al.

[Objective] This study aimed to clarify the evolutionary trends of China’s ecological compensation mechanism and to further promote the construction of ecological civilization and a beautiful China. [Methods] From the perspective of institutional change, the study employed the Institutional Analysis and Development (IAD) framework to track, examine, and deconstruct policy changes about China’s ecological compensation mechanism from 1978 to 2023. [Results] The study found that: (1) From the perspective of institutional change, the evolution of the ecological compensation mechanism has experienced three stages—an exploratory stage of “polluters pay”, a formative stage of “beneficiaries pay”, and a refinement stage of “beneficiaries pay, protectors compensated”. The government has always been the primary participant in the ecological protection actions, dominating the direction of ecological compensation mechanism changes. (2) In terms of the internal logic of the institutional change, government leadership, clarifying the rights-responsibilities-benefits of the entities, transitioning from separate management to integrated management, and the marketization of ecological compensation are the main features and inherent pattern of China’s ecological compensation mechanism changes. [Conclusion] We should focus on four aspects to improve the ecological compensation system: improving the property rights system of natural resource assets and the management system of national territorial space of natural resources, forming a diversified and market-oriented ecological compensation method led by the government and participated by all parties, establishing a digital driven investigation and monitoring system of ecological resource protection and utilization, and forming a closed-loop mechanism of transforming lucid waters and lush mountains into mountains of gold and silver and then feeding back clear waters and green mountains.

To improve the effectiveness of dairy product safety governance, it is necessary to explore the development and mechanism of dairy product safety governance in China from a policy perspective. The texts of policies concerning dairy products from 2002 to 2021 were quantified by the grounded theory to form a dairy product safety assurance system including governance elements and behaviors. Then, based on the quantitative results and social network analysis, the evolutionary process and mechanism of dairy product safety governancein China were dissected. It was found that China’s dairy safety governance has gone through an evolutionary process from mandatory government supervision, emergency governance, government-led and enterprise-assisted governance to social co-governance. The whole evolution process reflects the country’s focus on the governance behaviors and modes, and reveals the mechanism of the comprehensive governance of dairy product safety. The governance actors work together on the governance elements through the interactions of the governance behaviors, and the governance role is reflected in the safety of dairy products through the governance elements, thus guaranteeing the quality and safety of dairy products.

The article discusses a study conducted by Shah and colleagues on the genetic characteristics and phylogeographic dynamics of lagoviruses. The study aimed to provide an update on the evolutionary history of lagoviruses and their emergence and re-emergence. However, the authors of this response argue that the methodologies used in the analysis were inappropriate and led to incorrect and misleading inferences. They highlight the importance of considering recombination in phylogenetic analysis and criticize the conclusions drawn by Shah et al. They also point out errors in the classification system proposed by Shah et al. and suggest that their analysis will only generate confusion in the already complex classification of lagoviruses. [Extracted from the article]

Objective To identify the pathogenetic characteristics of an aggregated outbreak of acute hemorrhagic conjunctivitis in a school in Bao'an District, Shenzhen in 2023, and to analyze its virological characteristics, providing a reference and basis for the rapid tracing of the source of infection and the handling of such outbreaks. Methods A total of 22 eye swab samples were collected from an AHC cluster in a school in Bao'an District, Shenzhen in 2023. Real-time fluorescence quantitative polymerase chain reaction(PCR) method was used to detect Enterovirus 70 (EV70) and Coxsackievirus A24 (CVA24) viruses in eye swab specimens collected from patients. The positive samples were performed by full sequencing of the viral gene (VP1 nucleotide). The sequenced data was compared with that from different periods and regions for CVA24, analyzing homologies and constructing a phylogenetic tree. Additionally, the nucleotide sequences were translated into amino acid sequences to analyze mutations at the amino acid sites. Results Among the 22 eye swab specimens collected, 16 samples were positive for CVA24 virus as determined by fluorescence quantitative PCR, with a positive rate of 72.73%, while all samples tested negative for EV70. VP1 primers were used to amplify 16 positive specimens, successfully sequencing the complete VP1 sequence from 14 samples. They were determined to be of the CVA24v GIV genotype. The genetic evolutionary analysis showed that the 14 CVA24v nucleotide sequences had 100.00% homology with each other, 85.14% homology with the prototype strain EH24/70 of CVA24v, and 77.27% homology with the prototype strain Joseph of CVA24. The phylogenetic tree showed that these isolates and the CVA24v strains circulating in Zhongshan City, Guangdong Province at the same time were on the same evolutionary clade, suggesting a close phylogenetic relationship. Compared with the amino acid sequence of the reference sequence before 2023, the amino acid sequence of the VP1 region of this epidemic strain formed a new mutation at the 16th site, with a substitution from leucine (L) to isoleucine (I). Conclusions The pathogen causing this outbreak of acute hemorrhagic conjunctivitis was the Coxsackievirus A24 variant, presenting a new variant site appears in its amino acid sequence. According to the results of the phylogenetic tree, the strain is presumed to originate from a strain circulating in Guangdong Province during the same period. [ABSTRACT FROM AUTHOR]

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Copyright of Journal of International Chinese Teaching is the property of Beijing Language & Culture University Press Co. Ltd. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The AP2/ERF gene family, referring to an exclusive class of transcription factors unique to plants, is involved in various biological processes, including plant growth and responses to environmental stresses like high salt and drought. In this study, the AP2/ERF gene in M. notabilis was comprehensively identified and bioinformatically analyzed based on the genomic data of M. notabilis. 106 members in the MnAP2/ERF gene family were identified in the M. notabilis genome and were categorized into five subfamilies: ERF, AP2, DREB, RAV, and Soloist, with the ERF subfamily representing 80.19% of the total. The MnAP2/ERF gene family was observed to be distributed on six chromosomes of M. notabilis. Members in the MnAP2/ERF gene family exhibited obvious differences in amino acid number, molecular weight, isoelectric point, and other properties. Approximately 68.87% of the MnAP2/ERF proteins were acidic, all exhibiting hydrophilic characteristics. Differences in conserved sequences and arrangement of AP2 domains were observed among distinct subfamilies, with genes in the same subfamily sharing similar conserved domain compositions. There were 47 genes without untranslated regions and 44 genes with two untranslated regions. The upstream functions of promoters were concentrated on light reactions and plant hormones. Evolutionarily, significant structural differences were identified, and 28 MnAP2/ERF gene family proteins could interact with each other. Moreover, 35 family genes were involved in 22 fragment repeat events, and 55 MnAP2/ERF and 84 AtAP2/ERF genes showed collinearity. The expression of the MnAP2/ERF gene family was significantly different in different parts, indicating that these gene family members were involved in different physiological activities. These results established a theoretical foundation for investigating the functional and evolutionary aspects of AP2/ERF gene family genes in M. notabilis, as well as exploring the root morphogenesis of M. notabilis. Additionally, this study contributes to a basis for the improvement of cultivar stress resistance of M. notabilis. [ABSTRACT FROM AUTHOR]

Microtubules, polymerized from α-tubulin (TUA) and β-tubulin (TUB) monomers, play a pivotal role in shaping plant morphogenesis according to developmental and environmental cues. Salix psammophila C. Wang & C. Y. Yang is an important shrub plant in sand-fixing afforestation in arid regions, with three significantly distinct plant types shaped under various environments, namely, upright, intermediate, and scattered types. However, how tubulin genes respond to the developmental and environmental signs in S. psammophila has been far less studied. Here, based on RNA-seq, Sanger sequencing, and real-time PCR (RT-PCR) data, we analyzed the phylogeny of tubulins and their expression profiles in S. psammophila among the three plant types. Furthermore, we analyzed the genetic structure and expression pattern of SpsTUB10 in S. psammophila under various abiotic stress treatments. In total, we identified 26 SpsTubulin genes in S. psammophila. The homologous alignment and phylogenetic analysis revealed that these SpsTubulin genes can be classified into two groups, corresponding to the TUA and TUB genes. The expression profiles of these SpsTubulin genes in various organs showed that most SpsTubulin genes were mainly expressed in the root. SpsTUB10 is a member of the TUB IIa group, consisting of two intros and three exons. The SpsTUB10 protein contains a typical GTPase domain and a C-terminal domain, with α-helix and random coil dominant in the secondary and tertiary structures. The RT-PCR results of SpsTUB10 showed an extremely significant difference in expression levels among the root and stem-developing organs between the upright and scattered types, and the transcript level of SpsTUB10 had a significantly negative correlation with the crown-height ratio. Under different treatments, we found that cold, osmotic stress, and short daylight could significantly increase SpsTUB10 expression levels compared to those in the controls, thereby supporting the positive role of SpsTUB10 in stress-induced responses. These results will provide evidence for the SpsTubulin genes' response to the developmental and environmental cues in S. psammophila. [ABSTRACT FROM AUTHOR]

In the present study, the diversity of two functional microbial communities; methanogenic archaea and soluble methane monooxygenase (sMMO) producing methanotrophic bacteria from rice paddy soil of different regions of Punjab, Pakistan were studied using phylogenetic analysis. Morphological and biochemical analysis showing the presence of different species of novel methanogenic archaea and sMMO-producing methanotrophic bacteria in rice paddy soil samples. The evolutionary analysis indicated a phylogram with five monophyletic groups (MPG-I to MPG-V). Results revealed that three isolated species (Sphingomonas sp. MG-1, Sphingomonas sp. MG-2 and Sphingomonas sp. MT-2) were in a close evolutionary relationship while the fourth isolated species (Sphingomonas sp. MT-1) appeared in MPG-II and showed strong evolutionary relationships with Sphingopyxis terrae and Novosphingobium capsulatum. The appearance of Sphingomonas sp. MT-1 in a different clade was also evidence of its distant evolutionary relationships with the other three isolated strains of Sphingomonas sp. (MG-2, MG-1 and MT-2). The strain designated as MT-1 was found to be rod-shaped with µmax 0.065±0.25 h-1 and 13.59±0.25 UmL-1 sMMO. The optimum pH and temperature for the growth of MT-1 and production of sMMO were 6.3 and 37 °C, respectively. The concentration of MG-1 and MT-1 was significantly higher in the soil of Faisalabad region (FSD) as compared to MG-2 and MT-2 in soil of Sargodha region (SGD). Overall FSD soil was observed to be more suitable for methanogenic and methanotrophic growth than SGD soil according to the conditions needed for microbial growth in soil. [ABSTRACT FROM AUTHOR]

The spread of digitalisation has led to the global penetration of digital finance in all sectors of the economy. The high relevance of the problem of digital finance necessitates deepening research in this area, in particular by carrying out a comprehensive analysis of the accumulated knowledge in it. The aim of the present research is to reveal the main trends and determinants of the evolution of scientific investigations in the field of digital finance by means of a bibliometric analysis of publications in the journals indexed by the Scopus scientometric database. This study was carried out in accordance with the traditional approach to bibliometric analysis and is aimed at the following objectives: determining the features of the scientific landscape in the field of digital finance by carrying out an evolutionary analysis of publication activity; identification of the main determinants for the development of research by mapping and clustering the existing array of publications using VOSviewer software. The time frame of the study was set as 2008 – 1st quarter of 2024. The results showed that the term «digital finance» is of an interdisciplinary nature. It is found that China is leading in the number of publications in this area, followed by the United States, Great Britain, and India by a notable margin. 8 clusters have been selected that characterise the key research areas. The results of the bibliometric analysis showed that the most significant development of research in the field of digital finance was in 2021-2023, with an emphasis on the development of fintech, banking services and cryptocurrencies. In 2023, it was found that the number of studies on the following issues increased: the Green Deal, COVID-19, ecosystem formation, and green energy. They are considered to be research areas that require further development in the near future.

Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribution of the SAP gene family to salt tolerance and drought resistance in sunflower.

ObjectiveTo analyze the genomic characteristics of the monkeypox virus (MPXV) strains isolated from local cases in Ji′nan city, Shandong province. MethodsBlood serum and vesicular fluid samples from suspected cases of MPXV infection reported in Ji′nan city from June to October 2023 were tested for MPXV nucleic acids. The complete genome sequence of MPXV was obtained using whole-genome sequencing (WGS) technology. Molecular genetic evolution of the MPXV genome sequence was performed using Mega 11 software, Bioedit software, and the Nextclade online comparison website. Systematic phylogenetic trees and nucleotide and amino acid sequence mutation analyses were performed. ResultsIn this study, the complete genome sequences of 7 strains of MPXV isolated from the cases in Ji′nan city were obtained by WGS, with a total genome length of 196 858 bp. The online comparison results uploaded to the Nexttrade website showed that all of them belonged to the IIb branch of the West African branch, and the lineage classification was C.1. The number of nucleotide variations with a depth greater than 50% is 86, and the total number of variations with an effect of ≥ intermediate is 39. ConclusionThe evolutionary distance between the sequences of MPXV strains isolated in Ji′nan city and those in China is relatively close, belonging to the same evolutionary branch, and no new branches have been found.

[ Objective ] Sugars will eventually be exported transporters ( SWEETs ) play an important role in growth and development of plants. The aims of the study were to elucidate the role of the SWEET gene family in sugar accumulation during the development of wolfberry , and to provide a reference for revealing the role of the SWEET genes in the development of wolfberry fruits. [ Methods ] In the present study , based on genomic data of wolfberry , LbaSWEETs were identified by bioinformatics method , and the ex- pression of LbaSWEETs during fruit development was analyzed using published transcriptional data. [ Results ] There were 37 members of the SWEET gene family , which were randomly distributed on 10 chromosomes , encoding 152 621 amino acids. The molecular weight of the proteins was 16.87 69.97 kD , and the isoelectric point was 4.96 9.86. Subcellular localizations were predicted to be located in the chloroplast or plasma membrane , most containing seven transmembrane helices. Phylogenetic analysis showed that 37 LbaSWEET proteins were divided into 4 subgroups , which had similar gene structures and conserved motifs. Analysis of promoter elements showed that LbaSWEET promoters were rich in hor- mone response , stress response , and growth response elements. Transcriptome and qRT-PCR analysis showed that the expression of LbaSWEET9 and LbaSWEET29 genes was increased significantly with fruit ripening. Pearson correlation analysis showed that the expression levels of LbaSWEET9 and Lba- SWEET29 genes were significantly positively correlated with fructose content. [ Conclusion ] LbaSWEET9 and LbaSWEET29 are the key genes that may play an important role in the accumulation of fructose sugar.

Abstract AP2 (APETALA2)/EREBP (ethylene-responsive element-binding protein), cytochrome c oxidase (COX) and nonspecific lipid transfer proteins (LTP) play important roles in the response to drought stress. This is the first study to identify the COX gene in Zea mays L. via genome-wide analysis. The qRT‒PCR results indicated that AP2/EREBP, COX and LTP were downregulated, with fold changes of 0.84, 0.53 and 0.31, respectively, after 12 h of drought stress. Genome-wide analysis identified 78 AP2/EREBP, 6 COX and 10 LTP genes in Z. mays L. Domain analysis confirmed the presence of the AP2 domain, Cyt_c_Oxidase_Vb domain and nsLTP1 in the AP2/EREBP, COX and LTP proteins, respectively. The AP2/EREBP protein family (AP2) includes five different domain types: the AP2/ERF domain, the EREBP-like factor (EREBP), the ethylene responsive factor (ERF), the dehydration responsive element binding protein (DREB) and the SHN SHINE. Synteny analysis of the AP2/EREBP, COX and LTP genes revealed collinearity orthologous relationships in O. sativa, H. vulgare and A. thaliana. AP2/EREBP genes were found on the 10 chromosomes of Z. mays L. COX genes were found on chromosomes 1, 3, 4, 5, 7 and 8. LTP genes were found on chromosomes 1, 3, 6, 8, 9 and 10. In the present study, the Ka/Ks ratios of the AP2/EREBP paralogous pairs indicated that the AP2/EREBP genes were influenced primarily by purifying selection, which indicated that the AP2/EREBP genes received strong environmental pressure during evolution. The Ka/Ks ratios of the COX-3/COX-4 paralogous pairs indicate that the COX-3/COX-4 genes were influenced primarily by Darwinian selection (driving change). For the LTP genes, the Ka/Ks ratios of the LTP-1/LTP-10, LTP-5/LTP-3 and LTP-4/LTP-8 paralogous pairs indicate that these genes were influenced primarily by purifying selection, while the Ka/Ks ratios of the LTP-2/LTP-6 paralogous pairs indicate that these genes were influenced primarily by Darwinian selection. The duplication time of the AP2/EREBP paralogous gene pairs in Z. mays L. ranged from approximately 9.364 to 100.935 Mya. The duplication time of the COX-3/COX-4 paralogous gene pair was approximately 5.217 Mya. The duplication time of the LTP paralogous gene pairs ranged from approximately 19.064 to 96.477 Mya. The major focus of research is to identify the genes that are responsible for drought stress tolerance to improve maize for drought stress tolerance. The results of the present study will improve the understanding of the functions of the AP2/EREBP, COX and LTP genes in response to drought stress.

Abstract Background 'Taishuu' has a crisp texture, abundant juice, and sweet flavor with hints of cantaloupe. The availability of mitochondrial genome data of Diospyros species is far from the known number of species. Results The sequencing data were assembled into a closed circular mitochondrial chromosome with a 421,308 bp length and a 45.79% GC content. The mitochondrial genome comprised 40 protein-coding, 24 tRNA, and three rRNA genes. The most common codons for arginine (Arg), proline (Pro), glycine (Gly), tryptophan (Trp), valine (Val), alanine (Ala), and leucine (Leu) were AGA, CCA, GGA, UGG, GUA, GCA, and CUA, respectively. The start codon for cox1 and nad4L protein-coding genes was ACG (ATG), whereas the remaining protein-coding genes started with ATG. There are four types of stop codons: CGA, TAA, TAG, and TGA, with TAA being the most frequently used stop codon (45.24%). In the D. kaki Thunb. 'Taishuu' mitochondrial genome, a total of 645 repeat sequences were identified, including 125 SSRs, 7 tandem repeats, and 513 dispersed repeats. Collinearity analysis revealed a close relationship between D. kaki Thunb. 'Taishuu' and Diospyros oleifera, with conserved homologous gene fragments shared among these species in large regions of the mitochondrial genome. The protein-coding genes ccmB and nad4L were observed to undergo positive selection. Analysis of homologous sequences between chloroplasts and mitochondria identified 28 homologous segments, with a total length of 24,075 bp, accounting for 5.71% of the mitochondrial genome. These homologous segments contain 8 annotated genes, including 6 tRNA genes and 2 protein-coding genes (rrn18 and ccmC). There are 23 homologous genes between chloroplasts and nuclei. Mitochondria, chloroplasts, and nuclei share two homologous genes, which are trnV-GAC and trnW-CCA. Conclusion In conclusion, a high-quality chromosome-level draft genome for D. kaki was generated in this study, which will contribute to further studies of major economic traits in the genus Diospyros.

Abstract Previously we isolated three Fusarium strains (a F. sacchari strain namely GXUF-1, and another two F. commune strains namely GXUF-2 and GXUF-3), and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila. Considering that Fusarium spp. are a group of widely distributed fungal pathogens, we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar (Guitang42), using a suitable inoculation method established based on infection assays using Badila. We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42, to different extents. To better investigate the potential pathogenicity mechanisms, we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains. The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7–48.2 Mb, with G + C contents of 48.0–48.5%, and 14,154–15,175 coding genes. The coding genes were annotated by multiple public databases, and potential pathogenic genes were predicted using proprietary databases (such as PHI, DFVF, CAZy, etc.). Furthermore, based on evolutionary analysis of the coding sequence, we found that contraction and expansion of gene families occurred in the three Fusarium strains. Overall, our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane, and provide clues to understand the pathogenic mechanisms of Fusarium spp. causing sugarcane root rot.

SUMMARY: Developing climate‐resilient crops is critical for future food security and sustainable agriculture under current climate scenarios. Of specific importance are drought and soil salinity. Tolerance traits to these stresses are highly complex, and the progress in improving crop tolerance is too slow to cope with the growing demand in food production unless a major paradigm shift in crop breeding occurs. In this work, we combined bioinformatics and physiological approaches to compare some of the key traits that may differentiate between xerophytes (naturally drought‐tolerant plants) and mesophytes (to which the majority of the crops belong). We show that both xerophytes and salt‐tolerant mesophytes have a much larger number of copies in key gene families conferring some of the key traits related to plant osmotic adjustment, abscisic acid (ABA) sensing and signalling, and stomata development. We show that drought and salt‐tolerant species have (i) higher reliance on Na for osmotic adjustment via more diversified and efficient operation of Na+/H+ tonoplast exchangers (NHXs) and vacuolar H+‐ pyrophosphatase (VPPases); (ii) fewer and faster stomata; (iii) intrinsically lower ABA content; (iv) altered structure of pyrabactin resistance/pyrabactin resistance‐like (PYR/PYL) ABA receptors; and (v) higher number of gene copies for protein phosphatase 2C (PP2C) and sucrose non‐fermenting 1 (SNF1)‐related protein kinase 2/open stomata 1 (SnRK2/OST1) ABA signalling components. We also show that the past trends in crop breeding for Na+ exclusion to improve salinity stress tolerance are counterproductive and compromise their drought tolerance. Incorporating these genetic insights into breeding practices could pave the way for more drought‐tolerant and salt‐resistant crops, securing agricultural yields in an era of climate unpredictability. Significance Statement: This work compare some of the key traits that differentiate between xerophytes (naturally drought‐tolerant plants) and mesophytes (to which majority of the crops belong). Incorporating these genetic insights into breeding practices could pave the way for more drought‐tolerant and salt‐resistant crops, securing agricultural yields in an era of climate unpredictability. [ABSTRACT FROM AUTHOR]

PIN-formed (PIN) proteins—specific transcription factors that are widely distributed in plants—play a pivotal role in regulating polar auxin transport, thus influencing plant growth, development, and abiotic stress responses. Although the identification and functional validation of PIN genes have been extensively explored in various plant species, their understanding in woody plants—particularly the endangered species Phoebe bournei (Hemsl.) Yang—remains limited. P. bournei is an economically significant tree species that is endemic to southern China. For this study, we employed bioinformatics approaches to screen and identify 13 members of the PIN gene family in P. bournei. Through a phylogenetic analysis, we classified these genes into five sub-families: A, B, C, D, and E. Furthermore, we conducted a comprehensive analysis of the physicochemical properties, three-dimensional structures, conserved motifs, and gene structures of the PbPIN proteins. Our results demonstrate that all PbPIN genes consist of exons and introns, albeit with variations in their number and length, highlighting the conservation and evolutionary changes in PbPIN genes. The results of our collinearity analysis indicate that the expansion of the PbPIN gene family primarily occurred through segmental duplication. Additionally, by predicting cis-acting elements in their promoters, we inferred the potential involvement of PbPIN genes in plant hormone and abiotic stress responses. To investigate their expression patterns, we conducted a comprehensive expression profiling of PbPIN genes in different tissues. Notably, we observed differential expression levels of PbPINs across the various tissues. Moreover, we examined the expression profiles of five representative PbPIN genes under abiotic stress conditions, including heat, cold, salt, and drought stress. These experiments preliminarily verified their responsiveness and functional roles in mediating responses to abiotic stress. In summary, this study systematically analyzes the expression patterns of PIN genes and their response to abiotic stresses in P. bournei using whole-genome data. Our findings provide novel insights and valuable information for stress tolerance regulation in P. bournei. Moreover, the study offers significant contributions towards unraveling the functional characteristics of the PIN gene family. [ABSTRACT FROM AUTHOR]

Previously we isolated three Fusarium strains (a F. sacchari strain namely GXUF-1, and another two F. commune strains namely GXUF-2 and GXUF-3), and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila. Considering that Fusarium spp. are a group of widely distributed fungal pathogens, we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar (Guitang42), using a suitable inoculation method established based on infection assays using Badila. We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42, to different extents. To better investigate the potential pathogenicity mechanisms, we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains. The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7–48.2 Mb, with G + C contents of 48.0–48.5%, and 14,154–15,175 coding genes. The coding genes were annotated by multiple public databases, and potential pathogenic genes were predicted using proprietary databases (such as PHI, DFVF, CAZy, etc.). Furthermore, based on evolutionary analysis of the coding sequence, we found that contraction and expansion of gene families occurred in the three Fusarium strains. Overall, our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane, and provide clues to understand the pathogenic mechanisms of Fusarium spp. causing sugarcane root rot. [ABSTRACT FROM AUTHOR]

Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization of lipid droplets (LDs) in seeds of oil crops. Despite the proposal of five oleosin clades (i.e., U, SL, SH, T, and M) in angiosperms, their evolution in eudicots has not been well-established. In this study, we employed Brassicales, an economically important order of flowering plants possessing the lineage-specific T clade, as an example to address this issue. Three to 10 members were identified from 10 species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, and Cleomaceae. Evolutionary and reciprocal best hit-based homologous analyses assigned 98 oleosin genes into six clades (i.e., U, SL, SH, M, N, and T) and nine orthogroups (i.e., U1, U2, SL, SH1, SH2, SH3, M, N, and T). The newly identified N clade represents an ancient group that has already appeared in the basal angiosperm Amborella trichopoda, which are constitutively expressed in the tree fruit crop Carica papaya, including pulp and seeds of the fruit. Moreover, similar to Clade N, the previously defined M clade is actually not Lauraceae-specific but an ancient and widely distributed group that diverged before the radiation of angiosperm. Compared with A. trichopoda, lineage-specific expansion of the family in Brassicales was largely contributed by recent whole-genome duplications (WGDs) as well as the ancient γ event shared by all core eudicots. In contrast to the flower-preferential expression of Clade T, transcript profiling revealed an apparent seed/embryo/endosperm-predominant expression pattern of most oleosin genes in Arabidopsis thaliana and C. papaya. Moreover, the structure and expression divergence of paralogous pairs was frequently observed, and a good example is the lineage-specific gain of an intron. These findings provide insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in nonmodel plants such as C. papaya. [ABSTRACT FROM AUTHOR]

Abstract Background Phospholipases As (PLAs) are acyl hydrolases that catalyze the release of free fatty acids in phospholipids and play multiple functions in plant growth and development. The three families of PLAs are: PLA1, PLA2 (sPLA), and patatin-related PLA (pPLA). The diverse functions that pPLAs play in the growth and development of a broad range of plants have been demonstrated by prior studies. Methods Genome-wide analysis of the pPLA gene family and screening of genes for expression verification and gene silencing verification were conducted. Additionally, pollen vitality testing, analysis of the pollen expression pattern, and the detection of POD, SOD, CAT, MDA, and H2O2 were performed. Result In this study, 294 pPLAs were identified from 13 plant species, including 46 GhpPLAs that were divided into three subfamilies (I-III). Expression patterns showed that the majority of GhpPLAs were preferentially expressed in the petal, pistil, anther, and ovule, among other reproductive organs. Particularly, GhpPLA23 and GhpPLA44, were found to be potentially important for the reproductive development of G. hirsutum. Functional validation was demonstrated by VIGS which showed that reduced expression levels of GhpPLA23 and GhpPLA44 in the silenced plants were associated with a decrease in pollen activity. Moreover, a substantial shift in ROS and ROS scavengers and a considerable increase in POD, CAT, SOD, and other physiological parameters was found out in these silenced plants. Our results provide plausibility to the hypothesis that GhpPLA23 and GhpPLA44 had a major developmental impact on cotton reproductive systems. These results also suggest that pPLAs are important for G. hirsutum’s reproductive development and suggest that they could be employed as potential genes for haploid induction. Conclusions The findings of the present research indicate that pPLA genes are essential for the development of floral organs and sperm cells in cotton. Consequently, this family might be important for the reproductive development of cotton and possibly for inducing the plant develop haploid progeny.

Abstract Background High-Affinity Potassium ions represent one of the most important and large group of potassium transporters. Although HAK genes have been studied in a variety of plant species, yet, remain unexplored in common bean. Results In the current study, 20 HAK genes were identified in common bean genome. Super-family “K_trans” domain was found in all PvHAK genes. Signals for localization of PvHAK proteins were detected in cell membrane. Fifty three HAKs genes, across diverse plant species, were divided into 5 groups based on sequential homology. Twelve pairs of orthologs genes were found in various plant species. PvHAKs genes were distributed unequally on 7 chromosomes with maximum number (7) mapped on chromosome 2 while only 1 PvHAK found on each chromosome 1, 4, and 6. Tandem gene duplication was witnessed in 2 paralog pairs while 1 pair exhibited segmental gene duplication. Five groups were made in PvHAK gene family based on Phylogeny. Maximum PvHAKs (10) were detected in Group-V while group-II composed of only 1 PvHAK gene. Variation was witnessed in number and size of motifs, and structure of PvHAKs associated with different groups. Light and hormone responsive elements contributed 57 and 24% share, respectively, to cis regulatory elements. qRT-PCR based results revealed significant increase in expression of all 4 PvHAK genes under low-potassium stress. Conclusion The current study provides valuable information for further functional characterization and uncovering the molecular mechanism associated with Potassium transportation in plants.

Whirly transcription factors are unique to plants, playing pivotal roles in managing leaf senescence and DNA repair. While present in various species, their identification in Brassica napus L. (B. napus) and their differences during hybridization and polyploidy has been elusive. Addressing this, our study delves into the functional and evolutionary aspects of the Whirly gene family during the emergence of B. napus, applying bioinformatics and comparative genomics. We identified six Whirly genes in B. napus. In Brassica rapa L. (B. rapa), three Whirly genes were identified, while four were found in Brassica oleracea L. (B. oleracea). The results show that the identified Whirly genes not only have homology but also share the same chromosomal positions. Phylogenetic analysis indicates that Whirly genes in monocots and dicots exhibit high conservation. In the evolutionary process, the Whirly gene family in B. napus experienced events of intron/exon loss. Collinearity insights point to intense purifying selection post-duplication. Promoter regions housed diverse cis-acting elements linked to photoresponse, anaerobic initiation, and methyl jasmonate responsiveness. Notably, elements tied to abscisic acid signaling and meristem expression were prominent in diploid ancestors but subdued in tetraploid B. napus. Tissue-specific expression unveiled analogous patterns within subfamily genes. Subsequent qRT-PCR analysis spotlighted BnAWHY1b’s potential significance in abiotic stress response, particularly drought. These findings can be used as theoretical foundations to understand the functions and effects of the Whirly gene family in B. napus, providing references for the molecular mechanism of gene evolution between this species and its diploid ancestors.

THAP9 is a transposable element-derived gene that encodes the THAP9 protein, which is homologous to the Drosophila P-element transposase (DmTNP) and can cut and paste DNA. However, the exact functional role of THAP9 is unknown. Here, we perform structure prediction, evolutionary analysis and extensive in silico characterization of THAP9, including predicting domains and putative post-translational modification sites. Comparison of the AlphaFold-predicted structure of THAP9 with the DmTNP CryoEM structure, provided insights about the C2CH motif and other DNA binding residues, RNase H-like catalytic domain and insertion domain of the THAP9 protein. We also predicted previously unreported mammalian-specific post-translational modification sites that may play a role in the subcellular localization of THAP9. Furthermore, we observed that there are distinct organism class-specific conservation patterns of key functional residues in certain THAP9 domains.

Callose is an important polysaccharide composed of beta-1,3-glucans and is widely implicated in plant development and defense responses. Callose synthesis is mainly catalyzed by a family of callose synthases, also known as glucan synthase-like (GSL) enzymes. Despite the fact that GSL family genes were studied in a few plant species, their functional roles have not been fully understood in woody perennials. In this study, we identified total of 84 GSL genes in seven plant species and classified them into six phylogenetic clades. An evolutionary analysis revealed different modes of duplication driving the expansion of GSL family genes in monocot and dicot species, with strong purifying selection constraining the protein evolution. We further examined the gene structure, protein sequences, and physiochemical properties of 11 GSL enzymes in Prunus mume and observed strong sequence conservation within the functional domain of PmGSL proteins. However, the exon–intron distribution and protein motif composition are less conservative among PmGSL genes. With a promoter analysis, we detected abundant hormonal responsive cis-acting elements and we inferred the putative transcription factors regulating PmGSLs. To further understand the function of GSL family genes, we analyzed their expression patterns across different tissues, and during the process of floral bud development, pathogen infection, and hormonal responses in Prunus species and identified multiple GSL gene members possibly implicated in the callose deposition associated with bud dormancy cycling, pathogen infection, and hormone signaling. In summary, our study provides a comprehensive understanding of GSL family genes in Prunus species and has laid the foundation for future functional research of callose synthase genes in perennial trees. [ABSTRACT FROM AUTHOR]