Chromosomal Location Research Articles

Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs.

Pseudomonas aeruginosa has increasing clinical relevance and commonly occupies the cystic fibrosis (CF) airways. Its ability to colonize and persist in diverse niches is attributed to its large accessory genome, where prophages represent a common feature and may contribute to its fitness and persistence. We focused on the CF airways niche and used 197 longitudinal isolates from 12 patients persistently infected by P. aeruginosa. We computationally predicted intact prophages for each longitudinal group and scored their long-term persistence. We then confirmed prophage inducibility and mapped their location in the host chromosome with lysate sequencing. Using comparative genomics, we evaluated prophage genomic diversity, long-term persistence and level of genomic maintenance. Our findings support previous findings that most P. aeruginosa genomes harbour prophages some of which can self-induce, and that a common CF-treating antibiotic, ciprofloxacin, can induce prophages. Induced prophage genomes displayed high diversity and even genomic novelty. Finally, all induced prophages persisted long-term with their genomes avoiding gene loss and degradation over four years of host replication in the stressful CF airways niche. This and our detection of phage genes which contribute to host competitiveness and adaptation, lends support to our hypothesis that the vast majority of prophages detected as intact and inducible in this study facilitated their host fitness and persistence.

The repetitive DNA landscape in the 'brizantha' agamic complex of Urochloa P. Beauv.

Urochloa P. Beauv. (formerly classified as Brachiaria (Trin.) Griseb.) is a genus of African perennial grasses that is extensively cultivated in tropical countries for cattle nutrition. Three of the most economically relevant species, Urochloa brizantha, U. decumbens, and U. ruziziensis, form the 'brizantha' agamic complex, which includes allopolyploid series with distinct subgenomes. Investigating the composition and organization of repetitive DNA, a major component of grass genomes, can provide insights into their genomic relationships and evolutionary history. This study aimed to characterize the repetitive DNA landscape of selected Urochloa species belonging to the 'brizantha' agamic complex; identify and compare major repeat classes across species and evaluate their potential as cytogenetic markers on mitotic chromosomes using fluorescent in situ hybridization (FISH). Clustering analysis revealed that repetitive DNA constitutes 56-65% of the genomes, with Ty3/Gypsy retrotransposons, particularly the Athila and Retand lineages, representing the most abundant repeat class. U. decumbens exhibited the highest proportion of Ty3/Gypsy retrotransposons, while U. ruziziensis had the highest satellite DNA content. The chromosomal location of representative satellites (UroSat-1a, UroSat-2a, and UroSat-3) was determined in all three species via FISH. UroSat-1a was detected in all centromeres, while UroSat-2a and UroSat-3 signals varied in number and position. Our findings validate the use of satDNA as cytogenetic markers in the Urochloa 'brizantha' agamic complex and revealed genomic relationships among different species and ploidy levels.

Identification and characterization of GRAS genes in passion fruit (Passiflora edulis Sims) revealed their roles in development regulation and stress response.

Twenty-nine GRAS genes were identified in passion fruit, the N-terminal regions and 3D (three-dimensional) structures were closely related with their tissue-specific expression patterns. Candidate PeGRASs for enhancing stress resistance were identified. Passion fruit (Passiflora edulis Sims) is a tropical fruit crop with significant edible and ornamental value, but its growth and development are highly sensitive to environmental conditions. The plant-specific GRAS gene family plays critical roles in regulating growth, development, and stress responses. Here, we performed the first comprehensive analysis of the GRAS gene family in passion fruit. A total of 29 GRAS genes were identified and named PeGRAS1 to PeGRAS29 based on their chromosomal locations. Phylogenetic analysis using GRAS proteins from passion fruit, Arabidopsis, and rice revealed that PeGRAS proteins could be classified into 10 subfamilies. Compared to Arabidopsis, passion fruit lacked members from the LAS subfamily but gained one GRAS member (PeGRAS9) clustered with the rice-specific Os4 subfamily. Structural analysis performed in silico revealed that most PeGRAS members were intron less and exhibited conserved motif patterns near the C-terminus, while the N-terminal regions varied in sequence length and composition. Members within certain subfamilies including DLT, PAT1, and LISCL with similar unstructured N-terminal regions and 3D structures, exhibited similar tissue-specific expression patterns. While PeGRAS members with difference in these structural features, even within the same subfamily (e.g., DELLA), displayed distinct expression patterns. These findings highlighted that the N-terminal regions of GRAS proteins may be critical for their specific functions. Moreover, many PeGRAS members, particularly those from the PAT1 subfamily, were widely involved in stress responses, with PeGRAS19 and PeGRAS26 likely playing roles in cold tolerance, and PeGRAS25 and PeGRAS28 in drought resistance. This study provides a foundation for further functional research on PeGRASs and offers potential candidates for molecular breeding aimed at enhancing stress tolerance in passion fruit.

Distinct checkpoint and homolog biorientation pathways regulate meiosis I in Drosophila oocytes.

Mitosis and meiosis have two mechanisms for regulating the accuracy of chromosome segregation: error correction and the spindle assembly checkpoint (SAC). We have investigated the function of several checkpoint proteins in meiosis I of Drosophila oocytes. Increased localization of several SAC proteins was found upon depolymerization of microtubules by colchicine. However, unattached kinetochores or errors in biorientation of homologous chromosomes do not induce increased SAC protein localization. Furthermore, the metaphase I arrest does not depend on SAC genes, suggesting the APC is inhibited even if the SAC is not functional. Two SAC proteins, ROD of the ROD-ZW10-Zwilch (RZZ) complex and MPS1, are also required for the biorientation of homologous chromosomes during meiosis I, suggesting an error correction function. Both proteins aid in preventing or correcting erroneous attachments and depend on SPC105R for localization to the kinetochore. We have defined a region of SPC105R, amino acids 123-473, that is required for ROD localization and biorientation of homologous chromosomes at meiosis I. Surprisingly, ROD removal from kinetochores and movement towards spindle poles, termed "streaming," is independent of the dynein adaptor Spindly and is not linked to the stabilization of end-on attachments. Instead, meiotic RZZ streaming appears to depend on cell cycle stage and may be regulated independently of kinetochore attachment or biorientation status. We also show that Spindly is required for biorientation at meiosis I, and surprisingly, the direction of RZZ streaming.

Epigenetic state and gene expression remain stable after CRISPR/Cas-mediated chromosomal inversions.

The epigenetic state of chromatin, gene activity and chromosomal positions are interrelated in plants. In Arabidopsis thaliana, chromosome arms are DNA-hypomethylated and enriched with the euchromatin-specific histone mark H3K4me3, while pericentromeric regions are DNA-hypermethylated and enriched with the heterochromatin-specific mark H3K9me2. We aimed to investigate how the chromosomal location affects epigenetic stability and gene expression by chromosome engineering. Two chromosomal inversions of different sizes were induced using CRISPR/Cas9 to move heterochromatic, pericentric sequences into euchromatic regions. The epigenetic status of these lines was investigated using whole-genome bisulfite sequencing and chromatin immunoprecipitation. Gene expression changes following the induction of the chromosomal inversions were studied via transcriptome analysis. Both inversions had a minimal impact on the global distribution of histone marks and DNA methylation patterns, although minor epigenetic changes were observed across the genome. Notably, the inverted chromosomal regions and their borders retained their original epigenetic profiles. Gene expression analysis showed that only 0.5-1% of genes were differentially expressed genome-wide following the induction of the inversions. CRISPR/Cas-induced chromosomal inversions minimally affect epigenetic landscape and gene expression, preserving their profiles in subsequent generations.

Genome-wide identification and expression analysis of GRAS transcription factors under cold stress in diploid and triploid Eucalyptus

The GRAS [GRI (Gibberellic Acid Insensitive), RGA (Repressor of GAI-3 mutant), and SCR (Scarecrow)] transcription factors play a pivotal role in the development and stress responses of plants. Eucalyptus is an important fast-growing tree species worldwide, yet its poor cold tolerance limits its cultivation range. This study conducted a bioinformatics analysis of Eucalyptus grandis GRAS family and investigated the expression patterns of GRAS genes in different ploidy Eucalyptus under cold treatment. This study identified 92 EgrGRAS genes, which were divided into eight subfamilies. Interspecies synteny analysis found that E. grandis and Populus trichocarpa have more syntenic GRAS gene pairs. Chromosome localization analysis revealed that 90 EgrGRAS genes were found to be unevenly distributed across 11 chromosomes. Gene structure analysis found similar intron-exon structures in EgrGRAS genes. Protein motif analysis revealed that proteins within the same subfamily have certain structural similarities. The physical and chemical properties of the proteins encoded by EgrGRAS genes vary, but the ranges of amino acid numbers, molecular weights, and isoelectric points (pI) are similar to those of GRAS proteins from other species. Subcellular localization prediction using software found that 56 members of EgrGRAS family are localized in the nucleus, with a few members localized in the cytoplasm, chloroplasts, and mitochondria. Tobacco subcellular localization experiments verified a nuclear-localized GRAS transcription factor. Cis-acting element analysis predicted that EgrGRAS genes are involved in the growth as well as the response to hormones, light induction, and low-temperature stress. Transcriptome data analysis and quantitative real-time PCR (qRT-PCR) experiments in diploid and triploid Eucalyptus urophylla found that some EgrGRAS genes exhibited upregulated expression under different cold treatment durations, with certain genes from the LISCL, PAT1, and DELLA subfamilies significantly upregulated in triploid Eucalyptus. These EgrGRAS transcription factors may play an important role in Eucalyptus response to cold stress. The study lays a molecular foundation for the breeding of cold-resistant Eucalyptus varieties.

Genome-Wide Characterization and Expression Profiling of YTH Domain-Containing RNA-Binding Protein Family in Taxus chinensis

N6-methyladenosine (m6A), the most common internal RNA modification in eukaryotes, plays a vital role in post-transcriptional regulation. The YT521-B homology (YTH) domain plays a pivotal role in the methylation-dependent recognition of m6A. In this study, we performed an in-depth analysis of the YTH domain-containing RNA-binding protein family in Taxus chinensis (T. chinensis), a species renowned for its rich content of taxol, a significant compound in cancer therapy. We identified and analyzed six YTH domain-containing proteins in T. chinensis, elucidating their phylogenetic relationships, conserved domain, gene structures, conserved motifs, and chromosomal locations. The prion-like domain analyses provided insights into their potential functions in liquid–liquid phase separation and mRNA metabolism. Quantitative tissue analysis revealed TcYTH1 as the most highly expressed gene among the six TcYTH members. Additionally, we investigated the expression profiles of TcYTH genes under various stress conditions, such as high light, ABA, and PEG treatments. The expression levels of all TcYTH genes changed significantly under stress, revealing their involvement in stress response mechanisms. Our research provides novel insights into the YTH genes family in T. chinensis, emphasizing their potential roles in growth regulation and stress tolerance. The identification and analysis of these genes lay the groundwork for future studies on their functional roles in plant biology.

Centromeric chromatin clearings demarcate the site of kinetochore formation.

The centromere is the chromosomal locus that recruits the kinetochore, directing faithful propagation of the genome during cell division. Using cryo-ET on human mitotic chromosomes, we reveal a distinctive architecture at the centromere: clustered 20- to 25-nm nucleosome-associated complexes within chromatin clearings that delineate them from surrounding chromatin. Centromere components CENP-C and CENP-N are each required for the integrity of the complexes, while CENP-C is also required to maintain the chromatin clearing. We find that CENP-C is required in mitosis, not just for kinetochore assembly, likely reflecting its role in organizing the inner kinetochore during chromosome segregation. We further visualize the scaffold of the fibrous corona, a structure amplified at unattached kinetochores, revealing crescent-shaped parallel arrays of fibrils extending >1μm. Thus, we reveal how the organization of centromeric chromatin creates a clearing at the site of kinetochore formation as well as the nature of kinetochore amplification mediated by corona fibrils.

Genome-wide analysis of TCP family genes and their constitutive expression pattern analysis in the melon (Cucumis melo).

TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done. The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions. The chromosomal location, gene structure, conserved motifs, protein domains, structural homology, cis-regulating elements, transcript expression patterns, and potential protein-protein interactions were analyzed using various databases and webtools. A total of 29 putative TCP genes are identified in melon. These genes were classified into two classes: Class-I (13 genes) and Class-II (16 genes). The results revealed that the putative CmTCP genes are distributed across nine of the twelve melon chromosomes and exhibit diverse expression patterns in different tissues which mostly indicates their potential role in floral organ development, lateral branching, growth and development. Phylogenetic analysis suggests that some CmTCP genes may have similar functions to their homologs in other plant species, while others may have undergone functional diversification. This study paves the way for future investigations into the specific roles of individual CmTCP genes in melon and for elucidating the mechanisms by which TCP proteins regulate leaf elongation, floral development, and lateral branching.

The first insight into Acanthocephalus (Palaeacanthocephala) satellitome: species-specific satellites as potential cytogenetic markers

Acanthocephalan parasites are often overlooked in many areas of research, and satellitome and cytogenetic analyzes are no exception. The species of the genus Acanthocephalus are known for their very small chromosomes with ambiguous morphology, which makes karyotyping difficult. In this study, we performed the first satellitome analysis of three Acanthocephalus species to identify species- and chromosome-specific satellites that could serve as cytogenetic markers. RepeatExplorer2 revealed a remarkably high number of species-specific repeats, with a predominance of satellite DNAs, alongside variations in repetitive content between sexes. Five satellites in A. anguillae, two in A. lucii and six in A. ranae were successfully mapped to chromosomes using FISH. Each satellite showed a clustered hybridization signal at specific chromosomal locations, which allowed us to create a schematic representation of the distribution of satellites for each species. These newly identified satellites proved to be useful chromosomal markers for the accurate identification of homologous chromosome pairs. No FISH-positive signals were observed on the supernumerary chromosomes of A. anguillae and A. lucii, supporting the hypothesis that these chromosomes have recent origin.

Comprehensive genomic analysis of SmbHLH genes and the role of SmbHLH93 in eggplant anthocyanin biosynthesis.

SmbHLH93can activate the expression of SmCHS, SmANS, SmDFR and SmF3H.Overexpression of SmbHLH93promotes anthocyanin biosynthesis. SmbHLH93can interact with SmMYB1 to promote anthocyanin accumulation. As an outstanding source of anthocyanins, eggplant (Solanum melongena L.) is extremely beneficial for human health. In the process of anthocyanin biosynthesis in eggplant, the basic helix-loop-helix (bHLH) transcription factor family plays a crucial role. However, the bHLH gene family is extensive, making it difficult to systematically screen and analyze their functions using conventional methods. We studied the phylogeny, gene structure, conserved motifs, promoter element, and chromosomal location of the 166 SmbHLH genes in the recently released eggplant genome. Through the analysis of transcriptomic data of eggplant peel treated with light, it was found that SmbHLH93 was the most responsive to light among those of unknown function. Additionally, it was discovered that SmbHLH93 plays a positive regulatory role in anthocyanin synthesis through dual-luciferase reporter assay(dual-LUC) and genetic transformation in Arabidopsis (Arabidopsis thaliana). Furthermore, experiments involving yeast two-hybrid (Y2H), luciferase complementation assay (Split-LUC), and tobacco transient transformation demonstrated that SmbHLH93 has the ability to interact with SmMYB1 in order to enhance anthocyanin accumulation. This study will serve as a foundation for exploring the role of SmbHLH transcription factors in anthocyanin biosynthesis in the future.

Genome-Wide Identification and Characterization of the CDPK Family of Genes and Their Response to High-Calcium Stress in Yinshania henryi.

Background/Objectives: Calcium-dependent protein kinases (CDPKs) are a crucial class of calcium-signal-sensing and -response proteins that significantly regulate abiotic stress. Yinshania henryi is a member of the Brassicaceae family that primarily grows in the karst regions of southwestern China, with a notable tolerance to high-calcium soils. Currently, the function of the CDPK family of genes in Y. henryi has yet to be explored. Methods: This study employed a comprehensive approach starting with bioinformatic methods to analyze the whole-genome sequencing data of Y. henryi and identified YhCDPK genes by combining phylogenetic characteristics and protein domain analysis. Results: It then delved into the physicochemical properties, gene structure, chromosomal localization, phylogenetic tree, and promoter cis-acting elements of these YhCDPK genes. Subsequently, RNA-seq data and qRT-PCR analysis were utilized to understand the expression patterns of YhCDPK genes. Twenty-eight YhCDPK genes were found to be unevenly distributed across six chromosomes; these can be classified into four subfamilies, with many cis-acting elements in their promoter regions involved in plant growth and stress responses. Furthermore, the differential expression patterns of YhCDPK genes under different concentrations of calcium treatments were investigated using RNA-seq data and qRT-PCR analysis. Conclusions: These results are a critical first step in understanding the functions of YhCDPK genes, and they lay a foundation for further elucidating the adaptability and response mechanism of YhCDPK genes in Y. henryi to the karst environment.

Ammonium Transporter 1 (AMT1) Gene Family in Pomegranate: Genome-Wide Analysis and Expression Profiles in Response to Salt Stress.

Understanding the ammonium (NH4+) uptake and transport systems, particularly AMT1 genes, is important for plant growth and defense. However, there is a lack of research on identifying and analyzing AMT1 genes in pomegranate, emphasizing the need for further investigation in this area. Five AMT1 genes (PgAMT1-1 to PgAMT1-5) were identified, all of which contain the PF00909 domain, a feature of ammonium transporters. Various characteristics of these genes, including gene length, coding sequence length, and chromosomal locations, were examined. This study evaluated the isoelectric point, hydropathicity, conserved domains, motifs, and synteny of the PgAMT1 proteins. Phylogenetic analysis confirmed the homology of PgAMT1 genes with previously reported AMT in Arabidopsis and tomato. The tissue-specific expression analysis of PgAMT1 genes revealed distinct patterns: PgAMT1-1 and PgAMT1-2 were predominantly expressed in flowers, PgAMT1-3 exhibited notable expression in roots, leaves, and flowers, PgAMT1-4 was primarily expressed in leaf tissue, while the expression of PgAMT1-5 was detected in both leaves and roots. The impact of salt-induced stress on AMT1 gene expression was also examined, revealing that PgAMT1-1, PgAMT1-2, and PgAMT1-4 expression is reduced under increased salt stress. These expression modifications can help regulate NH4+ assimilation in conditions of elevated salinity, maintaining cellular homeostasis and ion balance. This study contributes to the comprehensive identification of the AMT1s gene family in pomegranate; however, further research on the functional characterization of the identified PgAMT1s is needed.

Identification and Analysis of Melon (Cucumis melo L.) SHMT Gene Family Members and Their Functional Studies on Tolerance to Low-Temperature Stress

Melon (Cucumis melo L.) is a significant cash crop globally and is cherished for its sweet and flavorful fruits, as well as its high nutritional values. However, its yield and quality are limited by various factors, including drought, salinity, and low temperatures. Low temperatures are one of the primary factors influencing the growth and development of melons, diminishing the viability, germination, and growth rate of melon seeds. Concurrently, low temperatures also reduce light absorption efficiency and fruit yields, thereby affecting melon growth and development. Serine hydroxymethyltransferase (SHMT), a conserved phosphopyridoxal-dependent enzyme, plays a crucial role in plant resistance to abiotic stressors. In this study, eight CmSHMT family genes were identified from the melon genome. We predicted their chromosomal locations, physicochemical properties, gene structures, evolutionary relationships, conserved motifs, cis-acting elements of promoters, and tissue-specific expression patterns. The expression levels of CmSHMT family genes in response to low-temperature stress was then analyzd using qRT-PCR. The phylogenetic results indicated that these CmSHMT genes were classified into four subfamilies and were unevenly distributed across five chromosomes, with relatively high conservation among them. Furthermore, our investigation revealed that the promoter regions of the CmSHMT family genes contain many cis-acting elements related to phytohormones, growth, and various stress responses. The relative expression levels of CmSHMT3, CmSHMT4, CmSHMT6, and CmSHMT7 were higher under low-temperature stress compared to the control group. Notably, the promoter region of CmSHMT3 contains cis-acting elements associated with low-temperature response (LTR) and abscisic acid response (ABRE). It is suggested that the mechanism through which CmSHMT3 responds to low-temperature stress treatments may be associated with hormonal regulation. These findings provide a foundation for the further exploration of CmSHMT family genes in melon and their functional roles in response to low-temperature stress, and they provide a theoretical basis for the targeted breeding of superior melon varieties with enhanced tolerance to low temperatures.

Negative DNA supercoiling enhances DARS2 binding of DNA-bending protein IHF in the activation of Fis-dependent ATP-DnaA production.

Oscillation of the active form of the initiator protein DnaA (ATP-DnaA) allows for the timely regulation for chromosome replication. After initiation, DnaA-bound ATP is hydrolyzed, producing inactive ADP-DnaA. For the next round of initiation, ADP-DnaA interacts with the chromosomal locus DARS2 bearing binding sites for DnaA, a DNA-bending protein IHF, and a transcription activator Fis. The IHF binding site is about equidistant between the DnaA and Fis binding sites within DARS2. The DARS2-IHF-Fis complex promotes ADP dissociation from DnaA and furnishes ATP-DnaA at the pre-initiation stage, which dissociates Fis in a negative-feedback manner. However, regulation for IHF binding as well as mechanistic roles of Fis and specific DNA structure at DARS2 remain largely unknown. We have discovered that negative DNA supercoiling of DARS2 is required for stimulating IHF binding and ADP dissociation from DnaA in vitro. Consistent with these, novobiocin, a DNA gyrase inhibitor, inhibits DARS2 function in vivo. Fis Gln68, an RNA polymerase-interaction site, is suggested to be required for interaction with DnaA and full DARS2 activation. Based on these and other results, we propose that DNA supercoiling activates DARS2 function by stimulating stable IHF binding and DNA loop formation, thereby directing specific Fis-DnaA interaction.

Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs

The Homo sapiens Chromosomal Location Ontology (HSCLO) is designed to facilitate the integration of human genomic features into biomedical knowledge graphs from releases GRCh37 and GRCh38 at multiple resolutions. HSCLO comprises two distinct versions, HSCLO37 and HSCLO38, each tailored to its respective human genome release. This ontology supports the efficient integration and analysis of human genomic data across scales ranging from entire chromosomes to individual base pairs, thereby enhancing data retrieval and interoperability within large-scale biomedical datasets. Unlike existing ontologies that primarily focus on genomic feature identification or annotation, HSCLO is specifically engineered to optimize the interoperability and scalability of genomic data within biomedical knowledge graphs. The utility and performance of HSCLO are demonstrated through a case study involving the integration of high-resolution chromatin interaction data, which reveals significant improvements in query efficiency and data linkage. HSCLO represents a valuable resource for advancing research in disease genetics, personalized medicine, and other domains that require complex genomic data integration.

Study of the SPL gene family and miR156-SPL module in Populus tomentosa: Potential roles in juvenile-to-adult phase transition and reproductive phase.

Populus tomentosa, a deciduous tree species distinguished by its significant economic and ecological value, enjoys a wide-ranging natural distribution. However, its long juvenile period severely restricts the advancement of breeding work. The SPL gene family, a distinctive class of transcription factors exclusive to the plant kingdom, is critical in various processes of plant growth and development. The miR156-SPL molecular module stands as an indispensable regulatory mechanism in the transition from the vegetative juvenile phase to the adult phase in plants. Consequently, this research endeavored a methodical and exhaustive exploration of the SPL gene family within the P.tomentosa species, synergistically integrating the miR156 family into the analysis. A total of 56 PtSPL genes were identified and subjected to a comprehensive analysis of their gene structure, conserved motifs, collinearity relationships, chromosomal localization, and promoter cis-acting elements. Further analysis of gene expression profiles confirmed the pivotal role of PtSPLs in the reproductive phase and tissue development of P. tomentosa. In addition, 11 members of miR156 in P. tomentosa were identified and their sequences analyzed, elucidating the miR156-SPL regulatory network. The target relationship between miR156k and PtSPLs was further validated by detecting the expression levels of PtSPLs in transgenic poplars overexpressing 35S::MIR156k. This comprehensive study lays a robust theoretical foundation for the continued exploration and application of the SPL genes in P. tomentosa, opening avenues for future research and potential advancements in plant biology and breeding strategies.

The characteristics of aminotransferases gene family in Ruditapes philippinarum and its response to salinity stresses.

Aminotransferase is involved in the regulation of amino acid metabolism, which can affect the balance and distribution of amino acids in the organism, help maintain the homeostasis of amino acids in the organism, and play an important role in the environmental adaptation of aquatic animals. In this study, a total of 28 aminotransferase genes were identified in the genome of R. philippinarum. The gene structure, protein structure, chromosome localization, and phylogenetic analysis of aminotransferase were conducted using bioinformatics. According to the gene structure and phylogenetic analysis of aminotransferase proteins, aminotransferase proteins can be categorized into class I and II, class III, and class V. RNA-seq data analysis showed that aminotransferase genes were differentially expressed at different developmental stages, tissues, and salinity stress. In addition, qPCR demonstrated that the expression levels of most aminotransferase genes increased significantly during salinity changes. We also measured the free amino acids content in the gills of R. philippinarum after 48 h of low and high salinity stress. The results indicated that the total free amino acids under low salinity stress (75.89 ± 3.31 mg/g) and high salinity stress (91.01 ± 3.31 mg/g) at 48 h were significantly decreased and increased compared with the control group (83.01 ± 3.12 mg/g), respectively. The results of this study provide a valuable reference for further research on the salinity adaptation of the aminotransferase gene in R. philippinarum.

Efficient Genetic Transformation and Suicide Plasmid-mediated Genome Editing System for Non-model Microorganism Erwinia persicina.

Erwinia persicina is a gram-negative bacterium that causes diseases in plants. Recently, E. persicina BST187 was shown to exhibit broad-spectrum antibacterial activity due to its inhibitory effects on bacterial acetyl-CoA carboxylase, demonstrating promising potential as a biological control agent. However, the lack of suitable genetic manipulation techniques limits its exploitation and industrial application. Here, we developed an efficient transformation system for E. persicina. Using pET28a as the starting vector, the expression cassette of the red fluorescent protein-encoding gene with the strong promoter J23119 was constructed and transformed into BST187 competent cells to verify the overexpression system. Moreover, suicide plasmid-mediated genome editing systems was developed, and lacZ was knocked out of BST187 genome by parental conjugation transfer using the recombinant suicide vector pKNOCK-sacB-km-lacZ. Therefore, both the transformation and suicide plasmid-mediated genome editing system will greatly facilitate genetic manipulations in E. persicina and promote its development and application. Key features • Our studies establish a genetic manipulation system for Erwinia persicina, providing a versatile tool for studying the gene function of non-model microorganisms. • Requires approximately 6-10 days to complete modification of a chromosome locus.

Identification and characterization of soybean phytochrome-interacting factors and their potential roles in abiotic stress

Phytochrome-interacting factors (PIFs) belong to a subfamily of the bHLH transcription factor family and play a pivotal role in plant light signal transduction, hormone signal pathways, and the modulation of plant responses to various abiotic stresses. The soybean (Glycine max) is a significant food crop, providing essential oil and nutrients. Additionally, it is a vital industrial raw material and a lucrative cash crop. Nevertheless, research on PIFs in soybean is relatively scarce. In this study, we conducted a comprehensive analysis of the gene structure, chromosomal location, conserved motifs, phylogenetic relationships, and expression patterns of the Glycine max PIF (GmPIF) genes. A total of 20 GmPIF genes were identified in the soybean genome. These are unevenly distributed on 12 soybean chromosomes. The analysis of gene duplication events revealed the existence of five pairs of duplicated genes within the GmPIF gene set. Conserved motif analysis demonstrated the presence of several conserved motifs that were generally aligned with the classification of PIF protein. Cis-acting elements in the GmPIF promoters were found to be responsive to light, heat, drought, and phytohormone signaling. The expression levels of certain GmPIF genes were significantly induced under shade, high temperature and drought stress conditions. The heterologous expression of the GmPIF6c/GmPIL1 in an Arabidopsis mutant resulted in a reduction in the elongation of the hypocotyl in response to shade. It is proposed that GmPIF6c/GmPIL1 may exert an inhibitory effect on shade avoidance. This study elucidated the evolution, structural and functions of GmPIF family members.Clinical trial numberNot applicable.