Chromosomal Location Research Articles

Histone methyltransferase NSD modulates gene silencing mechanisms on Drosophila chromosome 4

The nuclear receptor-binding SET domain protein (NSD) gene family encodes histone methyltransferases that mono- and di-methylate lysine 36 on histone H3 (H3K36). Here, we examine the effects of NSD loss-of-function on transcription and heterochromatin formation in Drosophila to elucidate the role of NSD in chromatin structure regulation. Transcriptome analysis showed that NSD deletion activated more genes on chromosome 4, predominantly heterochromatic, than on other chromosomes. We further analyzed the position-effect variegation of fly eyes due to mini-white (mw+) transgenes inserted at various chromosomal loci and found that NSD deletion promoted mw+ transgene expression on chromosome 4. Additionally, NSD deletion reduced the binding of heterochromatin markers HP1a and H3K9 to chromosome 4. These findings suggest that NSD deletion disrupts chromosome 4 heterochromatin structure by reducing HP1a binding, implying NSD's role as an epigenetic regulator of chromosome 4 silencing.

Genome-Wide Analysis and Expression Profiling of Glyoxalase Gene Families Under Abiotic Stresses in Cucumber (Cucumis sativus L.)

The glyoxalase pathway, consisting of glyoxalase I (GLYI) and glyoxalase II (GLYII), is an enzymatic system that converts cytotoxic methylglyoxal to non-toxic S-D-lactoylglutathione. Although the GLY gene family has been analyzed in Arabidopsis, rice, grape, cabbage, and soybean, cucumber studies are lacking. Here, we analyzed the cucumber GLY gene family, identifying 13 CsGLYI and 2 CsGLYII genes. Furthermore, we investigated the physicochemical properties, phylogenetic relationships, chromosomal localization and colinearity, gene structure, conserved motifs, cis-regulatory elements, and protein–protein interaction networks of the CsGLY family. They were primarily localized in the cytoplasm, chloroplasts, and mitochondria, with a minor presence in the nucleus. The classification of CsGLYI and CsGLYII genes into five classes closely resembled the homologous genes in Arabidopsis and soybean. Additionally, hormone-responsive elements dominated the promoter region of GLY genes, alongside light- and stress-responsive elements. The predicted interaction proteins of CsGLYIs and CsGLYIIs exerted a significant role in cellular respiration, amino acid synthesis, and metabolism, as well as methylglyoxal catabolism. In addition, the expression profiles of GLY genes were distinct in different tissues of cucumber as well as under diverse abiotic stresses. This study is conducive to the further exploration of the functional diversity among glyoxalase genes and the mechanisms of stress responses in cucumber.

Chromosomal Localization and Diversity Analysis of 5S and 18S Ribosomal DNA in 13 Species from the Genus Ipomoea

Background: Sweet potato (Ipomoea batatas (L.) Lam.), a key global root crop, faces challenges due to its narrow genetic background. This issue can be addressed by utilizing the diverse genetic resources of sweet potato’s wild relatives, which are invaluable for its genetic improvement. Methods: The morphological differences in leaves, stems, and roots among 13 Ipomoea species were observed and compared. Chromosome numbers were determined by examining metaphase cells from root tips. Fluorescence in situ hybridization (FISH) was used to identify the number of 5S and 18S rDNA sites in these species. PCR amplification was performed for both 5S and 18S rDNA, and phylogenetic relationships among the species were analyzed based on the sequences of 18S rDNA. Results: Three species were found to have enlarged roots among the 13 Ipomoea species. Chromosome analysis revealed that I. batatas had 90 chromosomes, Ipomoea pes-tigridis had 28 chromosomes, while the remaining species possessed 30 chromosomes. Detection of rDNA sites in the 13 species showed two distinct 5S rDNA site patterns and six 18S rDNA site patterns in the 12 diploid species. These rDNA sites occurred in pairs, except for the seven 18S rDNA sites observed in Ipomoea digitata. PCR amplification of 5S rDNA identified four distinct patterns, while 18S rDNA showed only a single pattern across the species. Phylogenetic analysis divided the 13 species into two primary clades, with the closest relationships found between I. batatas and Ipomoea trifida, as well as between Ipomoea platensis and I. digitata. Conclusions: These results enhance our understanding of the diversity among Ipomoea species and provide valuable insights for breeders using these species to generate improved varieties.

Genome-Wide Identification of MKK Gene Family and Response to Hormone and Abiotic Stress in Rice.

Mitogen-activated protein kinase (MAPK/MPK) cascades are pivotal and highly conserved signaling modules widely distributed in eukaryotes; they play essential roles in plant growth and development, as well as biotic and abiotic stress responses. With the development of sequencing technology, the complete genome assembly of rice without gaps, T2T (Telomere-to-Telomere)-NIP (version AGIS-1.0), has recently been released. In this study, we used bioinformatic approaches to identify and analyze the rice MPK kinases (MKKs) based on the complete genome. A total of seven OsMKKs were identified, and their physical and chemical properties, chromosome localization, gene structure, subcellular localization, phylogeny, family evolution, and cis-acting elements were evaluated. OsMKKs can be divided into four subgroups based on phylogenetic relationships, and the family members located in the same evolutionary branch have relatively similar gene structures and conserved domains. Quantitative real-time PCR (qRT-PCR) revealed that all OsMKKs were highly expressed in rice seedling leaves. The expression levels of all OsMKKs were more or less altered under exogenous hormone and abiotic stress treatments, with OsMKK1, OsMKK6, and OsMKK3 being induced under almost all treatments, while the expression of OsMKK4 and OsMKK10-2 was repressed under salt and drought treatments and IAA treatment, respectively. In this study, we also summarized the recent progress in rice MPK cascades, highlighted their diverse functions, and outlined the potential MPK signaling network, facilitating further studies on OsMKK genes and rice MPK cascades.

Genome-Wide Identification and Expression Analysis of the PsTPS Gene Family in Pisum sativum

This study aimed to explore the role of the trehalose-6-phosphate synthase (TPS) gene family in the adaptation of peas to environmental stress. A comprehensive analysis of the PsTPS gene family identified 20 genes with conserved domains and specific chromosomal locations. Phylogenetic analysis delineated evolutionary relationships, while gene structure analysis revealed compositional insights, and motif analysis provided functional insights. Cis-regulatory element identification predicted gene regulation patterns. Tissue-specific and stress-induced expression profiling highlighted eight genes with ubiquitous expression, with PsTPS15 and PsTPS18 displaying elevated expression levels in roots, nodules, and young stems, and PsTPS13 and PsTPS19 expression downregulated in seeds. Transcriptome analysis identified a differential expression of 20 PsTPS genes, highlighting the significance of 14 genes in response to drought and salinity stress. Notably, under drought conditions, the expression of PsTPS4 and PsTPS6 was initially upregulated and then downregulated, whereas that of PsTPS15 and PsTPS19 was downregulated. Salinity stress notably altered the expression of PsTPS4, PsTPS6, and PsTPS19. Taken together, these findings elucidate the regulatory mechanisms of the PsTPS gene family and their potential as genetic targets for enhancing crop stress tolerance.

Elucidating genetic variability between randomly bred domestic cats and Persian domestic cats from different geographical locations using microsatellite markers.

The domestic cat (Felis catus) is a newly evolved species in the family Felidae that has developed some great features among mammals. It is critical to conserve these species and prevent inbreeding from reducing their genetic diversity by understanding their genetic relationships and applying the information to breeding management. The diverse population was an excellent choice for studying genetic diversity and inbreeding phenomena. To conduct this research, 128 individuals from 8 populations, including Azerbaijan, Persian, Ahar, Uermia, Tehran, Karaj, Turkish and Shop cat (both genders), were randomly selected from different geographical regions. We selected eight STR markers with different chromosomal locations based on polymorphism and observed allele numbers in the next step. DNA extraction was performed using tail hair root, PCR and electrophoresis, and gel staining was performed according to routine laboratory protocol. For statistical analysis, CONVERT versions POPGENE, ARLEQUIN GenAlEx and R script analysis. Remarkably, our results showed that 23 alleles were identified in 128 samples. The highest number of alleles belonged to the FCa096 locus (eight alleles) in the Persian population, followed by FCa045 (seven alleles) in the Persian and Ahar populations. Another new finding is that the lowest number of alleles belonged to the 35 and FCa77 locus (two alleles). In addition, pairwise differentiation between and within populations was examined using the genetic distance index. Overall, the results showed that the degree of differentiation within the population is high in the Turkish population compared to other population groups and lower in the Azerbaijan population. In addition, principal component discriminant analysis-based analysis based on the ADAGENET package shows the distribution of samples by geographical location. The results show that genetic mixing between populations is high. On this basis, we conclude that randomly bred domestic cats have a higher level of diversity than Persian domestic cats. This is an interesting topic for future work.

Genome-Scale Identification of Wild Soybean Serine/Arginine-Rich Protein Family Genes and Their Responses to Abiotic Stresses.

Serine/arginine-rich (SR) proteins mostly function as splicing factors for pre-mRNA splicing in spliceosomes and play critical roles in plant development and adaptation to environments. However, detailed study about SR proteins in legume plants is still lacking. In this report, we performed a genome-wide investigation of SR protein genes in wild soybean (Glycine soja) and identified a total of 31 GsSR genes from the wild soybean genome. The analyses of chromosome location and synteny show that the GsSRs are unevenly distributed on 15 chromosomes and are mainly under the purifying selection. The GsSR proteins can be phylogenetically classified into six sub-families and are conserved in evolution. Prediction of protein phosphorylation sites indicates that GsSR proteins are highly phosphorylated proteins. The protein-protein interaction network implies that there exist numerous interactions between GsSR proteins. We experimentally confirmed their physical interactions with the representative SR proteins of spliceosome-associated components such as U1-70K or U2AF35 by yeast two-hybrid assays. In addition, we identified various stress-/hormone-responsive cis-acting elements in the promoter regions of these GsSR genes and verified their expression patterns by RT-qPCR analyses. The results show most GsSR genes are highly expressed in root and stem tissues and are responsive to salt and alkali stresses. Splicing analysis showed that the splicing patterns of GsSRs were in a tissue- and stress-dependent manner. Overall, these results will help us to further investigate the biological functions of leguminous plant SR proteins and shed new light on uncovering the regulatory mechanisms of plant SR proteins in growth, development, and stress responses.

Crucial role of a takeout protein in white-backed planthopper Sogatella furcifera (Horváth) orientation towards its host rice plants.

The takeout (TO) gene family impacts diverse physiological and behavioral functions in insects, yet specific olfactory-associated roles for the family have yet to be fully elucidated. To provide insights into TO function in rice planthoppers, the genomes of three rice planthoppers (white-backed planthopper, brown planthopper and small brown planthopper) were searched for TO homologs and their degree of conservation assessed via chromosomal localization, exon-intron boundaries, phylogenetic relationships and protein domains/motifs. We performed a tissue-specific expression analysis of the 20 TO genes in the white-backed planthopper (WBPH, Sogatella furcifera) and found that SfTO17 is enriched in adult antennae. RNAi-mediated knockdown of SfTO17 impaired WBPH olfaction and reduced host-seeking responses following exposure to rice plants. The binding profile of β-ionone, hexyl benzoate and benzyl benzoate with recombinant SfTO17 was evaluated via competitive fluorescence binding assays. Conformational prediction of SfTO17 coupled with molecular docking analyses revealed several amino acid residues potentially critical for odorant binding. This study demonstrates the olfactory function of SfTO17 in WBPH and highlights its potential as a target for controlling this rice pest. © 2024 Society of Chemical Industry.

Competition between homologous chromosomal DNA and exogenous donor DNA to repair CRISPR/Cas9-induced double-strand breaks in Aspergillus niger

BackgroundAspergillus niger is well-known for its high protein secretion capacity and therefore an important cell factory for homologous and heterologous protein production. The use of a strong promoter and multiple gene copies are commonly used strategies to increase the gene expression and protein production of the gene of interest (GOI). We recently presented a two-step CRISPR/Cas9-mediated approach in which glucoamylase (glaA) landing sites (GLSs) are introduced at predetermined sites in the genome (step 1), which are subsequently filled with copies of the GOI (step 2) to achieve high expression of the GOI.ResultsHere we show that in a ku70 defective A. niger strain (Δku70), thereby excluding non-homologous end joining (NHEJ) as a mechanism to repair double-stranded DNA breaks (DSBs), the chromosomal glaA locus or homologous GLSs can be used to repair Cas9-induced DSBs, thereby competing with the integration of the donor DNA containing the GOI. In the absence of exogenously added donor DNA, the DSBs are repaired with homologous chromosomal DNA located on other chromosomes (inter-chromosomal repair) or, with higher efficiency, by a homologous DNA fragment located on the same chromosome (intra-chromosomal repair). Single copy inter-chromosomal homology-based DNA repair was found to occur in 13–20% of the transformants while 80–87% of the transformants were repaired by exogenously added donor DNA. The efficiency of chromosomal repair was dependent on the copy number of the potential donor DNA sequences in the genome. The presence of five homologous DNA sequences, resulted in an increased number (35–61%) of the transformants repaired by chromosomal DNA. The efficiency of intra-chromosomal homology based DSB repair in the absence of donor DNA was found to be highly preferred (85–90%) over inter-chromosomal repair. Intra-chromosomal repair was also found to be the preferred way of DNA repair in the presence of donor DNA and was found to be locus-dependent.ConclusionThe awareness that homologous chromosomal DNA repair can compete with donor DNA to repair DSB and thereby affecting the efficiency of multicopy strain construction using CRISPR/Cas9-mediated genome editing is an important consideration to take into account in industrial strain design.

Genome-Wide Identification and Expression Analysis of the ALKB Homolog Gene Family in Potato (Solanum tuberosum L.).

N6-methyladenosine (m6A) is an abundant and pervasive post-transcriptional modification in eukaryotic mRNAs. AlkB homolog (ALKBH) proteins play crucial roles in RNA metabolism and translation, participating in m6A methylation modification to regulate plant development. However, no comprehensive investigations have been conducted on ALKBH in potato. Here, 11 StALKBH family genes were identified in potato and renamed according to BLASTP and phylogenetic analyses following the Arabidopsis genome. The characteristics, sequence structures, motif compositions, phylogenetics, chromosomal locations, synteny, and promoter cis-acting element predictions were analyzed, revealing distinct evolutionary relationships between potato and other species (tomato and Arabidopsis). Homologous proteins were classified into seven groups depending on similar conserved domains, which implies that they possess a potentially comparable function. Moreover, the StALKBHs were ubiquitous, and their expression was examined in the various tissues of a whole potato, in which the StALKBH genes, except for StALKBH2, were most highly expressed in the stolon and flower. Multiple hormone and stress-response elements were found to be located in the promoters of the StALKBH genes. Further qRT-PCR results suggest that they may be significantly upregulated in response to phytohormones and abiotic stress (except for cold), and the expression of most of the StALKBH genes exhibited positively modulated trends. Overall, this study is the first to report a genome-wide assessment of the ALKBH family in potato, providing valuable insights into candidate gene selection and facilitating in-depth functional analyses of ALKBH-mediated m6A methylation mechanisms in potato.

R2R3-MYB transcription factor GmMYB68 is involved in the accumulation of soybean isoflavones

We aimed to investigate the regulatory function of the soybean transcription factor R2R3-MYB (GmMYB68) in isoflavone biosynthesis. Through comprehensive subcellular and chromosomal localization analyses, we found that GmMYB68 was predominantly localized to the nucleus and mapped to chromosome Gm04. Notably, SSR markers near this gene significantly correlated with seed isoflavone content. GmMYB68 overexpression markedly increased isoflavone contents, confirming its positive role in regulating isoflavone synthesis. GmMYB68 also played a crucial role in the response of soybean to abiotic stress. Using RNA-seq and yeast one-hybrid techniques, we discovered an intricate interaction between GmMYB68 and key isoflavone biosynthesis genes GmCHS7 and GmCHS8. These findings provide novel insights into the mechanisms underlying isoflavone biosynthesis. Furthermore, using yeast two-hybrid experiments, we identified proteins interacting with GmMYB68, suggesting roles in the synthesis of physiologically active compounds and abiotic stress response. We not only elucidated the regulatory mechanisms of GmMYB68 in isoflavone biosynthesis and abiotic stress response but also constructed a molecular network encompassing GmMYB68, GmCHS7, and GmCHS8. This network provides a theoretical basis for a better understanding of and strategies for improving soybean isoflavone biosynthesis.

Genome-wide identification of the Phospholipase D (PLD) gene family in Chinese white pear (Pyrus bretschneideri) and the role of PbrPLD2 in drought resistance

The Chinese white pear (Pyrus bretschneideri), a vital fruit crop, is highly susceptible to abiotic stresses, especially drought, which poses a major threat to its growth and productivity. Phospholipase D (PLD) genes are pivotal in orchestrating plant responses to abiotic stresses, acting as key regulators in stress adaptation mechanisms. This study systematically identified and functionally characterized the entire PLD gene family in P. bretschneideri through a comprehensive genome-wide analysis. A total of 20 PbrPLD genes were identified, and they were categorized into five subfamilies based on phylogenetic analysis. chromosome localization, gene structure, and conserved motif analyses revealed that these genes have diverse evolutionary histories. Cis-acting element analysis and expression profiling under drought stress indicated that several PbrPLD genes, particularly PbrPLD2, are strongly induced by drought. Overexpression of PbrPLD2 in both Arabidopsis thaliana and pear demonstrated enhanced drought tolerance through improved stomatal closure and increased expression of drought-responsive genes. These findings highlight the critical role of PbrPLD2 in drought resistance and provide a theoretical and experimental foundation for molecular breeding in pear and other fruit crops.

Molecular epidemiological analysis of blaNDM-5-producing Klebsiella pneumoniae ST2407-K25 causing infection outbreaks in pediatric patients based on whole genome sequencing

BackgroundPediatric patients are vulnerable to the threat of carbapenem-resistant Klebsiella pneumoniae (CRKP) due to their limited immunity and few available antibiotics. Especially when these pathogens exhibit hypervirulent phenotypes, they are often associated with poor clinical outcomes.MethodsIn this study, we investigated a CRKP outbreak in pediatric patients from 2019 to 2021 in a teaching hospital in China based on whole genome sequencing. We sequenced twenty-nine CRKP isolates isolated from unduplicated pediatric patients to understand their genetic relationships, virulence factors, resistance mechanisms, and transmission trajectories. Conjugation experiments were performed to evaluate the horizontal transfer ability of carbapenem resistance determinants in twenty-nine CRKP isolates. We then characterized these isolates for biofilm formation ability and serum resistance. Genetic relatedness, comparison of plasmids, and chromosomal locus variation of CRKP isolates were analyzed by bioinformatics.ResultsAll the isolates were carbapenemase-producers harbouring blaNDM−5. Among them, twenty-eight isolates belonged to the ST2407 group, with the consistent capsular serotype K25. The virulence-related factors: ureA, fim, ybtA, irp1/irp2, and mrkA were prevalent in these isolates. Additionally, most CRKP isolates showed moderately adherent biofilm formation. Although the ST2407 clonal group did not exhibit serum resistance, the heterogeneous level of serum resistance was related to the disruption of oqxR. Conjugation and WGS revealed that the blaNDM−5 carried by the twenty-eight CRKP ST2407 isolates was located on nonconjugative IncX3 plasmids associated with deleting the T4SS-encoding genes. Clonal transmission of CRKP ST2407 in pediatric patients was suggested by the phylogenetic tree.ConclusionsOur study provides evidence of the clonal spread of blaNDM−5-producing K. pneumoniae in pediatric patients and the necessity for the T4SS system for horizontal transfer of the IncX3 plasmid carrying blaNDM−5. Additionally, the disruption of oqxR may have affected the serum resistance of CRKP. The results of this study emphasize the importance of continuously monitoring for CRKP infection in pediatric patients to prevent recurrent infections.

Development and evaluation of a panel of newly screened Y chromosome InDels for inferring paternal ancestry information in Southwest China.

Y-InDels (insertions/deletions) are genetic markers which are extremely understudied. It is unknown whether this type of markers can be utilized for genetic ancestry inference. We have developed an innovative Y chromosome ancestry inference system tailored for forensic applications. This panel amplifies 21 Y chromosome loci, encompassing Y-InDels and Y-SNPs (Single Nucleotide Polymorphism), utilizing the capillary electrophoresis (CE) platform. The system performed well at DNA concentrations greater than 0.125 ng/ul and produced accurate results at a 1:100 mixing ratio of male and female DNA. The Cumulative probability of matching (CPM) was between 0.95 and 0.97 in the experimental population. The system's efficacy in inferring ancestral origins was demonstrated through intercontinental population discrimination, revealing high discrimination power between African and East Asian populations. Population genetic analyses conducted on Han, Qiang and Hui populations in Southwest China, where the smallest FST value was 0.0002 between Han Chinese in Beijing (from 1000 Genomes Project) and Qiang Chinese from Sichuan (CQSC). Phylogenetic tree construction further illuminated distinct haplotypes among populations, with ethnically unique haplotypes observed in 34.6% of Hui and 7.1% of Qiang populations. K-fold cross-validation show the system's inference abilities at the intercontinental level. In addition, our investigations identified potential associations between the Y-InDel locus Y: 15,385,547 (GRCh37) and haplogroup R1a1a1b2a2- Z2124, as well as locus Y: 13,990,180 (GRCh37) and haplogroup F-M89. In conclusion, we have established a Y-chromosome inference system tailored for grassroots-level application, underscoring the value of incorporating Y-InDel markers in forensic analyses.

Genome-Wide Identification and Expression Analysis of the MADS-Box Gene Family in Cassava (Manihot esculenta)

The MADS-box gene family constitutes a vital group of transcription factors that play significant roles in regulating plant growth, development, and signal transduction processes. However, research on the MADS-box genes in cassava (Manihot esculenta) has been relatively limited. To gain deeper insights into the functions of the MADS-box genes in cassava development, in this study, we undertook a comprehensive genome-wide identification of the MADS-box gene family in cassava. We identified a total of 86 MADS-box genes with complete domains in the cassava genome, designated as MeMADS01 to MeMADS86. Through bioinformatic analyses, we investigated the basic physicochemical properties, conserved motifs, chromosomal locations, and phylogenetic relationships of the cassava MADS-box genes. The MADS-box gene family of cassava exhibited conservation, as well as species-specific characteristics, with intron loss being a predominant mode of evolution for the MADS-box genes. Expression pattern variations in the MeMADS genes across different tissues offer insights into their potential functions. Time-ordered gene co-expression network (TO-GCN), transcriptome data, and RT-qPCR analysis suggested the responsiveness of the MADS-box genes to drought stress. Meanwhile, MeMADS12 might be involved in regulating flowering under drought conditions via an ABA (abscisic acid)-dependent pathway. These findings provide valuable resources for a deeper understanding of the biological roles of the MADS-box genes in cassava.

Characterization and Expression of the Cytochrome P450 Genes in Daphnia magna Exposed to Cerium Oxide Nanoparticles.

As cerium oxide nanoparticles (nCeO2) continue to infiltrate aquatic environments, the resulting health risks to exposed aquatic organisms are becoming evident. Cytochrome P450 (CYP) enzymes are integral to the detoxification processes in these species. Herein, we conducted a genomic analysis of CYPs in Daphnia magna, encompassing phylogenetic relationships, gene structure, and chromosomal localization. We identified twenty-six CYPs in D. magna, categorizing them into four clans and seven families, distributed across six chromosomes and one unanchored scaffold. The encoded CYP proteins varied in length from 99 to 585 amino acids, with molecular weights ranging from 11.6 kDa to 66.4 kDa. A quantitative real-time PCR analysis demonstrated a significant upregulation of CYP4C1.4, CYP4C1.5, CYP4C1.6, CYP4c3.3, and CYP4c3.6 in D. magna exposed to 150 mg/L nCeO2 for 24 h. The transcript levels of CYP4C1.3, CYP18a1, CYP4C1.1, and CYP4c3.9 were notably downregulated in D. magna exposed to 10 mg/L nCeO2 for 48 h. A further transcriptomic analysis identified differential expression patterns of eight CYP genes, including CYP4C1.3, in response to nCeO2 exposure. The differential regulation observed across most of the 26 CYPs highlights their potential role in xenobiotic detoxification in D. magna, thereby enhancing our understanding of CYP-mediated toxicological responses to metal nanoparticles in aquatic invertebrates.

Establishing of 3D-FISH on frozen section and its applying in chromosome territories analysis in Populus trichocarpa.

Fluorescence in situ hybridization with frozen sections of root tips showed difference of chromosome territories distribution between autosome and sex-chromosome homologous pairs in Populus trichocarpa. The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biologic processes. Three-dimensional fluorescence in situ hybridization (3D-FISH) is a powerful tool for analyzing CTs, but its application in plants is limited. In this study, we established a 3D-FISH technique using frozen sections of Populus trichocarpa root tips, which was an improvement over the use of paraffin sections and enabled us to acquire good FISH signals. Using chromosome-specific oligo probes, we were able to analyze CTs in interphase nuclei in three dimensions. The distribution of chromosome pairs 17 and 19 in the 3D-preserved nuclei of P. trichocarpa root tip cells were analyzed and showed that the autosome pair 17 associated more often than sex chromosome 19. This research lays a foundation for further study of the spatial position of chromosomes in the nucleus and the relationship between gene expression and spatial localization of chromosomes in poplar.

Genome-Wide Identification and Expression Profiling of the BES1 Gene Family in Medicago sativa

Brassinosteroid (BR) signaling is regulated by BRI1-EMS SUPPRESSOR 1 (BES1) transcription factors, which are crucial for plant growth, development, and stress responses. Despite their importance, BES1 gene studies in Medicago sativa L. are limited, hindering our understanding of the BR signaling in this species. This study identified four BES1 genes in M. sativa; characterized their properties, conserved motifs, cis-regulatory elements, and chromosomal location; and explored their functions in development and stress responses. A phylogenetic analysis grouped these genes into two subfamilies. Transcript profiling showed widespread and tissue-specific expression patterns. A qRT-PCR analysis unveiled that most MsBESI genes were upregulated under salt and drought treatments, except MsG0280009980, which was suppressed. This research lays the groundwork for enhancing M. sativa stress resistance and understanding the BES1 gene family’s function.

Systematic analysis of the ARF gene family in Fagopyrum dibotrys and its potential roles in stress tolerance.

The auxin response factor (ARF) is a plant-specific transcription factor that regulates the expression of auxin response genes by binding directly to their promoters. They play an important role in the regulation of plant growth and development, as well as in the response to biotic and abiotic stresses. However, the identification and functional analysis of ARFs in Fagopyrum dibotrys are still unclear. In this study, a total of 26 FdARF genes were identified using bioinformatic methods. Their chromosomal location, gene structure, physical and chemical properties of their encoded protein, subcellular location, phylogenetic tree, conserved motifs and cis-acting elements in FdARF promoters were analyzed. The results showed that 26 FdARF genes were unevenly distributed on 8 chromosomes, with the largest distribution on chromosome 4 and the least distribution on chromosome 3. Most FdARF proteins are located in the nucleus, except for the proteins FdARF7 and FdARF21 located to the cytoplasm and nucleus, while FdARF14, FdARF16, and FdARF25 proteins are located outside the chloroplast and nucleus. According to phylogenetic analysis, 26 FdARF genes were divided into 6 subgroups. Duplication analysis indicates that the expansion of the FdARF gene family was derived from segmental duplication rather than tandem duplication. The prediction based on cis-elements of the promoter showed that 26 FdARF genes were rich in multiple stress response elements, suggesting that FdARFs may be involved in the response to abiotic stress. Expression profiling analysis showed that most of the FdARF genes were expressed in the roots, stems, leaves, and tubers of F. dibotrys, but their expression exhibits a certain degree of tissue specificity. qRT-PCR analysis revealed that most members of the FdARF gene were up- or down-regulated in response to abiotic stress. The results of this study expand our understanding of the functional role of FdARFs in response to abiotic stress and lay a theoretical foundation for further exploration of other functions of FdARF genes.

Genome-wide investigation and analysis of U-box E3 ubiquitin-protein ligase gene family in kiwifruit (Actinidia chinensis) in response to the yeast antagonist, Wickerhamomyces anomalus

ABSTRACT Although the ubiquitin ligase U-box protein family is a vital component of plant development and stress response, the exact role of kiwifruit U-box genes family is not known. The study identified 73 putative U-box genes from the kiwifruit genome. Chromosomal localisation, phylogenetic analysis, physicochemical properties, gene structure, motifs, and promoters of these genes were analysed. Distribution of Actinidia chinensis PUB (AcPUB) genes exhibited varying densities across 27 chromosomes. The study found that U-box clusters were classified into groups I–VII in phylogenetic analyses of a variety of plants, including kiwifruit, Arabidopsis thaliana, and rice, with most of the genes in kiwifruit being related to rice. The conserved motif analyses revealed that all the AcPUB genes have typical U-box structural domains. Analysis of the cis-acting elements suggested that AcPUBs expression may be responsive to several hormones and stresses. RNA-Seq analysis showed that six kiwifruit U-box genes were differentially expressed after induction by Wickerhamomyces anomalus, suggesting a potential involvement of these U-box genes in the kiwifruit's response to W. anomalus, which might include mechanisms related to resistance. Overall, our findings provide valuable insights into the function and structure of U-box genes that will help develop new genomic technologies and study plant resistance.