Somatic Number Research Articles

Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements.

Budding yeast (Saccharomyces cerevisiae) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and proteins. The Saccharomyces Genome Database (SGD) is a scientific resource that provides information about the genome and biology of S. cerevisiae. For more than 30 years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation for budding yeast along with search and analysis tools to explore these data. Here we describe recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface. These activities are part of our continuing effort to promote insights gained from yeast to enable the discovery of functional relationships between sequence and gene products in fungi and higher eukaryotes.

Spectro-photometry and radial distribution of multiple stellar populations in globular clusters from gaia XP spectra

Abstract Understanding the formation of multiple populations in globular clusters (GCs) represents a challenge for stellar population studies. Nevertheless, the outermost cluster regions, likely to hold clues about the initial configuration of GC stars, remain underexplored. We use synthetic spectra reflecting the chemical compositions of first- and second-population (1P, 2P) stars in 47 Tucanae to identify spectral regions sensitive to these populations. This led us to define new photometric bands that effectively distinguish 1P and 2P giant stars using Gaia XP spectra. Testing these filters, we constructed the pseudo two-color diagrams dubbed chromosome maps (ChMs) and, for the first time, identified 1P and 2P stars in the cluster’s outermost regions and beyond its tidal radius. We constructed similar diagrams for NGC 3201, NGC 6121, NGC 6752, and NGC 6397, thus exploring GCs with different metallicities. The ChMs effectively distinguished multiple populations in the outer regions of all clusters, except for the metal-poor NGC 6397. Our findings, together with literature results from more-internal regions, show that the 2P stars of 47 Tucanae are more-centrally concentrated than the 1P. A similar pattern is seen for 2P stars with extreme chemical composition of NGC 3201. The multiple populations of NGC 6121, and NGC 6752 share the same radial distributions. These radial behaviors are consistent with the GC formation scenarios where 2P stars originate in the central regions. Noticeably, results on NGC 3201 are in tension with the conclusion from recent work that its 1P is more centrally concentrated than the 2P and might form with more central concentration.

Integration of Genome-Wide Identification and Transcriptome Analysis of Class III Peroxidases in Paeonia ostii: Insight into Their Roles in Adventitious Roots, Heat Tolerance, and Petal Senescence

As a plant-specific gene family, class III peroxidases (PODs) play an important role in plant growth, development, and stress responses. However, the POD gene family has not been systematically studied in Paeonia ostii. In this study, a total of 57 PoPOD genes were identified in the P. ostii genome. Subsequently, phylogenetic analysis and chromosome mapping revealed that PoPODs were classified into six subgroups and were unevenly distributed across five chromosomes. The gene structure and conserved motifs indicated the potential for functional divergence among the different subgroups. Meanwhile, four PoPODs were identified as tandem duplicated genes, with no evidence of segmental duplication. Using RNA-seq data from eight different tissues, multiple PoPODs exhibited enhanced expression in apical and adventitious roots (ARs). Next, RNA-seq data from AR development combined with trend analysis showed that PoPOD30/34/43/46/47/57 are implicated in the formation of ARs in tree peony. Through WGCNA based on RNA-seq, two key genes, PoPOD5/15, might be involved in heat tolerance via ABA and MeJA signaling. In addition, real-time quantitative PCR (qRT-PCR) analysis indicated that PoPOD23 may play an important role in flower senescence. These findings deepened our understanding of POD-mediated AR development, heat tolerance, and petal senescence in tree peony.

Identification and Expression Analysis of TCP Transcription Factors Under Abiotic Stress in Phoebe bournei.

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes-PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15-under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family's functional characteristics and stress resistance regulation in P. bournei.

Karyotypes and chromosomal mapping of some repetitive DNAs in two stingless bee species (Apidae: Meliponini), with the description of a B chromosome in Plebeia genus.

Cytogenetic studies on stingless bees have significantly contributed to our understanding of karyotypic evolution and the composition of euchromatin and heterochromatin regions, including repetitive sequences. In this study, we performed classical cytogenetics, chromosomal banding, and mapping of some repetitive sequences in two stingless bee species, Frieseomelitta trichocerata and Plebeia poecilochroa. The species exhibit the typical diploid chromosome number of each genera, 2n=30 for Frieseomelitta and 2n=34 for Plebeia. Additionally, some individuals of P. poecilochroa presented a small heterochromatic B chromosome, showing a numeric variation of n=17 to 18 in males and 2n=34 to 35 in females. In both species heterochromatin is primarily distributed in the short arm and centromeric regions. Centromeric regions were found to be AT-rich in both species, while subterminal/terminal regions of the short arms of one and six chromosomes presented GC-rich sites in P. poecilochroa and F. trichocerata, respectively. The rDNA clusters mapped on two chromosome pairs in F. trichocerata, and in only one in P. poecilochroa. Microsatellites (GA)n, (GAG)n, and (CAA)n were predominantly mapped in euchromatic regions, while the telomeric motif (TTAGG)n mapped to the ends of most chromosomes, including the B chromosome of P. poecilochroa. The other repetitive probes used, including the rDNA clusters, do not label the B chromosome of P. poecilochroa. Our cytogenetic data highlight both similarities and differences when compared to other congeneric species, expanding the chromosomal data for both genera.

The burst of satellite DNA in Leptidea wood white butterflies and their putative role in karyotype evolution.

Satellite DNAs (satDNAs) are abundant components of eukaryotic genomes, playing pivotal roles in chromosomal organization, genome stability and evolution. Here, we combined cytogenetic and genomic methods to characterize the satDNAs in the genomes of Leptidea butterflies. Leptidea is characterized by the presence of a high heterochromatin content, large genomes and extensive chromosomal reshuffling as well as the occurrence of cryptic species. We show that, in contrast to other Lepidoptera, satDNAs constitute a considerable proportion of Leptidea genomes, ranging between 4.11%-11.05%. This amplification of satDNAs, together with the hyperactivity of transposable elements, contributes to the substantial genome expansion in Leptidea. Using chromosomal mapping, we show that, particularly LepSat01-100 and LepSat03-167 satDNAs, are preferentially localized in heterochromatin exhibiting variable distribution that could influence in the highly diverse karyotypes within the genus. The satDNAs also exhibit W-chromosome accumulation, suggesting their involvement in sex chromosome evolution. Our results provide insights into the dynamics of satDNAs in Lepidoptera genomes and highlight their role in genome expansion and chromosomal organization, which could influence the speciation process. The high proportion of repetitive DNAs in the genomes of Leptidea underscores the complex evolutionary dynamics revealing the interplay between repetitive DNAs and genomic architecture in the genus.

Fluorescence in situ hybridization analysis of Oligonucleotide 5S rDNA, 45S rDNA, and (TTTAGGG)3 locations in Gloriosa superba L.

Gloriosa superba L. is a horticulturally and medicinally important plant native to Africa. However, the few cytogenetic studies of the species are mainly focused on chromosome counting and chromosome morphology-based karyotyping. Fluorescence in situ hybridization (FISH) is a powerful tool for the detection of DNA repetitive elements in a specific region of a chromosome. Here, detailed karyotypes of G. superba were constructed by FISH using 5S and 45S rDNAs, and telomeric repeat (TTTAGGG)3 oligonucleotides. Twenty-two chromosomes were observed. Two 5S rDNA hybridization signals were detected in the proximal regions of the short arms of one pair of chromosomes, which were adjacent to the (TTTAGGG)3 terminal signals. Four 45S rDNA signals were detected near the centromere region of the short arm of the four chromosomes, but one of these was very weak and almost undetectable compared to the others. Telomeric repeat hybridization signals were distributed at the terminal region of each chromosome. The chromosomes displayed were intact and the chromosome counts were accurate. Chromosome length ranged from 3.46 to 9.31 μm. These results will facilitate the cytogenetic mapping of other major repeats, thus contributing to an improved understanding of the G. superba genome structure and evolutionary history.

Genome-Wide Identification and Expression Analysis of SNAP Gene Family in Wheat

Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution, physicochemical properties, conserved motifs, and cis-acting elements of the TaSNAP family members. Results: The TaSNAP family comprises members that encode proteins ranging between 120 and 276 amino acids, with isoelectric points spanning from 4.87 to 7.92. Phylogenetic analysis elucidated the categorization of the eight TaSNAP into three distinct subfamilies, wherein members of the same subfamily display marked similarities in their gene structures. Chromosomal mapping revealed the distribution of TaSNAP family members across chromosomes 2A, 2B, 2D, 7A, 7B, and 7D. Utilizing the Plant CARE tool, we identified ten elements linked to plant hormones and four associated with stress responses. Expression analysis via qRT-PCR was performed to assess the levels of the eight TaSNAP genes in various tissues and under diverse abiotic stress conditions. The results indicated heightened expression of most genes in roots compared to spikes. Notably, under ABA stress, the majority of genes exhibited upregulation, whereas certain genes were downregulated under PEG stress, implying a substantial role for SNAP protein in wheat growth and development. Conclusions: This study conducted a comprehensive bioinformatics analysis of each member of the wheat SNAP family, laying a crucial foundation for future functional investigations.

Chromosomal mapping of 5S rDNA in two species of the genus Acanthocephalus (Echinorhynchida)

Chromosomal mapping of 5S rDNA in two Acanthocephala species was performed for the first time using fluorescence in situ hybridization (FISH) with a 5S rDNA probe. The 5S rDNA PCR products from the genomes of both species were sequenced and aligned and an identical 141 bp long coding region was determined. The same patterns of 5S rDNA gene cluster distribution were observed, with FISH signal restricted to a single autosomal chromosome pair. A preference for distal positioning on the chromosomes (subtelomeric position) was observed in both species. In addition, two-color FISH was performed to examine the mutual positions of 5S and 18S rDNA on the chromosomes. Our knowledge of the organization of the Acanthocephala genome is extremely limited and its chromosomes are poorly studied. Any new information about the location of chromosomal markers as important features of the respective karyotype may be useful in solving evolutionary questions.

Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements.

Budding yeast (Saccharomyces cerevisiae) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and proteins. The Saccharomyces Genome Database (SGD) is a scientific resource that provides information about the genome and biology of S. cerevisiae. For more than 30 years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation for budding yeast along with search and analysis tools to explore these data. Here we describe recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface. These activities are part of our continuing effort to promote insights gained from yeast to enable the discovery of functional relationships between sequence and gene products in fungi and higher eukaryotes.

Genome-Wide Identification of CAMTA Gene Family in Oat (Avena sativa) and Expression Analysis under Various Abiotic Stresses

Oat (Avena sativa) is one of the most important cereal crops and cool-season forage grasses in the world. The calmodulin-binding transcription activator (CAMTA) gene family is one of the largest families in plants, and it plays vital roles in multiple biological processes. However, the CAMTA genes in oats, especially those involved in abiotic stress, have not yet been elucidated. Herein, our findings reveal the presence of 20 distinct AsCAMTA genes, which were clustered into three subfamilies based on their gene structure and conserved motifs, indicating functional similarities within each subgroup. Chromosomal mapping indicated an uneven distribution across 10 chromosomes, suggesting a complex evolutionary history marked by potential gene duplication events. The results showed that most AsCAMTA genes contained stress-related cis-elements. The study further investigated the expression patterns of these genes under abiotic stress conditions utilizing RT-qPCR analysis. The results identified three AsCAMTA genes (AsCAMTA5, AsCAMTA7, and AsCAMTA19) that exhibited significant up-regulation under salt stress, with AsCAMTA7 also showing a marked increase in expression under drought stress. These findings suggest a pivotal role of AsCAMTA5, AsCAMTA7, and AsCAMTA19 genes in mediating the responses to various abiotic stresses by integrating multiple stress signals in oats. This investigation provides valuable insights into the potential functions of AsCAMTA genes in the stress response mechanisms of oats, laying a foundation for further functional studies aimed at enhancing abiotic stress tolerance in crops.

Exploring the Roles of the Swi2/Snf2 Gene Family in Maize Abiotic Stress Responses.

The maize Snf2 gene family plays a crucial role in chromatin remodeling and response to environmental stresses. In this study, we identified and analyzed 35 members of the maize Snf2 gene family (ZmCHR1 to ZmCHR35) using the Ensembl Plants database. Each protein contained conserved SNF2-N and Helicase-C domains. Phylogenetic analysis revealed six groups among the Snf2 proteins, with an uneven distribution across subfamilies. Physicochemical analysis indicated that the Snf2 proteins are hydrophilic, with varied amino acid lengths, isoelectric points, and molecular weights, and are predominantly localized in the nucleus. Chromosomal mapping showed that these genes are distributed across all ten maize chromosomes. Gene structure analysis revealed diverse exon-intron arrangements, while motif analysis identified 20 conserved motifs. Collinearity analysis highlighted gene duplication events, suggesting purifying selection. Cis-regulatory element analysis suggested involvement in abiotic and biotic stress responses. Expression analysis indicated tissue-specific expression patterns and differential expression under various stress conditions. Specifically, qRT-PCR validation under drought stress showed that certain Snf2 genes were upregulated at 12 h and downregulated at 24 h, revealing potential roles in drought tolerance. These findings provide a foundation for further exploration of the functional roles of the maize Snf2 gene family in development and stress responses.

Glycoside hydrolases reveals their differential role in response to drought and salt stress in potato (Solanum tuberosum)

Glycoside hydrolases (GHs) are important in metabolic processes involving diverse carbohydrate-based substances found inside plant tissues. Potatoes (Solanum tuberosum) are rich in starchy carbohydrates, suggesting the role of GHs in their metabolic pathways. In this study, we examine the GH superfamily in potato where 366 potential GHs were identified using a similarity search method. Genes were subjected to further characterisation to gain insights into their structural composition, functional properties and distribution patterns across tissue types. Several in silico methodologies were also employed to investigate the physicochemical features, conserved motifs, chromosomal mapping, duplication events, syntenic links with tomato (Solanum lycopersicum), subcellular localisations, secondary structures and phylogenetic relationships. Cis-elements in StGHs revealed that the promoters of StGHs contain cis-elements that are responsive to phytohormones that are involved in plant growth and development, and are associated with stress responses. RNA-seq data identified significant changes in expression levels of GH16, GH17, GH18, GH19 and GH28 members under stress conditions. Expression patterns of several GHs were confirmed using real time quantitative PCR in response to stress. StGH16.24 expression increased after 3 days of drought stress, whereas StGH16.30 continuously increased under salt stress. Potential interactions between potato miRNAs and StGH revealed 393 and 627 interactions under drought and salt stress, respectively. Our findings offer insights into specific functions of GHs in diverse developmental stages and stress-related challenges in potato and other plants.

Satellite DNAs and the evolution of the multiple X1X2Y sex chromosomes in the wolf fish Hoplias malabaricus (Teleostei; Characiformes)

Multiple sex chromosomes usually arise from chromosomal rearrangements which involve ancestral sex chromosomes. There is a fundamental condition to be met for their long-term fixation: the meiosis must function, leading to the stability of the emerged system, mainly concerning the segregation of the sex multivalent. Here, we sought to analyze the degree of differentiation and meiotic pairing properties in the selected fish multiple sex chromosome system present in the wolf-fish Hoplias malabaricus (HMA). This species complex encompasses seven known karyotype forms (karyomorphs) where the karyomorph C (HMA-C) exhibits a nascent XY sex chromosomes from which the multiple X1X2Y system evolved in karyomorph HMA-D via a Y-autosome fusion. We combined genomic and cytogenetic approaches to analyze the satellite DNA (satDNA) content in the genome of HMA-D karyomorph and to investigate its potential contribution to X1X2Y sex chromosome differentiation. We revealed 56 satDNA monomers of which the majority was AT-rich and with repeat units longer than 100 bp. Seven out of 18 satDNA families chosen for chromosomal mapping by fluorescence in situ hybridization (FISH) formed detectable accumulation in at least one of the three sex chromosomes (X1, X2 and neo-Y). Nine satDNA monomers showed only two hybridization signals limited to HMA-D autosomes, and the two remaining ones provided no visible FISH signals. Out of seven satDNAs located on the HMA-D sex chromosomes, five mapped also to XY chromosomes of HMA-C. We showed that after the autosome-Y fusion event, the neo-Y chromosome has not substantially accumulated or eliminated satDNA sequences except for minor changes in the centromere-proximal region. Finally, based on the obtained FISHpatterns, we speculate on the possible contribution of satDNA to sex trivalent pairing and segregation.

Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics.

High dimensional nature of the chromosomal conformation contact map ('Hi-C Map'), even for microscopically small bacterial cell, poses challenges for extracting meaningful information related to its complex organization. Here we first demonstrate that an artificial deep neural network-based machine-learnt (ML) low-dimensional representation of a recently reported Hi-C interaction map of archetypal bacteria Escherichia coli can decode crucial underlying structural pattern. The ML-derived representation of Hi-C map can automatically detect a set of spatially distinct domains across E. coli genome, sharing reminiscences of six putative macro-domains previously posited via recombination assay. Subsequently, a ML-generated model assimilates the intricate relationship between large array of Hi-C-derived chromosomal contact probabilities and respective diffusive dynamics of each individual chromosomal gene and identifies an optimal number of functionally important chromosomal contact-pairs that are majorly responsible for heterogenous, coordinate-dependent sub-diffusive motions of chromosomal loci. Finally, the ML models, trained on wild-type E. coli show-cased its predictive capabilities on mutant bacterial strains, shedding light on the structural and dynamic nuances of ΔMatP30MM and ΔMukBEF22MM chromosomes. Overall our results illuminate the power of ML techniques in unraveling the complex relationship between structure and dynamics of bacterial chromosomal loci, promising meaningful connections between ML-derived insights and biological phenomena.

Satellitome Analysis of Adalia bipunctata (Coleoptera): Revealing Centromeric Turnover and Potential Chromosome Rearrangements in a Comparative Interspecific Study.

Eukaryotic genomes exhibit a dynamic interplay between single-copy sequences and repetitive DNA elements, with satellite DNA (satDNA) representing a substantial portion, mainly situated at telomeric and centromeric chromosomal regions. We utilized Illumina next-generation sequencing data from Adalia bipunctata to investigate its satellitome. Cytogenetic mapping via fluorescence in situ hybridization was performed for the most abundant satDNA families. In silico localization of satDNAs was carried out using the CHRISMAPP (Chromosome In Silico Mapping) pipeline on the high-fidelity chromosome-level assembly already available for this species, enabling a meticulous characterization and localization of multiple satDNA families. Additionally, we analyzed the conservation of the satellitome at an interspecific scale. Specifically, we employed the CHRISMAPP pipeline to map the satDNAs of A. bipunctata onto the genome of Adalia decempunctata, which has also been sequenced and assembled at the chromosome level. This analysis, along with the creation of a synteny map between the two species, suggests a rapid turnover of centromeric satDNA between these species and the potential occurrence of chromosomal rearrangements, despite the considerable conservation of their satellitomes. Specific satDNA families in the sex chromosomes of both species suggest a role in sex chromosome differentiation. Our interspecific comparative study can provide a significant advance in the understanding of the repeat genome organization and evolution in beetles.

Comprehensive characterization and expression profiling of BBX gene family in soybean in response to UV-B stress

The BBX gene family encodes transcription factors that regulate several biological processes, such as plant growth, development, and stress response. They have been identified and thoroughly studied in numerous plant species. The functional role of the BBX gene family against UV-B stress in soybean has not been well documented. Herein, this study focused on a comprehensive investigation of the GmBBX genes in soybean and their expression patterns in response to UV-B exposure. A total of 184 BBX genes were identified and analyzed to determine the conserved domain. Single and double B-box and CCT domains were found across these proteins, indicating potential functional diversity. The protein physicochemical properties showcased diverse characteristics, highlighting molecular size, stability, and hydrophobicity. Phylogenetic analysis revealed five distinct clades, showcasing a non-uniform distribution of GmBBX genes. Chromosomal mapping showed a non-uniform distribution of GmBBX genes across the 20 chromosomes of soybean. The highest number of genes (26) were found on chromosome 13, whereas chromosomes 5 and 15 displayed the lowest number of genes (3 genes each). Gene structure analysis revealed variations in exon-intron patterns, while motif composition analysis unveiled conserved motifs among GmBBX proteins. Gene duplication indicated that the expansion of the GmBBX genes was linked with tandem and dispersed duplications. Gene ontology analysis revealed enrichment of terms associated with light stimulus, response to abiotic stress, and molecular functions such as zinc ion binding. The promoter region reveals cis-acting elements related to hormones, light, and stress responses. The GmBBX genes exhibited differential expression in response to UV-B stress, suggesting their possible role in plant defense against UV-B stress. This study will provide a solid foundation for further analysis of the molecular mechanisms of GmBBX genes in soybean against UV-B stress.

OMEGACat. III. Multiband Photometry and Metallicities Reveal Spatially Well-mixed Populations within ω Centauri’s Half-light Radius

ω Centauri, the most massive globular cluster in the Milky Way, has long been suspected to be the stripped nucleus of a dwarf galaxy that fell into the Galaxy a long time ago. There is considerable evidence for this scenario including a large spread in metallicity and an unusually large number of distinct subpopulations seen in photometric studies. In this work, we use new Multi-Unit Spectroscopic Explorer spectroscopic and Hubble Space Telescope photometric catalogs to investigate the underlying metallicity distributions as well as the spatial variations of the populations within the cluster up to its half-light radius. Based on 11,050 member stars, the [M/H] distribution has a median of (−1.614 ± 0.003) dex and a large spread of ∼1.37 dex, reaching from −0.67 to −2.04 dex for 99.7% of the stars. In addition, we show the chromosome map of the cluster, which separates the red giant branch stars into different subpopulations, and analyze the subpopulations of the most metal-poor component. Finally, we do not find any metallicity gradient within the half-light radius, and the different subpopulations are well mixed.

Chromosome Mapping of Ribosomal DNA Clusters in Four Leaf-cutting Ant Species of the Genus Acromyrmex, with Description of a Triploid Individual in A. laticeps

The increase of cytogenetic data in the leaf-cutting genus Acromyrmex has shown interesting contributions to the evolutionary and taxonomic approaches, including the creation of a new genus and the description of chromosomal patterns allowing comparative studies within Acromyrmex as well as between this genus and other similar taxa. The conserved chromosome number in Acromyrmex is a notable feature, with some distinguishable chromosomes among the species. In this study, we describe the diploid karyotype of Acromyrmex laticeps in addition to an individual with all the metaphases triploids, suggesting a triploid individual. To the best of our knowledge, this is the first report of polyploidy in a fungus-growing ant. Furthermore, we mapped 18S ribosomal DNA on the chromosomes of A. laticeps and three other Acromyrmex species. Among them, three species showed the ribosomal DNA cluster pattern observed in other previously studied members of this genus, with a terminal location in the largest subtelocentric pair. Meanwhile, Acromyrmex balzani had these ribosomal DNA clusters in its entire short arm. The role of triploidy in ant evolution has also been discussed. The increase in chromosomal data of leaf-cutting ants may provide significant insights into the evolution of this peculiar ant group.

Genome-wide analysis of XTH gene family in cucumber (Cucumis sativus) against different insecticides to enhance defense mechanism

This study investigates how plants protect themselves, specifically looking at a group of genes called Xyloglucan Endotransglucosylase/Hydrolase (XTH) in cucumber plants. A detailed investigation of CsXTH genes, uncover their evolutionary background, structural motifs, regulatory networks, and functional responsibilities. The investigation utilized various bioinformatics tools and databases to highlight the dynamic interplay between CsXTH genes and abiotic stress responses. The investigation begins with a phylogenetic analysis that reveals the cladding of CsXTH genes into four categories. Further unraveling the conserved motif and domain analyses expose the coordination of xyloglucan modification, highlighting essential motifs and domains shared among these genes. Analyzing cis-regulatory elements helps us understand the complex networks that control the defense mechanisms of cucumber plants. Among these elements, CGTCA-motif and TGACG-motif stand out as key players in interpreting environmental signals and coordinating stress responses. The microRNA Csa-miR169 is becoming a key player in regulating the expression of CsXTH genes, and controlling the biological responses of cucumber plants. Chromosome mapping, Ka/Ks calculations, and protein-protein interaction analysis offer insights into the structural and evolutionary dynamics of CsXTH genes. Additionally, the study explores sub-cellular localization, uncovering the diverse cellular compartments where CsXTH genes are active. Finally, through chrysophanol and physcion, we unveil the adaptable functions of specific CsXTH genes in response to distinct treatments, underscoring their role in orchestrating cucumber's adaptive strategies.