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The study of plant resistance to stress and adversity is one of the hot scientific issues. With the frequent occurrence of extreme weather, millet, as a typical drought-resistant and barren crop, plays an increasingly important role in the adjustment of crop planting structure. This paper, reviewed the research progress of stress-related gene families and gene mining in recent years, and prospected the development prospect of stress-related functional genes in millet, in order to provide reference for the development of stress-related directions in millet, the analysis of resistance mechanism and the breeding of resistant varieties. [ABSTRACT FROM AUTHOR]

Invasive species offer uniquely replicated model systems to study rapid adaptation. The common myna (Acridotheres tristis) has been introduced to over a dozen countries and is classified as one of the most invasive birds in the world. Their multiple invasions provide an opportunity to identify repeated adaptation, as invasive populations originated from multiple source populations. We compared whole‐genome resequencing data from 80 individuals from four native and seven invasive populations, representing two independent introduction pathways. Results from two different selection scan methods were combined and identified a strongly selected region on chromosome 8 that spans two copies of AMY2A, part of the alpha‐amylase gene family, a putative ncRNA and an insertion–deletion structural variant (SV) that contains an ERVK transposable element (TE). Outlier SNPs and the SV are polymorphic in native populations, but fixed or close‐to‐fixed in the two invasive pathways, with the fixation of the same alleles in two independent lineages providing evidence for parallel selection on standing variation. Intriguingly, the second copy of AMY2A has a non‐conservative missense mutation at a phylogenetically conserved site. This mutation, alongside variation in the SV, TE and ncRNA, provide possible routes for changes to protein function or expression. AMY2A has been associated with human commensalism in house sparrows, and genes in this family have been linked to adaptation to high‐starch diets in humans and dogs. This study illustrates the value of replicated analyses within and across species to understand rapid adaptation at the molecular level. [ABSTRACT FROM AUTHOR]

Background : The rumen fluke, Calicophoron daubneyi, is the major paramphistome species infecting ruminants within Europe. Adult flukes reside within the rumen where they are in direct contact with a unique collection of microorganisms. Here, we report a 1.76-Gb draft genome for C. daubneyi, the first for any paramphistome species. Results: Several gene families have undergone specific expansion in C. daubneyi, including the peptidoglycan-recognition proteins (PGRPs) and DM9 domain-containing proteins, which function as pattern-recognition receptors, as well as the saposin-like proteins with putative antibacterial properties, and are upregulated upon arrival of the fluke in the microbe-rich rumen. We describe the first characterisation of a helminth PGRP and show that a recombinant C. daubneyi PGRP binds to the surface of bacteria, including obligate anaerobes from the rumen, via specific interaction with cell wall peptidoglycan. We reveal that C. daubneyi eggshell proteins lack L-DOPA typically required for eggshell crosslinking in trematodes and propose that C. daubneyi employs atypical eggshell crosslinking chemistry that produces eggs with greater stability. Finally, although extracellular digestion of rumen ciliates occurs within the C. daubneyi gut, unique ultrastructural and biochemical adaptations of the gastrodermal cells suggest that adult flukes also acquire nutrients via uptake of volatile fatty acids from rumen fluid. Conclusions: Our findings suggest that unique selective pressures, associated with inhabiting a host environment so rich in microbial diversity, have driven the evolution of molecular and morphological adaptations that enable C. daubneyi to defend itself against microorganisms, feed and reproduce within the rumen. [ABSTRACT FROM AUTHOR]

BackgroundCasesConclusionPathogenic variants in KIF11, a kinesin family gene, cause MCLMR and FEVR. In MCLMR, chorioretinal atrophy is present in the majority of cases and can be a helpful diagnostic sign.We present the cases of two patients with chorioretinal atrophy and microcephaly who carry novel KIF11 mutations. Both patients have relatively good central vision similar inferior lacunae of retinal atrophy with relative sparing of the foveal center with.Two cases with classic features of MCLMR have foveal sparing that expands the associated spectrum of ocular findings. [ABSTRACT FROM AUTHOR]

Aggregation of antimicrobial peptides (AMPs) enhances their efficacy by destabilising the bacterial cell wall, membrane, and cytosolic proteins. Developing aggregation-prone AMPs offers a promising strategy to combat antibiotic resistance, though predicting such AMPs and understanding bacterial responses remain challenging. Octopus bimaculoides , a cephalopod species, lacks known AMP gene families, yet its protein fragments were used to predict AMPs via artificial intelligence tools. Four peptides (Oct-P1, Oct-P2, Oct-P3, and Oct-P4) were identified based on their aggregation propensity. Among them, Oct-P2 reduced the viability of Escherichia coli and Staphylococcus aureus by up to 90 %, confirmed by confocal laser scanning microscopy and scanning electron microscopy. It further aggregated plasmid DNA in vitro , and the presence of extracellular DNA reduced their antibacterial activity. With knockout mutants, it revealed that Oct-P2 was internalized into bacterial cells, possibly through membrane transport proteins, enhancing its antibacterial effect. Aggregation-induced emission assays and molecular dynamics simulations revealed that Oct-P2 aggregates with transcription promoter DNA, inhibiting transcription and translation in vitro. This dual-target mechanism not only highlights the potential of Oct-P2 as a lead template for new antimicrobial drug development, but also opens a new window for discovering AMPs from protein fragments against the upcoming challenge of bacterial infections. A popular strategy for identifying antimicrobial peptides (AMPs) in specific genomes uses the conserved regions of AMP families, but this strategy has limitations in organisms lacking classical AMP gene families, such as Octopus. Fragments from non-antimicrobial proteins serve as a rich source for the identification of new AMPs. In this study, we used artificial intelligence tools to search for potential candidate AMP sequences from non-antimicrobial proteins in Octopus bimaculoides. The successful identification of aggregation-prone AMPs was shown to decrease bacterial viability, increase permeability, and reduce biomass. One candidate, Oct-P2, kills the gram-negative bacteria E. coli by aggregating with DNA and inhibiting transcription and translation, suggesting a new intracellular mechanism of AMP activity. [Display omitted] [ABSTRACT FROM AUTHOR]

Background: The plant-specific YABBY transcription factor family plays several activities, including responding to abiotic stress, establishing dorsoventral polarity, and developing lateral organs. Cucumis sativus L. commonly referred to as cucumber and one of the first vegetable crops with a fully sequenced genome. Results: In this work, we examined the application of NAA, CPPU, and GA4 + 7 to inflict parthenocarpy in the cucumber ZK line. The expression pattern of YABBY genes throughout fruit development and performed a genomic census of cucumber (Cucumis sativus L.). Based on peptide classification, we discovered eight CsYABBY genes and divided them into five subfamilies. Similarities in motif composition and exon-intron structure were also observed. The cis-elements and gene ontology (GO) analysis revealed the involvement of CsYABBY genes in vegetative growth and the transition of vegetative to the reproductive phase. The expression analysis revealed the differential expression response to NAA, CPPU, and GA4 + 7. In particular, the CsYABBY1 was induced sharply by NAA and CPPU but not GA4 + 7. The transient expression of CsCRC disclosed that it is localized in the nucleus. Conclusion: These findings point to the possibility that CsYABBY1 and CsCRC may positively affect fruit development and could be utilized to generate parthenocarpic cucumber fruits. [ABSTRACT FROM AUTHOR]

Background: Calmodulin-binding transcription activator (CAMTA) proteins play significant roles in signal transduction, growth and development, as well as abiotic stress responses, in plants. Understanding their involvement in the low-temperature stress response of teak is vital for revealing cold resistance mechanisms. Results: Through bioinformatics analysis, the CAMTA gene family in teak was examined, and six CAMTA genes were identified in teak. The encoded proteins were predicted to be located in the nucleus and exhibited hydrophilic properties, with molecular weights ranging from 103.4 to 123.3 kDa and isoelectric points ranging from 5.49 to 7.55. On the basis of protein sequence homology, the CAMTA family could be divided into three subgroups. Domain and 3D structure analyses demonstrated that all the TgCAMTA proteins contained the typical CAMTA domain with the CaMBD binding domain, which was exposed on the surface. Expression analysis of different tissues revealed the expression of TgCAMTA genes in teak roots, stems, leaves, flowers, fruits, and branches. Furthermore, the promoter region contained various cis-acting elements related to light, hormone, and abiotic stress responses. After low-temperature stress treatment, different expression patterns of TgCAMTAs were observed in teak roots, stems, and leaves, with TgCAMTA1 showing the highest expression level in leaves compared with stems. Transgenic lines carrying the TgCAMTA1/3 promoter::GUS construct cold stress induction of TgCAMTA1/3 genes revealed the presence of multiple low-temperature responsive cis-acting elements in the TgCAMTA1/3 promoter region. Subcellular localization analysis indicated that these genes were functional predominantly in the nucleus. Compared with wild-type Arabidopsis, TgCAMTA1/3-overexpressing Arabidopsis presented increased tolerance to freezing stress, with increased expression of AtCOR genes. Moreover, under low-temperature conditions, TgCAMTA3-overexpressing Arabidopsis presented significantly elevated expression levels of genes related to the CBF signaling pathway, including AtCBF1/2/3. Conclusions: Our findings add significantly to the existing knowledge regarding cold stress tolerance and help elucidate cold response mechanisms in teak. [ABSTRACT FROM AUTHOR]

The sunflower (Helianthus annuus L.), belonging to the Asteraceae family, is the world's fourth most important oil crop. Sunflower cultivars are categorized into oilseed and confectionery types. Here, we present chromosome-level genome assemblies of two Chinese sunflower cultivars-oilseed and confectionery-using PacBio HiFi and Hi-C sequencing. The oilseed cultivar, OXS, has a genome assembly spanning 3.03 Gb with 99.58% of sequences anchored to 17 chromosomes and a contig N50 length of 154.78 Mb. The first published confectionery cultivar genome, YDS, mirrors this closely with a 3.02 Gb assembly, contig N50 length of 153.87 Mb and 99.40% of sequences mapped similarly. Gene completeness reached 98.2% for OXS and 98.4% for YDS, with LTR Assembly Index scores of 24.73 and 25.85, respectively. Comparative genomics identified rapidly evolving gene families linked to synthesis, growth, and stress defense. Additionally, we found high collinearity between the YDS and OXS genomes, despite three significant inversions, and detected 15,056 large deletions and insertions. These findings lay a robust foundation for advanced genomic research and breeding innovations in sunflowers. [ABSTRACT FROM AUTHOR]

The Jacalin-related lectins (JRLs) gene family play a crucial role in regulating plant development and responding to environmental stress. However, a systematic bioinformatics analysis of the JRL gene family in Gramineae plants has been lacking. In this study, we identified 101 JRL proteins from five Gramineae species and classified them into eight distinct clades. Most of the AtJRL proteins clustered in the same group and were differentiated from the Gramineae JRL proteins. The analysis of protein motifs, gene structures and protein domain revealed that the JRL genes play diverse functions in Gramineae plants. Duplication events indicated that tandem duplication significantly contributed to the expansion of the JRL family, with most JRL members underwent purifying selection. Tissue expression profile analysis showed that most OsJRL genes were highly expressed in the roots, while ZmJRL genes exhibited high expression in inflorescences. Furthermore, the expression level of OsJRL and ZmJRL genes were influenced by drought, cold, heat and salt stresses, respectively, implying that these genes play important roles in response to various abiotic stresses. RT-qPCR results demonstrated that OsJRL4 was up-regulated under PEG6000 and NaCl stresses, while OsJRL12 and OsJRL26 were down-regulated under PEG6000. These findings provide comprehensive insights into the JRL gene family in Gramineae plants and will facilitate further functional characterization of JRLs. [ABSTRACT FROM AUTHOR]

Sophora flavescens is a traditional Chinese medicinal herb rich in various bioactive secondary metabolites, such as alkaloids and flavonoids, and exhibits remarkable resistance to abiotic stress. The WRKY transcription factor (TF) family is one of the largest plant-specific TF families and plays a crucial role in plant growth, development, and responses to abiotic stress. However, a comprehensive genome-wide analysis of the WRKY gene family in S. flavescens has not yet been conducted. In this study, we identified 69 SfWRKY genes from the S. flavescens genome and classified them into seven distinct subfamilies based on phylogenetic analysis. Transposed duplications and dispersed duplications were found to be the primary driving forces behind the expansion of the SfWRKY family. Additionally, several cis -acting elements related to the stress response and hormone signaling were discovered within the promoter regions of SfWRKYs. Transcriptomic analyses across five tissues (leaves, flowers, pods, roots, and stems) revealed that genes exhibiting high expression levels in specific tissues generally showed high expression across all the examined tissues. Coexpression network constructed based on metabolomic and transcriptomic analyses of root and pod development indicated that SfWRKY29 may play a significant role in regulating the biosynthesis of secondary metabolites during tissue development. The RT-qPCR results of gene expression analysis revealed that several SfWRKY genes were significantly induced in response to the accumulation of secondary metabolites or salt stress. Our study systematically analyzed WRKY TFs in S. flavescens , which provides valuable reference data for further studies on the key roles of SfWRKY genes in growth development as well as their responses under salt stress conditions. [ABSTRACT FROM AUTHOR]

Rice is susceptible to cold temperatures, especially during the seedling stage. Despite extensive research into the cold tolerance mechanisms of rice, the number of cloned genes remains limited. Plant subtilisin-like proteases (SUBs or SBTs) are protein-hydrolyzing enzymes which play important roles in various aspects of plant growth as well as the plant response to biotic and abiotic stress. The rice SUB gene family consists of 62 members, but it is unknown whether they are involved in the response to cold stress. In this study, we observed that a loss-of-function SUB4 mutant exhibited enhanced cold tolerance at the seedling stage. The sub4 mutant seedlings exhibited improved survival rates and related physiological parameters, including relative electrolyte conductivity, chlorophyll content, malondialdehyde content, and antioxidant enzyme activity. Transcriptomic analysis revealed that differentially expressed genes responsive to cold stress in the sub4 mutants were primarily associated with metabolism and signal transduction. Notably, the majority of cold-responsive genes were associated with cell wall functions, including those related to cell wall organization, chitin catabolic processes, and oxidoreductases. Our findings suggest that SUB4 negatively regulates the cold response in rice seedlings, possibly by modifying the properties of the cell wall. [ABSTRACT FROM AUTHOR]

To explore CRT gene family members and their responses to low-temperature stress, bioinformatics methods were used to identify the CRT gene family in pepper. In this study, a total of 4 CRT gene family members were identified by screening. The genes were found to be located on different chromosomes, and phylogenetic tree and collinearity analyses were performed. In addition, the cis-acting elements identified in the 2.0 kb upstream promoter regions of the 4 CaCRTs described in this study can be divided into three categories. The expression patterns of CRTs in different tissues and organs under low-temperature stress were analysed. Virus-induced gene silencing (VIGS) technology was used to verify the function of CaCRT1, and the results revealed that CaCRT1 participated in the pepper response to low-temperature stress and the accumulation of excessive reactive oxygen species (ROS) and malondialdehyde (MDA). In summary, this study systematically verified the regulatory role of CaCRT gene family members in pepper under low-temperature stress and provided a foundational understanding for further research on the biological functions of pepper CRT genes. [ABSTRACT FROM AUTHOR]

Introduction The importance of identifying relevant indicators of antidepressant efficacy is highlighted by the low response rates to antidepressant treatment for depression. The ABC gene family, encoding ATP-dependent transport proteins facilitating the transport of psychotropic drugs, has drawn attention. This study delved into the relationship between antidepressant efficacy and seven single nucleotide polymorphisms of ABCB1 and ABCB6 genes. Methods A total of 549 depressed patients participated in the study, and all completed a 6-week course of antidepressant treatment. Cognitive function was assessed at baseline and post-treatment. Patients were categorized based on post-treatment HAMD-17 scores (with HAMD≤7 indicating remission), and comparisons were made between different groups in terms of allelic gene frequencies and genotypes. Logistic regression was used to explore the interaction between cognitive function and genotype on efficacy. Dual-luciferase reporter assays were performed to compare the regulatory effects of rs1109866 allele variants on the ABCB6 promoter. Results There were no notable differences in allelic gene frequencies and genotypes between the remission and non-remission groups. Nonetheless, a significant interaction was identified between the rs1109866 genotype and language fluency-related indicators concerning efficacy (p=0.029) before correction. The dual-luciferase reporter assays demonstrated markedly higher fluorescence intensity of rs1109866-C compared to that of rs1109866-T (p<0.001). Discussion Relying solely on genetic polymorphisms of ABC family genes as predictors of antidepressant treatment response may not be sufficient. However, the interaction between the rs1109866 and cognition plays a pivotal role. The potentially enhanced transcriptional activity of rs1109866-C might offer insight into its impact on antidepressant efficacy. [ABSTRACT FROM AUTHOR]

Chemokines play a crucial role in immune responses by facilitating the migration of cells expressing corresponding chemokine receptors along concentration gradients. Photobacterium damselae subsp. Damselae (PDD) and Nocardia seriolae (NS) are known to induce substantial mortality in silver pomfret populations, yet there exists a dearth of research regarding the immune response of CCLs in PDD‐ or NS‐infected silver pomfret. In our investigation, we identified 10 PaCCLs, which include one fish‐specific CCL (PaCCL44). Phylogenetic analysis revealed considerable diversity in CCL types and copy numbers among various teleost fishes. Notably, silver pomfret lacks specific CCL genes, with most PaCCLs exhibiting heightened expression levels in immune‐related organs such as the spleen and kidney, and some being expressed in mucosal immune‐related organs like the skin and gills. Transcriptome analysis conducted on silver pomfret infected with NS and PDD elucidated that the expression changes of PaCCLs primarily manifested in the spleen during the initial stages of NS infection, shifting to the kidney in later stages. Conversely, the expression changes of PaCCLs following PDD infection predominantly occurred in the kidney. In vitro studies using silver pomfret spleen cell lines demonstrated an early peak in PaCCLs expression during infection, followed by gradual decline with NS treatment and rapid diminishment with PDD treatment. These findings suggest that PaCCLs primarily support the innate immunity of silver pomfret, potentially exhibiting chemotactic effects in the early infection stages, such as the synergistic action of PaCCL4 and PaCCL25, and later serving as direct antibacterial agents. NS invasion is characterised by a chronic infection affecting multiple organs, whereas PDD primarily inflicts severe damage to the kidney. PaCCL19a and PaCCL19b are specific to PDD, and their expression levels may decrease in the later stages of infection due to PDD immune escape. These data offer initial insights into understanding the mechanism underlying the innate immune response of the CCL gene family in silver pomfret and provide theoretical underpinnings for fish culture practices. [ABSTRACT FROM AUTHOR]

Magnolia sieboldii K. Koch (M. sieboldii) stands as an elegant tree species within the Magnoliaceae family, esteemed for its exquisite beauty, cultural significance and economic advantages. The species faces challenges in seed germination under natural conditions, primarily attributed to morphological dormancy. Despite its significance, the molecular mechanisms governing M. sieboldii seed germination remain elusive, compounded by the absence of genomic resources specific to this species. In this study, we present the first chromosome‐scale genome assembly of M. sieboldii, with a total genome size of 2.01 Gb, including 1096 scaffolds assigned to 19 chromosomes (N50 = 102.4 Mb). Phylogenetic analyses, incorporating 13 plant species, illuminate the evolutionary independence of Magnoliids from monocots and eudicots, positioning them as a sister clade. Through RNA‐seq analysis, we identify pivotal genes and pathways contributing to seed dormancy and germination. In addition, our investigation delves into the the far‐red‐impaired response (FAR1) transcription factor gene family, revealing their enrichment throughout evolution and their involvement in the intricate process of seed germination. This comprehensive genome sequencing initiative offers invaluable insights into the biological attributes of M. sieboldii, with a specific emphasis on unravelling the complexities of seed dormancy and germination. [ABSTRACT FROM AUTHOR]

• Eighteen quinoa gibberellin oxidase genes were identified. • They were divided into four subfamilies: C19GA2ox, C20GA2ox, GA3ox, and GA20ox. • CqGAox genes were specifically expressed during seed germination. • CqGAox genes were expressed to maintain endogenous GAs in plants exposed to stress. Pre-harvest sprouting (PHS) is an urgent problem in the quinoa breeding process. Gibberellin oxidases are key enzymes in the biosynthesis and degradation of gibberellins, playing a significant role in the regulation of active gibberellins (GAs). In this study, 18 CqGAox genes were identified in quinoa and characterized according to phylogenetic relationships, gene structure, conserved motifs, codon use pattern, and expression patterns. Based on their phylogenetic relationships, the CqGAox genes were classified into four groups: C19CqGA2ox, C20CqGA2ox, CqGA3ox , and CqGA20ox. Evolutionary analyses showed that homologous GAox genes from Arabidopsis, rice, and quinoa have been subject to purifying selection during evolution. According to the codon use patterns, mutational stress may cause codon bias in CqGAox genes. Prediction of promoter cis-regulatory elements suggested that the CqGAox genes contained multiple elements that responded to phytohormones and stress. We further evaluated the transcriptional responses of CqGAox genes during quinoa seed germination and under low-temperature stress treatments of seedlings. Moreover, qRT-PCR was used to confirm the changes in CqGAox gene expression during quinoa seed germination under GA 3 and paclobutrazol (PAC) treatments. Compared with the control, expression of CqGAox genes was significantly altered by treatment with GA 3 or PAC. These findings indicated that the CqGAox genes are essential for regulating GA biosynthesis and degradation. This study lays the foundation for further investigations of the roles of CqGAox genes in GA-regulated quinoa seed germination and provides potential targets for addressing the challenge of quinoa PHS. [ABSTRACT FROM AUTHOR]

High-temperature-induced early bolting poses a pressing challenge in annual leaf lettuce cultivation. ABF transcription factors, or ABA-responsive element binding factors, are crucial components of the ABA signalling pathway. In this study, we identified 8 members of the ABF gene family in leaf lettuce, categorising them into groups A, B, and C through phylogenetic analysis. All LsABFs exhibited a conserved domain, RMIKNRESAARSRARKQAY (Bzip_plant_BZIP46), as revealed by multiple sequence alignment. A total of 1242 cis-acting elements were detected, with 323 elements screened. Predictive analysis indicated 304 phosphorylation sites. Expression patterns of LsABFs were similar, peaking on the 8th day, implicating their role in bolting. Silencing LsABF1 positively impacted lettuce bolting, signifying its regulatory potential. This study establishes a theoretical foundation for comprehending the molecular mechanisms governing ABF genes in high-temperature-induced bolting in leaf lettuce. [ABSTRACT FROM AUTHOR]

Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of their genomic information has impeded evolutionary studies and genome-based breeding efforts. Here, we present reference genomes for Lilium sargentiae (lily, 35.66 Gb) and Gloriosa superba (flame lily, 5.09 Gb). The giant lily genome is shaped by recent long terminal repeat retroelements. Phylogenetic analysis reveals diverse, independent origins of lily cultivars. Gene families involved in sucrose and starch metabolism are significantly expanded in the lily genome. Key homologs of XTH22, SOC1, and AP1/FUL-like genes regulate the development, bud growth transition, and floral bud growth transition of lily bulbs. Colchicine biosynthetic gene clusters are identified in G. superba but are absent in L. sargentiae, highlighting independent colchicine evolution in Colchicaceae. These genomic insights enhance understanding of Liliales evolution, providing a foundation for future breeding and molecular research. Lilies are perennial plants with ornamental flowers and large genomes. The authors assemble genomes of two Liliales species, analyze lily phylogeny, flower and stem development (bulbs in lilies, rhizomes in flame lilies), bulb growth transitions, and colchicine biosynthesis. [ABSTRACT FROM AUTHOR]

The INDETERMINATE DOMAIN (IDD) gene family, encoding a class of C2H2 transcription factor, played diverse roles in land plants. The IDD family in tobacco (Nicotiana tabacum) has not been characterized. In this study, 26 NtIDDs were identified in the tobacco genome. Phylogenetic analysis showed that NtIDDs were divided into five groups. Motif analysis revealed that the ID domain was conserved in NtIDDs. Gene duplication analysis demonstrated that segmental/whole-genome duplication and dispersed duplication would have occurred in NtIDDs. Cis- element analysis predicted that hormone-, stress-, and development-related elements are located in NtIDD promoters. Expression analysis revealed tissue preference patterns and differential hormone responses in NtIDDs. Further investigations on the function of NtIDD9 exhibited increased leaf angle degrees in RNA silencing plants. Cellular localization suggested that NtIDD9 expressed in the endodermis of the leaf petiole base. Subcellular localization analysis revealed that the NtIDD9 protein was located in the nucleus. Hormone quantification found that the levels of auxin, ABA, JA, and GA were significantly changed in NtIDD9 -silenced plants. Thus, the study suggested that NtIDD9 played a crucial role in modulation of leaf angle development. Overall, these findings lay foundations for future function and mechanism research on IDDs in tobacco. [ABSTRACT FROM AUTHOR]

Acylation represents a pivotal biochemical process that is instrumental in the modification of secondary metabolites throughout the growth and developmental stages of plants. The BAHD acyltransferase family within the plant kingdom predominantly utilizes coenzyme A thioester as the acyl donor, while employing alcohol or amine compounds as the acceptor substrates to facilitate acylation reactions. Using bioinformatics approaches, the LjBAHD gene family members in the genome of Leonurus japonicus (L. japonicus) were identified and characterized including gene structure, conserved motifs, cis -acting elements, and potential gene functions. To elucidate the roles of BAHD genes in various tissues of L. japonicus , the expression profiles of LjBAHD family members across different organs were scrutinized. Under drought stress treatment, some LjBAHDs were upregulation, suggesting their potential involvement in drought response. Notably, a detailed study was conducted on a specific HCT gene (i.e., LjBAHD 25) within the BAHD gene family. Analysis of its expression patterns suggested a role for LjBAHD 25 in the phenylpropanoid metabolism pathway in L. japonicus , contributing to the biosynthesis of secondary metabolites with unique bioactivity. The findings of this study have established a scientific foundation for the subsequent development and functional validation of the BAHD gene family in L. japonicus. [ABSTRACT FROM AUTHOR]

BACKGROUND: The crucial role of insect chitinase in molting, pupation, and emergence renders it a promising target for pest control strategies. Despite the extensive investigation of chitinase genes in various pests, there is still a lack of systematic identification and functional analysis related to aphid chitinase. RESULTS: We systematically identified a total of nine chitinase/chitinase‐like genes and one ENGase gene, which included eight Cht genes, one IDGF gene, and one ENGase gene. Through phylogenetic analysis, the chitinase proteins were classified into nine distinct groups (I, II, III, V, VI, VIII, X, other, and ENGase). The expression profile revealed that the epidermis exhibited relatively high expression levels for three chitinase genes: MpCht5, MpCht7, and MpCht10. Furthermore, transcriptional levels of nine chitinase genes were up‐regulated following treatment with 20‐hydroxyecdysone (20E) hormone. Silencing MpCht3, MpCht5, MpCht7, MpCht10, and MpCht11‐2 via RNA interference (RNAi) during the molting stage resulted in nymph shrinking, hindering normal molting and leading to death. Additionally, it was observed that silencing of MpIDGF induced the body color of the aphids to change from reddish brown to colorless after molting, culminating in eventual mortality. CONCLUSION: Our findings suggest that chitinase/chitinase‐like genes play a crucial role in the molting process of Myzus persicae. Utilizing RNAi technology, we aimed to elucidate the precise function of MpCht genes in the molting mechanism of M. persicae, this discovery establishes a significant theoretical foundation for future research on aphid control, with chitinase as the target. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Peas (Pisum sativum L.) serve as a vital model for plant development and stress research. The kinesin (KIN) gene family, encoding essential motor proteins, remains understudied in peas. Our research conducted a comprehensive genomic analysis of the KIN genes in peas, identifying 105 genes categorized into seven subfamilies based on evolutionary relationships, gene structures, conserved motifs, and interaction networks. A comparative analysis with Arabidopsis and soybean KIN gene families showed a non-uniform distribution of PsKIN genes across subfamilies. Homology analysis revealed that the PsKIN family has undergone segmental duplication and is under negative selection pressures, with conserved genes on chromosomes Ps5, Ps6, and Ps7 playing a significant role in pea evolution. Transcriptomics revealed 38 PsKIN genes with distinct tissue-specific expression, with PsKIN76 , PsKIN96 , PsKIN82 , and PsKIN103 showing significant levels in roots, lateral roots, stems, petals, and seeds, respectively. Differential expression under drought and saline stress was observed, with PsKIN8 , PsKIN11 , PsKIN54 upregulated under drought, and PsKIN47 and PsKIN51 under saline stress. These genes are potential candidates for improving plant stress tolerance. This study offers insights into the pea KIN gene family, highlighting their potential in enhancing plant stress tolerance and setting a stage for future research. [ABSTRACT FROM AUTHOR]

Background: SARS-CoV-2 and COVID-19 are still active in the population. Some patients remained PCR-positive for more than 4 weeks, called "persistently PCR-positive". Recent evidence suggests a link between the gut microbiota and susceptibility to COVID-19, although no studies have explored persistent PCR conditions. We aimed to evaluate the relationship between persistent positive SARS-CoV-2 RT-PCR, the gut microbiome, and individual host determinants. Methods: A shotgun metagenomic analysis was conducted on fecal samples from 28 individuals affected by COVID-19. Patients were divided into two groups: those who had cleared the virus within 30 days (designated as the control group) (n = 15), and those who remained PCR-positive beyond 30 days (called the PCR+ group) (n = 13). We also investigated the correlation between prolonged viral clearance and several additional factors, including clinical parameters, immune responses, microbial metabolites, and dietary habits. Results: The composition and functionality of the microbiome varied based on the duration of positivity as determined by PCR. Compared to the control group, the persistent PCR+ group exhibited elevated pathogen levels and augmented diversity in functional gene families (p-value < 0.05). A multi-omics analysis integrating metagenomics, metabolites, and metadata also revealed the specific contribution of certain blood markers in this group, including basophils, IgM, IgG (both general and specific for SARS-CoV-2), and markers of liver damage. Unhealthy diet was identified as a significant factor influencing the duration of PCR positivity. Conclusions: These findings indicate that the gut microbiome may play a role in delayed viral clearance and persistent positive RT-PCR results. Our study also contributes to the understanding of the role of host factors as mediators linking the gut microbiota and disease outcomes. Further large-scale studies must confirm these data; however, they suggest the relevance of monitoring microbiome changes in the early post-viral years to control SARS-CoV-2 and providing individual healthcare support. [ABSTRACT FROM AUTHOR]

In common bean (Phaseolus vulgaris L.), leaf photosynthesis is significantly reduced under drought conditions. Previous studies have shown that some drought-tolerant cultivars use the pod walls to compensate the decreased photosynthesis rate in leaves by acting as temporary reservoirs of carbohydrates to support seed filling. Here, we describe a comprehensive molecular characterization of sucrose synthase (SUS, EC 2.4.1.13) gene family through a genome-wide analysis and evaluated the effects of terminal drought on reproductive structures, specifically the pod walls. Seven PvSUS genes were located on six different chromosomes and had 8–16 intron–exon structures (8–16 exons). The PvSUS protein sequences revealed conserved catalytic domains, with molecular weights ranging from 90.5 kDa to 105.1 kDa and lengths from 799 to 929 amino acids. Phylogenetic analysis grouped these sequences into three main clusters with seven subgroups, indicating divergence from SUS sequences in other plant species. Using a docking sequence, we predicted three-dimensional (3-D) structures and evaluated the active sites. Bioinformatics analysis of promoter regions suggested that PvSUS genes may respond to light, hormone signaling, and stress stimuli. Greenhouse experiments were conducted using the cv. OTI, identified as having intermediate drought tolerance. Plants at the R8 growth stage were maintained with regular irrigation at 100% field capacity (FC) or with water restriction to maintain 50% of field capacity. Pods were harvested 5 days, 10 days, 15 days, and 20 days after anthesis. An increase in PvSUS activity under water restriction was associated with higher levels of fructose, while sucrose concentration also increased. qRT-PCR analysis revealed that PvSUS1 , PvSUS3 , and PvSUS4 were strongly expressed during seed development under water restriction. The fluorescent sucrose analog esculin indicated that transport across the plasma membrane might contribute to the increase in the pith cell diameter of pedicels. The results provide a systematic overview of the PvSUS gene family in P. vulgaris , offering a framework for further research and the potential functional application of PvSUS genes. [ABSTRACT FROM AUTHOR]

The ATP-dependent zinc metalloprotease (FtsH) protein gene family is essential for plant growth, development, and stress responses. Although FtsH genes have been identified in various plant species, the FtsH gene family in wheat (Triticum aestivum) remains unstudied. In this study, we identified 11 TaFtsH genes with uneven chromosomal distribution, significant variations in gene sequence length, and differing intron numbers among individual members. Additionally, these proteins exhibit similar physicochemical characteristics as well as secondary and tertiary structures. The FtsH genes can be classified into eight groups, each characterized by similar structures and conserved motifs. Intraspecific and interspecific comparisons further revealed extensive gene duplications within the TaFtsH gene family, indicating a closer relationship to maize. Analysis of cis-acting elements in the promoter regions of TaFtsH genes revealed developmental and stress-responsive elements in most of the genes. Expression pattern analysis showed that TaFtsH genes are expressed in all wheat tissues, though with varying patterns. TaFtsH genes displayed differential responses to CdCl2, ZnSO4, and MnSO4 stress treatments. Gene Ontology (GO) enrichment analysis indicated that TaFtsH genes are involved in protein hydrolysis. Barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) technology confirmed the function of TaFtsH-1, indicating that silencing TaFtsH-1 enhances common wheat's resistance to cadmium (Cd) toxicity. In summary, this study offers an in-depth understanding of the FtsH gene family in wheat, establishing a solid basis for comprehending its functions, genetic mechanisms, and improving wheat's tolerance to heavy metal contamination. [ABSTRACT FROM AUTHOR]

Alanine-rich, alpha-helical type I antifreeze proteins (AFPs) in fishes are thought to have arisen independently in the last 30 Ma on at least four occasions. This hypothesis has recently been proven for flounder and sculpin AFPs, which both originated by gene duplication and divergence followed by substantial gene copy number expansion. Here, we examined the origins of the cunner (wrasse) and snailfish (liparid) AFPs. The cunner AFP has arisen by a similar route from the duplication and divergence of a GIMAP gene. The coding region for this AFP stems from an alanine-rich region flanking the GTPase domain of GIMAPa. The AFP gene has remained in the GIMAP gene locus and has undergone amplification there along with the GIMAPa gene. The AFP gene originated after the cunner diverged from its common ancestor with the closely related spotty and ballan wrasses, which exhibit similar gene synteny but lack AFP genes. Snailfish AFPs have also recently evolved because they are confined to a single genus of this family. In these AFP-producing species, the AFP locus does not share any similarity to functional genes. Instead, it is replete with repetitive DNAs and transposons, several stretches of which could encode alanine tracts with a dominant codon (GCC) that matches the bias observed in the AFP genes. All four known instances of type I AFPs occurring in fishes are independent evolutionary events that occurred soon after the onset of Northern Hemisphere Cenozoic glaciation events. Collectively, these results provide a remarkable example of convergent evolution to one AFP type. [ABSTRACT FROM AUTHOR]

The high-affinity nitrate transporter 2 (NRT2) protein plays an important role in nitrate uptake and transport in plants. In this study, the NRT2s gene family were systematically analyzed in alfalfa. We identified three MsNRT2 genes from the genomic database. They were named MsNRT2.1-2.3 based on their chromosomal location. The phylogenetic tree revealed that NRT2 proteins were categorized into two main subgroups, which were further confirmed by their gene structure and conserved motifs. Three MsNRT2 genes distributed on 2 chromosomes. Furthermore, we studied the expression patterns of MsNRT2 genes in six tissues based on RNA-sequencing data from the Short Read Archive (SRA) database of NCBI, and the results showed that MsNRT2 genes were widely expressed in six tissues. After leaves and roots were treated with drought, salt, abscisic acid (ABA) and salicylic acid (SA) for 0–48 h, and we used quantitative RT-PCR to analyze the expression levels of MsNRT2 genes and the results showed that most of the MsNRT2 genes responded to these stresses. However, there are specific genes that play a role under specific treatment conditions. This result provides a basis for further research on the target genes. In summary, MsNRT2s play an irreplaceable role in the growth, development and stress response of alfalfa, and this study provides valuable information and theoretical basis for future research on MsNRT2 function. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis Complex (MTBC), the etiological agent of tuberculosis (TB), demonstrates considerable genotypic diversity with distinct geographic distributions and variable virulence profiles. The pe-ppe gene family is especially noteworthy for its extensive variability and roles in host immune response modulation and virulence enhancement. We sequenced an Mtb genotype L2.1 isolate from Chiangrai, Northern Thailand, using second and third-generation sequencing technologies. Comparative genomic analysis with two additional L2.1 isolates and two L2.2.AA3 (Asia Ancestral 3 Beijing) isolates revealed significant pe-ppe gene variations. Notably, all L2.1 isolates harbored three copies of pe_pgrs3-pe_pgrs4-like genes (pe_pgrs3*, pe_pgrs4*, and pe_pgrs4), different from L2.2.AA3 and H37Rv strains. Additionally, ppe53 was duplicated in all but H37Rv, and ppe50 was deleted in L2.1 isolates, contrasting with an extended ppe50 in an L2.2 isolate (Mtb 18b), which contains an additional SVP motif. Complete deletion of ppe66 and loss of wag22 were observed in L2.1 isolates. These findings highlight the high structural variability of the pe-ppe gene family, emphasizing its complex roles in Mtb-host immune interactions. This genetic complexity offers potentially critical insights into mycobacterial pathogenesis, with significant implications for vaccine development and diagnostics. [ABSTRACT FROM AUTHOR]

The bagrada bug, Bagrada hilaris (Burmeister), is an emerging agricultural pest in the Americas, threatening agricultural production in the southwestern United States, Mexico and Chile, as well as in the Old World (including Africa, South Asia and, more recently, Mediterranean areas of Europe). Substantive transcriptomic sequence resources for this damaging species would be beneficial towards understanding its capacity for developing insecticide resistance, identifying viruses that may be present throughout its population and identifying genes differentially expressed across life stages that could be exploited for biomolecular pesticide formulations. This study establishes B. hilaris transcriptomic resources for eggs, 2nd and 4th larval instars, as well as male and female adults. Three gene families involved in xenobiotic detoxification—glutathione S-transferases, carboxylesterases and cytochrome P450 monooxygenases—were phylogenetically characterized. These data were also qualitatively compared with previously published results for two closely related pentatomid species—the brown marmorated stink bug, Halyomorpha halys (Stål), and the harlequin bug, Murgantia histrionica (Hahn)—to elucidate shared enzymatic components of terpene-based sex pheromone biosynthetic pathways. Lastly, the sequence data were screened for potential RNAi- and virus-related content and for genes implicated in insect growth and development. [ABSTRACT FROM AUTHOR]

Butyric acid (BA) can potentially enhance the function of the intestinal barrier. However, the mechanisms by which BA protects the intestinal mucosal barrier remain to be elucidated. Given that the Ras homolog gene family, member A (RhoA)/Rho-associated kinase 2 (ROCK2)/Myosin light chain kinase (MLCK) signaling pathway is crucial for maintaining the permeability of the intestinal epithelium, we further investigated whether BA exerts a protective effect on epithelial barrier function by inhibiting this pathway in LPS-induced Caco2 cells. First, we aimed to identify the optimal treatment time and concentration for BA and Lipopolysaccharide (LPS) through a CCK-8 assay. We subsequently measured Trans-epithelial electrical resistance (TEER), FITC-Dextran 4 kDa (FD-4) flux, and the mRNA expression of ZO-1, Occludin, RhoA, ROCK2, and MLCK, along their protein expression levels, and average fluorescence intensity following immunofluorescence staining. We then applied the ROCK2 inhibitor Y-27632 and reevaluated the TEER, FD-4 flux, and mRNA, and protein expression of ZO-1, Occludin, RhoA, ROCK2, and MLCK, as well as their distribution in Caco2 cells. The optimal treatment conditions were determined to be 0.2 mmol/L BA and 5 μg/mL LPS for 24 hours. Compared with LPS treatment alone, BA significantly mitigated the reduction in the TEER, decreased FD-4 flux permeability, increased the mRNA expression of ZO-1 and Occludin, and normalized the distribution of ZO-1 and Occludin in Caco2 cells. Furthermore, BA inhibited the expression of RhoA, ROCK2, and MLCK, and normalized their localization within Caco2 cells. Following treatment with Y-27632, the epithelial barrier function, along with the mRNA and protein expression and distribution of ZO-1 and Occludin were further normalized upon inhibition of the pathway. These findings contribute to a deeper understanding of the potential mechanisms through which BA attenuates LPS-induced impairment of the intestinal epithelial barrier. [ABSTRACT FROM AUTHOR]

ABSTRACT Hereditary spastic paraplegias (HSP) are a diverse group of neurodegenerative diseases characterized by lower limb spasticity and weakness. To date, over 80 genes have been associated with HSP, but many families remain without a molecular diagnosis.In this study, linkage analysis and whole‐exome sequencing (WES) were performed to identify the causal gene in a HSP family with autosomal recessive inheritance. Multipoint linkage analysis revealed a maximum significant multipoint LOD score of 4.6 on chromosome 4. WES analysis focused on this region led to the identification of a homozygous missense variant in AIMP1 (c.223G>A). Minigene assays showed that the presumed missense variant in AIMP1 caused loss of the exon 3 donor splice site. Ultimately, this led to the use of an alternative splice site within the intron and the insertion of a premature stop codon.The identification of a novel AIMP1 causal variant contributes to the growing list of HSP genes. Furthermore, it shows that, considering also previous reported cases, disruption of AIMP1 causes a spectrum of disorders ranging from intellectual disability to more complex neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

Introduction: The basic helix-loop-helix (bHLH) transcription factor family is one of the largest gene families in plants, extensively involved in plant growth, organ development, and stress responses. However, limited studies of this family are available in sea buckthorn (Hippophae rhamnoides). Methods: In this study, we identified 144 bHLH genes in H. rhamnoides (HrbHLH) through a genome-wide search method, then explored their DNA and protein sequences and physicochemical properties. Results and discussion: According to the sequence similarities, we classified them into 15 groups with specific motif structures. To explore their expressions, we performed gene expression profiling using RNA-Seq and identified 122 HrbHLH mRNAs were highly expressed, while the remaining 22 HrbHLH genes were expressed at very low levels in all 21 samples. Among these HrbHLH genes, HrbHLH47, HrbHLH74, HrbHLH90, HrbHLH131 showed the highest expression level in the root nodule, root, leaf, stem and fruit tissues. Furthermore, eleven HrbHLH genes displayed increased expressions during the fruit development process of sea buckthorn. Finally, we validated the expression patterns of HrbHLH genes using reverse transcription quantitative real-time PCR (QPCR). This comprehensive analysis provides a useful esource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs. [ABSTRACT FROM AUTHOR]

Roses (Rosa chinensis) are among the most cherished ornamental plants globally, yet they are highly susceptible to infections by Botrytis cinerea , the causative agent of gray mold disease. Here we inoculated the resistant rose variety 'Yellow Leisure Liness' with B. cinerea to investigate its resistance mechanisms against gray mold disease. Through transcriptome sequencing, we identified 578 differentially expressed genes (DEGs) that were significantly upregulated at 24, 48, and 72 hours post-inoculation, with these genes significantly enriched for three defense response-related GO terms. Further domain analysis of the genes in these GO terms reveal that 21 DEGs contain the Bet v 1 family domain, belonging to the major latex protein (MLP) gene family, suggesting their potential key role in rose disease resistance. Furthermore, we systematically identified 46 RcMLP genes in roses and phylogenetically categorized them into two distinct subfamilies: group I and II. Genomic duplication analysis indicates that tandem duplication is the main driver for the expansion of the RcMLP family, and these genes have undergone by purifying selection. Additionally, detailed analyses of gene structure, motif composition, and promoter regions reveal that RcMLP genes contain numerous stress-responsive elements, with 32 RcMLP genes harboring fungal elicitor/wound-responsive elements. The constructed potential transcription factor regulatory network showed significant enrichment of the ERF transcription factor family in the regulation of RcMLP genes. Gene expression analysis reveal that DEGs are mainly distributed in subfamily II, where four highly expressed genes (RcMLP13 , RcMLP28 , RcMLP14 , and RcMLP27) are identified in a small branch, with their fold change exceeding ten folds and verified by qRT-PCR. In summary, our research results underscore the potential importance of the RcMLP gene family in response to B. cinerea infection and provide comprehensive basis for further function exploration of the MLP gene family in rose resistance to fungal infections. [ABSTRACT FROM AUTHOR]

Global adaptation occurs when all populations of a species undergo selection toward a common optimum. This can occur by a hard selective sweep with the emergence of a new globally advantageous allele that spreads throughout a species' natural range until reaching fixation. This evolutionary process leaves a temporary trace in the region affected, which is detectable using population genomic methods. While selective sweeps have been identified in many species, there have been few comparative and systematic studies of the genes involved in global adaptation. Building upon recent findings showing repeated genetic basis of local adaptation across independent populations and species, we asked whether certain genes play a more significant role in driving global adaptation across plant species. To address this question, we scanned the genomes of 17 plant species to identify signals of repeated global selective sweeps. Despite the substantial evolutionary distance between the species analyzed, we identified several gene families with strong evidence of repeated positive selection. These gene families tend to be enriched for reduced pleiotropy, consistent with predictions from Fisher's evolutionary model and the cost of complexity hypothesis. We also found that genes with repeated sweeps exhibit elevated levels of gene duplication. Our findings contrast with recent observations of increased pleiotropy in genes driving local adaptation, consistent with predictions based on the theory of migration-selection balance. [ABSTRACT FROM AUTHOR]

Background: A diverse range of pollutants, including heavy metals, agrochemicals, pharmaceutical residues, illicit drugs, personal care products, and other anthropogenic contaminants, pose a significant threat to aquatic ecosystems. The Winam Gulf of Lake Victoria, heavily impacted by surrounding human activities, faces potential contamination from these pollutants. However, studies exploring the presence of antibiotic resistance genes (ARGs) in the lake remain limited. In the current study, a shotgun metagenomics approach was employed to identify ARGs and related pathways. Genomic DNA was extracted from water and sediment samples and sequenced using the high‐throughput Illumina NovaSeq platform. Additionally, phenotypic antibiotic resistance was assessed using the disk diffusion method with commonly used antibiotics. Results: The analysis of metagenomes sequences from the Gulf ecosystem and Comprehensive Antibiotic Resistance Database (CARD) revealed worrying levels of ARGs in the lake. The study reported nine ARGs from the 37 high‐risk resistant gene families previously documented by the World Health Organization (WHO). Proteobacteria had the highest relative abundance of antibiotic resistance (53%), Bacteriodes (4%), Verrucomicrobia (2%), Planctomycetes Chloroflexi, Firmicutes (2%), and other unclassified bacteria (39%). Genes that target protection, replacement, change, and antibiotic‐resistant efflux were listed in order of dominance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed antibiotic resistance to beta‐lactamase and vancomycin. Phenotypic resistance to vancomycin, tetracycline, sulfamethoxazole, erythromycin, trimethoprim, tetracycline, and penicillin was reported through the zone of inhibition. Conclusions: This study highlights that the Winam Gulf of Lake Victoria in Kenya harbors a diverse array of antibiotic‐resistant genes, including those conferring multidrug resistance. These findings suggest that the Gulf could be serving as a reservoir for more antibiotic‐resistant genes, posing potential risks to both human health and aquatic biodiversity. The insights gained from this research can guide policy development for managing antibiotic resistance in Kenya. [ABSTRACT FROM AUTHOR]

Background: Calcium-dependent protein kinases (CDPKs), play multiple roles in plant development, growth and response to bio- or abiotic stresses. Calmodulin-like domains typically contain four EF-hand motifs for Ca²⁺ binding. The CDPK gene family can be divided into four subgroups in Arabidopsis, and it has been identified in many plants, such as rice, tomato, but has not been investigated in alfalfa (Medicago sativa subsp. sativa) yet. Results: In our study, 38 non-redundant MsCDPK genes were identified from the "XinJiangDaYe" alfalfa genome. They can be divided into four subgroups which is the same as in Arabidopsis and Medicago truncatula, and there were 15, 12,10 and 1 in CDPK I, II, III and IV, respectively. RNA-seq analysis revealed tissue-specificity of 38 MsCDPK genes. After researching the transcriptome data, we found these 38 MsCDPK members responsive to drought, salt, and cold stress treatments. Further analysis showed that the expression of almost all the MsCDPKs is regulated by abiotic stresses. In addition, we chose MsCDPK03, MsCDPK26, MsCDPK31 and MsCDPK36 for RT-qPCR validation which was from CDPK I-IV subgroups respectively. The result showed that the expression of these four genes was significantly induced by drought, salt and cold treatments. The subcellular location experiment showed that these four proteins were all located in nucleus. Conclusion: In our study, we identified 38 distinct MsCDPK genes within the alfalfa genome, which were classified into four groups. We conducted a comprehensive analysis of various gene features, including physicochemical properties, phylogenetic relationships, exon-intron structures, conserved motifs, chromosomal locations, gene duplication events, cis-regulatory elements, 3D structures, and tissue-specific expression patterns, as well as responses to drought, salt, and cold stresses. These results also provide a solid foundation for further investigations into the functions of MsCDPKs aimed at improving drought tolerance in autotetraploid cultivated alfalfa through genetic engineering. [ABSTRACT FROM AUTHOR]

Background: The COBRA-like (COBL) gene family is a crucial glycosylphosphatidylinositol (GPI)-anchored proteins that participate in various biological processes in plants by regulating the arrangement of cell wall microfibrils. While the functions of COBL genes have been analyzed in several plant species, their roles in cotton's response to abiotic stress remain unexplored. Results: This study identified and characterized the COBL gene family in Gossypium hirsutum, revealing a total of 39 COBL family members classified into five subgroups. Transcriptome analysis indicated that the transcription levels of several GhCOBL genes were upregulated following PEG treatment, with GhCOBL22 being significantly induced. Further silencing of the GhCOBL22 gene through virus-induced gene silencing (VIGS) technology demonstrated that this gene's silencing reduced cotton's drought stress tolerance. Under drought stress conditions, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) enzymes, along with proline (PRO) content, were lower in GhCOBL22-silenced plants compared to control plants, while the accumulation of malondialdehyde (MDA) was significantly higher. Moreover, silencing the GhCOBL22 gene also led to reductions in the levels of cellulose, hemicellulose, and lignin content in cotton leaves. Conclusion: A systematic survey of gene structure, motif composition, and evolutionary relationships of the COBL gene family was conducted in Gossypium hirsutum. Subsequent expression and functional studies indicated that GhCOBL22 plays a significant role in cotton's drought tolerance. These findings enhance our understanding of the biological functions of the COBL family and highlight the critical role of the GhCOBL22 gene in cotton's response to drought stress. [ABSTRACT FROM AUTHOR]

Background: The three-amino-acid-loop-extension (TALE) superfamily genes are broadly present in plants and play important roles in plant growth, development, and abiotic stress responses. So far, the TALE family in B.napus have not been systematically studied, especially their potential roles in response to abiotic stress. Results: In this study, we identified 74 TALE family genes distributed on 19 chromosomes in the B. napus genome using bioinformatics methods. Phylogenetic analysis divided the BnTALE superfamily into two subfamilies, the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Moreover, the KNOX subfamily could be further categorized into three clades (KNOX Class I, KNOX Class II, and KNOX Class III). BnTALE members in the same subclass or branch of the phylogenetic tree generally showed similar gene structures and conserved domain compositions, which may indicate that they have similar biological functions. The BnTALE promoter regions contained many hormone-related elements and stress response elements. Duplication events identification analysis showed that WGD/segmental duplications were the main drivers of amplification during the evolution of TALE genes, and most of the duplicated BnTALE genes underwent purifying selection pressures during evolution. Potential protein interaction network analysis showed that a total of 12,615 proteins might interact with TALE proteins in B. napus. RNA-seq and qRT-PCR analyses showed that the expression of BnTALE was tissue-differentiated and can be induced by abiotic stresses such as dehydration, cold, and NaCl stress. In addition, weighted gene co-expression network analysis (WGCNA) identified four co-expression modules containing the most BnTALE genes, which would be notably related to dehydration and cold stresses. Conclusions: Our study paves the way for future gene functional research of BnTALE and facilitate their applications in the genetic improvement of B. napus in response to abiotic stresses. [ABSTRACT FROM AUTHOR]

Pheromones play a pivotal role in chemical communication across various taxa, with protein-based pheromones being particularly significant in amphibian courtship and reproduction. In this study, we investigate the Emei music frog (Nidirana daunchina), which utilizes both acoustic and chemical signals for communication. Base on a de novo assembled genome of a male Emei music frog, we identify substantial expansion in four pheromone-related gene families associated with chemical communication. Notably, six members of the two-domain three-finger protein (2D-TFP) family, belonging to the sodefrin precursor-like factor (SPF) pheromone system, exhibited high and specific expression in the male post-axillary glands during the breeding season. Structural and evolutionary analyses confirm the presence of the SPF system across amphibians, classifiable into four distinct classes (two within urodeles and two within anurans). We propose a complete regulatory network governing SPF secretion via the hypothalamic-pituitary-testicular-breeding gland axis, and suggest testosterone synthesis as the pivotal pathway. Behavioral experiments further reveal a previously unknown female-attractant role of SPF in anurans. Overall, these findings not only highlight the underestimated diversity and function of pheromones in anurans, but also provide important insights into the evolution of protein-based pheromones in vertebrates. Multi-omics techniques facilitate a comprehensive understanding of the function and regulatory mechanisms of SPF pheromones in Anurans, shedding lights on the protein pheromones evolutionary and multi-modal communication in vertebrates. [ABSTRACT FROM AUTHOR]

Background: Chitinases (CHIs) are glycosidases that degrade chitin, playing critical roles in plant responses to both abiotic and biotic stress. Despite their importance, the CHI family's systematic analysis and evolutionary pattern in F. tataricum (Tartary buckwheat) yet to be explored. Results: This study analyzed their phylogenetic relationships, conserved motifs, gene structures, syntenic relationships, physiological functions, and biochemical properties. This research identified 26 FtCHIs and examined their expression patterns under different salt stress conditions and across various tissues. Differential expression analysis revealed a significant upregulation of multiple FtCHIs in response to salt stress, which RT-qPCR further validated. Additionally, subcellular localization experiments demonstrated that Ft_chitinaseIV-2 is localized in vacuoles. The results of transient·transformation showed that·overexpression of Ft_chitinaseIV-2 could·enhance the salt tolerance of plants. Conclusions: The findings provide new insights into the role of CHIs in stress tolerance and lay the groundwork for future research on the functional characterization of FtCHIs. Understanding the molecular mechanisms of CHI-mediated stress responses could contribute to developing stress-resistant crops. [ABSTRACT FROM AUTHOR]

Hexokinases (HXK) not only facilitate carbohydrate metabolism but also play important roles in sugar sensing in higher plants. HXK gene families have been extensively discussed in many plant species; however, comprehensive information regarding HXKs in sorghum remains unclear. To address this gap, we identified 7 putative sorghum HXKs (SbHXK1 to SbHXK7), and the features of their conserved domains, gene structure, evolutionary tree, and cis-acting elements were systematically characterized to reveal the evolutionary conservation between different plant species. Based on expression profiling, we found that different expression patterns of SbHXKs were associated with different physiological processes, including abiotic stresses. Further qRT-PCR verification under salt and sucrose treatment confirmed that SbHXK2, SbHXK4, and SbHXK5 may play very important roles under high osmotic pressure. Notably, SbHXKs are predominantly localized in the cytoplasm, in contrast to some rice and Arabidopsis HXKs, which are localized in chloroplasts or mitochondria, suggesting divergent roles for SbHXKs. In summary, our study provides a theoretical foundation for understanding the HXK gene family and offers fundamental insights of SbHXKs in sorghum. [ABSTRACT FROM AUTHOR]

Background: Quinoa, as a new food crop, has attracted extensive attention at home and abroad. However, the natural disaster of spike germination seriously threatens the quality and yield of quinoa. Currently, there are limited reports on the molecular mechanisms associated with spike germination in quinoa. Results: In this study, we utilized transcriptome sequencing technology and successfully obtained 154.51 Gb of high-quality data with a comparison efficiency of more than 88%, which fully demonstrates the extremely high reliability of the sequencing results and lays a solid foundation for subsequent analysis. Using these data, we constructed a weighted gene co-expression network (WGCNA) related to starch, sucrose, α-amylase, and phenolic acid metabolites, and screened six co-expression modules closely related to spike germination traits. Two of the modules associated with physiological indicators were analyzed in depth, and nine core genes were finally predicted. Further functional annotation revealed four key transcription factors involved in the regulation of dormancy and germination processes: gene LOC110698065, gene LOC110696037, gene LOC110736224, and gene LOC110705759, belonging to the bHLH, NF-YA, MYB, and FAR1 gene families, respectively. Conclusions: These results provide clues to identify the core genes involved in quinoa spike germination. This will ultimately provide a theoretical basis for breeding new quinoa varieties with resistance. [ABSTRACT FROM AUTHOR]

NF-Y is a class of heterotrimeric transcription factor composed of three subunits; NF-YA, NF-YB, and NF-YC. This complex binds to the CCAAT box found in eukaryotic promoters and is involved in the plant development and proliferation at various stages. Although many studies were conducted on NF-Y gene family in various species, but no study has been reported yet in switchgrass (Panicum virgatum L.). In this study, 47 PvNF-Y genes (17 PvNF-YA, 18 PvNF-YB, and 12 PvNF-YC) have been identified and named according to their subfamily. Chromosome location analysis revealed that all 47 PvNF-Y genes are randomly distributed across nine chromosomes. Moreover, multiple sequence alignment showed the DNA-binding domain and NF-YA/NFYB interacting domains flanking with non-conserved domains. In addition, prediction of functional similarities among PvNF-Ys genes phylogenetic tree was constructed corresponding to Arabidopsis. The gene structure, conserved domains and motifs analysis of PvNF-Ys genes demonstrated their specificity and functional conservation. Cis-regulatory elements analysis identified numerous key CREs that are significantly associated with light, hormone, stress and plant development responses. Expression profiling indicated higher expression levels of many PvNF-YA genes during drought and heat stress. Additionally, qRT-PCR analysis showed that some PvNF-Ys genes have high expression level in root. In conclusion, the findings of this study could provide a foundation for further cloning and functional analysis of NF-Y genes in switchgrass. [ABSTRACT FROM AUTHOR]

UDP-glycosyltransferases (UGTs) widely exist in plants and play essential roles in catalyzing the glycosylation reaction associated with metabolic processes. UGT gene family has been identified in many species to date. However, the comprehensive identification and systematic analysis have not been documented yet in the latest potato genome. In this study, a total of 295 UGT members (StUGT) were identified and found to be unevenly distributed on twelve chromosomes of potato. All StUGT genes were classified into 17 groups (A-P, R) and the UGT genes within the same groups have similar structural characterization. Tandem duplication was the major driving force for the StUGT gene expansion. The prediction of cis-acting elements showed that the development process, light, phytohormone, and abiotic stress-responsive elements generally existed in StUGT promoter regions. Analysis of spatial and temporal expression patterns demonstrated that StUGT genes were widely and differentially expressed in various tissues. Additionally, to investigate the salt stress-responsive genes, we analyzed the expression profiles of the StUGT genes under salt treatment. A total of 50 and 20 StUGT genes were continuously up- and down-regulated, respectively, implicating that these genes were involved in the regulation of salt tolerance. Among them, the StUGT178 gene, which was significantly induced by salt stress and contains salt-responsive element, was considered as one of the most relevant candidate genes. Transient transformation of the StUGT178 promoter in tobacco revealed that the transcriptional activation activity of the StUGT178 gene was strengthened under salt treatment. Furthermore, the heterologous expressions of the promoter and coding protein of the StUGT178 gene in Arabidopsis further demonstrated that the StUGT178 gene significantly responds to salt treatment, and enhanced salinity tolerance by regulating antioxidant enzyme activity and H2O2 accumulation. These results provide comprehensive information for a better understanding of the StUGT genes and offer a foundation for uncovering their function associated with salt stress in potato. [ABSTRACT FROM AUTHOR]

Background: O-Methyltransferase (OMTs) is a class of conserved multifunctional enzymes that play important roles in plant developmental regulation, hormone signaling, secondary metabolite synthesis and abiotic stress response. The GiOMT gene family has been identified and analyzed in species such as citrus, alfalfa, Populus and grape, but has not been reported in Glycyrrhiza inflata Bat. Results: In this study, we systematically identified and analyzed the GiOMT gene family of G. inflata by bioinformatics, and analyzed their physicochemical properties, conserved motifs, conserved structural domains, gene structures, phylogenetic relationships, chromosomal localization and fragment duplications, and the expression patterns of GiOMT genes in combination with transcriptomic data and qRT-PCR. The results showed that a total of 41 GiOMTs were identified in G. inflata, which were named GiOMT1 ~ GiOMT41 based on their chromosomal locations. Protein characterization showed that 29 GiOMT proteins were hydrophilic and 12 GiOMT proteins were hydrophobic. Subcellular predicted localization revealed that most GiOMT proteins localized in the cytoplasm and chloroplasts. Phylogenetic relationships showed that the OMT genes of three species, G. inflata, Arabidopsis and alfalfa, were distributed in three taxa, while the GiOMT genes were distributed in taxa I and II. Promoters of GiOMT genes contained light responsive element and many hormone responsive elements. The expression levels of GiOMT genes under UV-B stress were varied, indicating that GiOMT gene was in response to abiotic stresses in G. inflata. Conclusion: In this study, we investigated the genome-wide identification, structure, evolution and expression analysis of the GiOMT gene in G. inflata. The basal sequence of GiOMT genes was highly conserved throughout the evolutionary history of G. inflata. Most of the GiOMT genes were highly expressed in roots and were involved in the response to UV-B stress. The GiOMT genes may lead to the accumulation of flavonoids and enhancement of G. inflata quality and drug activity in G. inflata under UV-B radiation. [ABSTRACT FROM AUTHOR]

Background: Sugar transporters (STs) play a critical role in the transportation of sugar, participating in plant growth and development, stress/defense responses, and signal transduction processes. Dendrobium catenatum (also known as Dendrobium officinale, hereinafter referred to as D. catenatum) is an important traditional Chinese medicinal herb with remarkable medicinal properties and possessing high economic value. Polysaccharides are the primary active components in D. catenatum, exhibiting diverse pharmacological activities. Sugar transporters function as material supplier and may play the essential roles in the polysaccharide biosynthesis, as well as the key reulators in the signaling and responses to abiotic stresses in Dendrobium plants. However, a comprehensive analysis of sugar transporters in D. catenatum remains elusive, thereby hindering our understanding of sugar partitioning within this species. Results: In this work, the members belonging to MST, SUT, and SWEET gene families were identified in four Dendrobium plants. A comprehensive study of sugar transporters was conducted in D. catenatum, including phylogenetic relationship, structural arrangement, regulatory networks, expression profiles, and potential functions analysis. Seven sugar transporters were found to be involved in the process of polysaccharide biosynthesis in D. catenatum. Red-blue light is an effective way to enhance the accumulation of polysaccharides, and exerts an influence on the expression of polysaccharide biosynthesis related genes. Conclusions: This study provide insight into the evolution and functional annotation of sugar transporters in Dendrobium, and establishing a foundation for future functional research of sugar transporters involved in polysaccharide biosynthesis and stress response. [ABSTRACT FROM AUTHOR]

Background: Gossypium raimondii serves as a widely used genomic model cotton species. Its genetic influence to enhance fiber quality and ability to adapt to challenging environments both contribute to increasing cotton production. The formins are a large protein family that predominately consists of FH1 and FH2 domains. The presence of the formin domains highly regulates the actin and microtubule filament in the cytoskeleton dynamics confronting various abiotic stresses such as drought, salinity, and cold temperatures. Results: In this study, 26 formin genes were analyzed and characterized in G. raimondii and mostly were found in the nucleus and chloroplast. According to the evolutionary phylogenetic relationship, GrFH were dispersed and classified into seven different groups and shared an ancestry relationship with MtFH. The GrFH gene structure prediction revealed diverse intron-exon arrangements between groups. The FH2 conserved domain was found in all the GrFH distributed on 12 different chromosomes. Moreover, 11 pairs of GrFH transpired segmental duplication. Among them, GrFH4-GrFH7 evolved 35 million years ago (MYA) according to the evolutionary divergence time. Besides, 57 cis-acting regulatory elements (CAREs) motifs were found to play a potential role in plant growth, development, and in response to various abiotic stresses, including cold stress. The GrFH genes mostly exhibited biological processes resulting in the regulation of actin polymerization. The ERF, GATA, MYB, and LBD, major transcription factors (TFs) families in GrFH, regulated expression in abiotic stress specifically salt as well as defense against certain pathogens. The microRNA of GrFH unveiled the regulatory mechanism to regulate their gene expression in abiotic stresses such as salt and cold. One of the most economic aspects of cotton (G.raimondii) is the production of lint due to its use in manufacturing fabrics and other industrial applications. The expression profiles of GrFH in different tissues particularly during the conversion from ovule to fiber (lint), and the increased levels (up-regulation) of GrFH4, GrFH6, GrFH12, GrFH14, and GrFH26 under cold conditions, along with GrFH19 and GrFH26 in response to salt stress, indicated their potential involvement in combating these environmental challenges. Moreover, these stress-tolerant GrFH linked to cytoskeleton dynamics are essential in producing high-quality lint. Conclusions: The findings from this study can contribute to elucidating the evolutionary and functional characterizations of formin genes and deciphering their potential role in abiotic stress such as cold and salt as well as in the future implications in wet lab. [ABSTRACT FROM AUTHOR]

The clinical presentation of T-cell large granular lymphocytic leukemia (T-LGLL) is extremely variable: 30% of patients have neutropenia with no associated symptoms, others present with bacterial infections and sepsis may occur. Tools to predict patient outcome are lacking. Stemming from preliminary results obtained by single cell-RNAseq we investigated by qPCR HSP and IFIT gene families in 27 LGLL patients (23T-LGLL and 4 NK-LGLL), including 11 with neutropenia and/or thrombocytopenia and 16 asymptomatic for the disease. HSP90AA1 and HSPA1B, among HSP family and CD279 exhibited a significantly higher expression in CD3 + CD57 + sorted cells of symptomatic LGLL patients compared to asymptomatic patients and healthy controls. Also, monocytes derived from symptomatic LGLL patients expressed high levels of CCL3, CCL4 and CCL5 mRNA and of IL-1β, IL-6, TNF, and PD-L1 mRNA, thus confirming a pro-inflammatory cytokine profile reminiscent of a non-classical phenotype. Overall, these data provide a rationale for considering HSP and CD279 genes as potential biomarkers for distinguishing symptomatic LGLL patients from asymptomatic ones, emphasizing the importance of further research to explore their implications for targeted therapy development. [ABSTRACT FROM AUTHOR]

ABSTRACT During the early stages of local adaptation and speciation, genetic differences tend to accumulate at certain regions of the genome leading to the formation of genomic islands of divergence (GIDs). This pattern may be due to selection and/or difference in the rate of recombination. Here, we investigate the possible causes of GIDs in Drosophila yakuba mayottensis, and reconfirm using field collection its association with toxic noni (Morinda citrifolia) fruits on the Mayotte island. Population genomics revealed lack of genetic structure on the island and identified 23 GIDs distinguishing D. y. mayottensis from generalist mainland populations of D. y. yakuba. The GIDs were enriched with gene families involved in the metabolism of lipids, sugars, peptides and xenobiotics, suggesting a role in host shift. We assembled a new genome for D. y. mayottensis and identified five novel chromosomal inversions. Twenty one GIDs (~99% of outlier windows) fell in low recombining regions or subspecies‐specific inversions. However, only two GIDs were in collinear, normally recombining regions suggesting a signal of hard selective sweeps. Unlike D. y. mayottensis, D. sechellia, the only other noni‐specialist, is known to be homosequential with its generalist relatives. Thus, whereas structural variation may disproportionally shape GIDs in some species, striking parallel adaptations can occur between species despite distinct genomic architectures. [ABSTRACT FROM AUTHOR]

ABSTRACT The largemouth bronze gudgeon (Coreius guichenoti), an endemic fish species, is distributed in the upper Yangtze River drainage. Due to anthropogenetic factors such as water pollution, overfishing, and dam construction, the wild populations of C. guichenoti have dramatically declined in recent decades. In this study, we generated a reference chromosomal‐level genome assembly of C. guichenoti on the basis of PacBio HiFi sequencing and Hi‐C scaffolding technologies. The final genome assembly was 1.10 Gb in length (contig N50: 28.64 Mb; scaffold N50: 42.39 Mb) with 25 chromosomes. The completeness score of the C. guichenoti genome was 96.4%, and high synteny was detected compared with Danio rerio and Ictalurus punctatus genomes. A total of 24 325 PCGs were annotated for the C. guichenoti genome. Comparative genomics analysis identified 986 expanded gene families in C. guichenoti, which were significantly enriched in GO items associated with the development and interaction of sperm and egg as well as immunity. Furthermore, positively selected genes (PSGs) detected in C. guichenoti were mainly associated with DNA repair, ATP binding, mitochondrion, and lipid homeostasis. Based on the reference genome and resequencing data, the polymorphic microsatellite (SSR) loci were comprehensively analyzed for C. guichenoti, and the top 15 tetra‐nucleotide SSR loci were selected for the construction of the genetic maker system after validation through PCR and genotyping. All of these 15 tetra‐nucleotide SSR loci without Hardy–Weinberg equilibrium (HWE) deviation showed high polymorphism, good amplification stability, and selective neutrality. The PID (sibs) curves revealed that the subset of four tetra‐nucleotide SSR loci (cgui1, cgui5, cgui3, cgui13) was sufficient for accurate identification of C. guichenoti individuals (PIDsib < 0.01). These 15 tetra‐nucleotide SSR loci could also serve as genetic markers in subsequent parentage identification and genetic diversity analysis. The chromosome‐level genome assembly and findings laid solid foundations for molecular breeding, genomic research, and biological conservation of C. guichenoti. [ABSTRACT FROM AUTHOR]