Gene Duplication Research Articles

Clinical and genetic analysis of a case with 2p23.2p22.1 duplication

To report on the phenotype of an adult patient with 2p23.2p22.1 duplication and explore its genotype-phenotype correlation. A pregnant woman who had presented at the Affiliated Drum Tower Hospital of Nanjing University Medical School on January 12, 2024 for a high risk signaled by NIPT was selected as the study subject. Amniotic fluid and peripheral blood samples were collected and subjected to chromosomal microarray analysis (CMA). The phenotype of the patient was observed, the medical history was taken, combined with the result of CMA assay, relevant database was searched for similar cases reported in the literature, and the correlation between genotype and phenotype was analyzed. The CMA result of the patient was arr[GRCh38]2p23.2p22.1(27961669_39280633)×3, which indicated a 11.31 Mb duplication. The woman was found to have short stature, learning disability, visual deficit, sleep disorder and other disorders. The duplication of PPP1CB and SOS1 genes within the 2p23.2p22.1 region can result in Noonan syndrome-like clinical manifestations such as short stature and reduced visual acuity. The duplication of the PPP1CB gene may be associated with the abnormal visual phenotype.

Genome-wide identification, gene cloning, subcellular location and expression analysis of the OPR gene family under salt stress in sweetpotato

BackgroundThe 12-oxo-phytodienoic acid reductase (OPR) enzyme is crucial for the synthesis of jasmonates (JAs), and is involved in the plant stress response. However, the OPR gene family in sweetpotato, an important horticultural crop, remains unidentified.ResultsIn this study, we employed bioinformatics techniques to identify nine IbOPR genes. Phylogenetic analysis revealed that these genes could be divided into Group I and Group II. Synteny analysis indicated that IbOPR evolution was driven by tandem duplication, whole-genome duplication (WGD), and segmental duplication events. The promoter sequences of IbOPRs were found to be associated with stress and hormonal responses. Additionally, we successfully cloned four IbOPRs from "Haida HD7791" and "Haida HD7798" using homologous cloning technology. These sequences were 1203 bp, 1200 bp, 1134 bp, and 1137 bp in length and encoded 400, 399, 377, and 378 amino acids, respectively. The protein sequence similarity between the salt-tolerant variety "Haida HD7791" and the salt-sensitive variety "Haida HD7798" was determined to be 96.75% for IbOPR2, 99.75% for IbOPR3, 92.06% for IbOPR6, and 98.68% for IbOPR7. Phylogenetic analysis categorized IbOPR2 and IbOPR3 proteins into Group II, while IbOPR6 and IbOPR7 proteins belonged to Group I. Subcellular localization experiments showed IbOPR2 protein present in the peroxisome, while IbOPR3, IbOPR6, and IbOPR7 proteins were found in the cytoplasm and nucleus. Salt stress induction experiments demonstrated that IbOPR2, IbOPR3, and IbOPR7 were significantly upregulated only in 'Haida HD7791' after 6 h. In contrast, IbOPR6 was induced in 'Haida HD7798' at 6 h but inhibited in 'Haida HD7791' at later time points (12, 24, 48, and 72 h), highlighting functional differences in salt stress responses.ConclusionsOur findings suggest that IbOPR2 may play a crucial role in sweetpotato's response to salt stress by participating in JAs synthesis. These results provide a foundation for future functional analyses of OPR genes in sweetpotato.

Experimental Evolution of Poxviruses.

Experimental evolution is the process of exposing virus populations to defined selective pressures in a laboratory setting to identify adaptive changes. Coupled with deep sequencing, this experimental approach allows for nucleotide-level resolution of poxvirus adaptive strategies over time. Here, we present a general method of poxvirus experimental evolution, Illumina-based deep sequencing, and bioinformatic analyses to identify structural changes (e.g., gene duplication) as well as local adaptive changes (e.g., small indels and single nucleotide polymorphisms).

Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises.

Many cellular processes and organismal behaviours are time-dependent, and asynchrony of these phenomena can facilitate speciation through reinforcement mechanisms. The Mojave and Sonoran desert tortoises (Gopherus agassizii and G. morafkai respectively) reside in adjoining deserts with distinct seasonal rainfall patterns and they exhibit asynchronous winter brumation and reproductive behaviours. We used whole genome sequencing of 21 individuals from the two tortoise species and an outgroup to understand genes potentially underlying these characteristics. Genes within the most diverged 1% of the genome (FST ≥ 0.63) with putatively functional variation showed extensive divergence in regulatory elements, particularly promoter regions. Such genes related to UV nucleotide excision repair, mitonuclear and homeostasis functions. Genes mediating chronobiological (cell cycle, circadian and circannual) processes were also among the most highly diverged regions (e.g., XPA and ZFHX3). Putative promoter variants had significant enrichment of genes related to regulatory machinery (ARC-Mediator complex), suggesting that transcriptional cascades driven by regulatory divergence may underlie the behavioural differences between these species, leading to asynchrony-based prezygotic isolation. Further investigation revealed extensive expansion of respiratory and intestinal mucins (MUC5B and MUC5AC) within Gopherus, particularly G. morafkai. This expansion could be a xeric-adaptation to water retention and/or contribute to differential Mycoplasma agassizii infection rates between the two species, as mucins help clear inhaled dust and bacterial. Overall, results highlight the diverse array of genetic changes underlying divergence, adaptation and reinforcement during speciation.

Identification and expression analysis of phosphate transporter (PHT) genesin Brachypodium distachyon in response to phosphorus deficiency.

Phosphorus (P) is a macronutrient that plays a crucial role in critical plant functions. Phosphate transporters (PHTs) ensure the acquisition and translocation of Pi in the plant, thereby playing a key role in maintaining normal plant growth under Pi deficiency conditions. In Brachypodium distachyon, the grass model system, the function of individual PHT genes, remains largely unknown. Here, we identified the complete PHT gene family in B. distachyon, for the first time, and analyzed their expression profiles under Pi deficiency. Overall, 25 PHT genes in B. distachyon (BdPHTs) were identified, which were divided into four clades (PHT1-4). BdPHT genes were found to be unevenly distributed across the five chromosomes. Both segmental and tandem duplication events contributed to PHT gene expansion in B. distachyon which underwent a strong purifying selection. Moreover, exon-intron organization and motif composition were conserved within each PHT group consolidating the classification of the phylogenetic tree. Motif composition differs among the four PHT groups, indicating their functional divergence. Gene expression analysis using real-time quantitative PCR revealed that two BdPHT1 genes (BdPHT1.9 and BdPHT1.10) were upregulated in leaves, and seven (BdPHT1.9, BdPHT1.8, BdPHT1.7, BdPHT1.11, BdPHT1.12, BdPHT1.5, and BdPHT1.13) in roots under P deficiency suggesting their involvement in P uptake and translocation. Therefore, these results lay the foundation for future functional analyses in B. distachyon to improve P deficiency tolerance in B. distachyon and other cereals.

Divergence in MiRNA targeting of AchAco and its role in citrate accumulation in kiwifruit

BackgroundMicroRNA (miRNA) is a crucial post-transcriptional regulatory factor in plant growth and development. Duplicated genes often exhibit functional divergence due to competition for the identical miRNA binding sites. Kiwifruit (Actinidia spp.) is an economically significant horticultural crop renowned for its distinctive flavor, which is largely attributable to elevated citrate levels during fruit development. However, the mechanisms through which miRNA-targeted modules evolve following duplication events and regulate citrate biosynthesis, thereby influencing the unique flavor profile of kiwifruits, remain poorly understood.ResultsIn this study, we examined the expression patterns of miRNAs and interactions with their targets in kiwifruit fruit samples from various pulp tissues and developmental stages. Our analysis identified 46 miRNAs, comprising 44 known miRNAs and two novel/kiwifruit-specific miRNAs, which targeted a total of 1,474 genes. Correlation analysis revealed weak relationships between the expression levels of miRNAs and their target genes. Among these targets, 27 tandemly duplicated genes, and 782 whole genome duplication (WGD) genes exhibited a loss of miRNA binding sites in one of their duplicated copies. Furthermore, weighted gene co-expression network analysis demonstrated that most duplicated genes clustered into distinct gene modules. These findings suggest that the loss of miRNA targets following duplications contributes to expression divergence among gene duplicates, thereby facilitating stable gene expression within the miRNA-targeted network. For instance, the aconitate hydratase genes AchAco4 and AchAco6 were each targeted by different miRNAs, ach-miR-3774 and ach-miR-10371, respectively. Notably, these genes exhibited distinct expression patterns compared to their duplicated counterparts.ConclusionsThis study enhances our understanding of how the miRNA-AchAco module regulates citrate content and provides insights into the molecular network that influences the flavor profile of kiwifruit.Clinical trial numberNot applicable.

SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads

Deletions and tandem duplications (commonly called CNVs) represent the majority of structural variations in a human genome. They can be identified using short reads, but because they frequently occur in repetitive regions, existing methods fail to detect most of them. This is because CNVs in repetitive regions often do not produce the evidence needed by existing short reads-based callers (split reads, discordant pairs or read depth change). Here, we introduce a new CNV short reads-based caller named SurVIndel2. SurVindel2 builds on statistical techniques we previously developed, but also employs a novel type of evidence, hidden split reads, that can uncover many CNVs missed by existing algorithms. We use public benchmarks to show that SurVIndel2 outperforms other popular callers, both on human and non-human datasets. Then, we demonstrate the practical utility of the method by generating a catalogue of CNVs for the 1000 Genomes Project that contains hundreds of thousands of CNVs missing from the most recent public catalogue. We also show that SurVIndel2 is able to complement small indels predicted by Google DeepVariant, and the two software used in tandem produce a remarkably complete catalogue of variants in an individual. Finally, we characterise how the limitations of current sequencing technologies contribute significantly to the missing CNVs.

A pivotal switch in β-domain determines the substrate selectivity of TPS genes involved in Gardenia jasminoides floral scent synthesis.

Plants have evolved a diverse array of secondary metabolites to enhance their adaptability to environmental stresses, with volatile terpenoids being a notable example. Gardenia (Gardenia jasminoides), celebrated for its unique fragrance, is a key natural source of volatile terpenoids. Using our chromosome-level genome and transcriptome data for G. jasminoides, we previously identified six terpene synthases (TPS) involved in the production of its floral scent. Here, we functionally characterized these six key TPS enzymes, aligning their product profiles with volatile organic compound (VOC) analysis. Notably, we identified two highly similar terpene synthases, GjTPS1 and GjTPS2, which share high sequence homology but differ in substrate selectivity. By leveraging AI-based predictions and site-directed mutagenesis, we pinpointed a single amino acid in the β-domain that acts as a "switch," modulating substrate selectivity-an unusual finding, as this residue is outside the active site region. Comparative genomic analyses with Coffea canephora and other eudicots revealed that G. jasminoides TPS genes primarily expanded through dispersed (DSD) and tandem duplications (TD). Our study is the first to reveal a "switch" in a previously deemed "non-functional" region, regulating substrate selectivity in TPS genes. These insights could facilitate breeding elite gardenia varieties and support the rational engineering of terpenoid synthases.

Hydroxylase-oriented mining and functional characterization of camptothecin 10-hydroxylase from Camptotheca acuminata Decne

The regiospecific C-10 hydroxylation of camptothecin (CPT) is challenging from a chemical perspective. This step bridges the natural-sourced CPT to an important industrial material, 10-hydroxycamptothecin (10HCPT). 10HCPT is naturally generated in a medicinal plant, Camptotheca acuminata Decne. Functionally active hydroxylase responsible for regiospecific C-10 hydroxylation of CPT is undoubtedly existed in this plant. Therefore, the multi-omics database of C. acuminata was utilized to perform hydroxylase-oriented mining and screening. Three CYP81 genes were identified and two of them, including CYP81BQ18 and CYP81B256 catalyzed hydroxylation of CPT at the C-10 position. CYP81B256 and CYP81BN24 displayed quercetin C-5’ hydroxylase activity. CYP81B256 exhibited better catalytic performance for CPT than CYP81BQ18 and CPT10H in vitro. Furthermore, CYP81BQ18 and CYP81B256 displayed CPT 10-hydroxylase activity in tobacco. Functional verification in planta suggested that the newly observed CYP81BQ18 and CYP81B256 were involved in 10HCPT biosynthesis in C. acuminata. Subcellular localization analysis revealed that these CYP81 genes were located on the endoplasmic reticulum. Evolutionary analysis indicated that CYP81B256 and CYP81BN24 probably evolved from a same ancestral gene via gene duplication, while CYP81BQ18 evolved independently and acted as a specie-specific hydroxylase. CYP81B256 acted as an evolutionary intermediate gene bridging the alkaloid and flavonoid metabolism in C. acuminata. This research provides valuable insights into the function and evolutionary origin of CYP81s in the regiospecific hydroxylation step for 10HCPT biosynthesis.

Genome‑wide identifcation and expression analysis of growth-regulating factors under drought in Brassica juncea

Growth-regulating factors (GRFs) are plant-specific transcription factors involved in the regulation of plant growth, development, and abiotic stress processes. However, the function of Brassica juncea (L.) Czern & Coss GRFs remain largely unknown. In this study, 34 BjGRF genes were identified in B. juncea. BjGRF members of the same subfamily were found to share a similar motif composition and gene structure. In total, 663 cis-acting elements were found in the promoter regions of BjGRF genes, which were related to light response, hormone response, environmental stresses, and plant growth/development. Additionally, 48 pairs of segmental duplication genes were identified during gene duplication events, and no tandemly duplicated genes were identified. qRT-PCR analysis showed that the 34 BjGRF genes were primarily expressed in the roots, followed by the leaves. Furthermore, the 10 BjGRF genes were screened in response to drought stress, and the expression patterns of the genes were relatively consistent, with a maximum expression level at 3 or 24 h, and the selected BjGRF03 and BjGRF32 might be involved in drought stress. This preliminary study clarifies the response of the BjGRF gene family to drought stress and provides ideas for further analyses of the biological functions of BjGRF genes.

Lineage-specific duplication and functional diversification of DOPA-decarboxylase genes in the Gryllidae family, as revealed in Gryllus bimaculatus.

The DOPA-decarboxylase (DDC) gene is crucial for dopamine synthesis and influences various biological functions in insects, including body coloration, behavior, learning, and sleep. However, its evolutionary impact remains largely unexplored. This study reports on the tandem duplication of two bona fide ddc genes (ddc1 and ddc2) in the Gryllidae cricket family. We herein investigated the function of ddc1 and ddc2 using Gryllus bimaculatus (Gb) as a model. Our results revealed that Gb'ddc1 was expressed systemically, with its expression being higher immediately after molting compared to the stage following melanin pigmentation. In homozygous knockout mutants of Gb'ddc1, generated via CRISPR/Cas9, reduced body color pigmentation and had translucent cuticles, decreased dopamine levels, and over-accumulated DOPA. These mutants died shortly after hatching, likely due to cuticle defects, underscoring the essential role of dopamine, produced by Gb'ddc1, in melanin synthesis. Conversely, Gb'ddc2 expression was confined to the ovary and was not up-regulated after molting. Homozygous knockout mutants of Gb'ddc2 exhibited no body color defects, whereas hatchability and embryonic development rates were significantly reduced. Interestingly, dopamine levels in the ovaries were significantly elevated in Gb'ddc2 mutants. This suggests that normal ovarian dopamine levels, modulated by Gb'ddc2, are vital for fertility maintenance. The function of Gb'ddc2 differs from that of typical ddc, indicating neofunctionalization through evolutionary duplication. Overall, Gb'ddc1 and Gb'ddc2 have distinct functions, and precise regulation of ovarian dopamine levels using these two ddc genes may have enhanced cricket fertility.

Evolution of thaumatin-like proteins in rosaceae and rapid response to cold stimulation coordinated with PmEOBⅡ in the floral scent formation process of Prunus mume

Prunus mume has a long history of cultivation in China as the ornamental plant. It has been observed for a long time that the colder weather the weather appear, the sweeter the flowers produce, coldness stress may contribute to the formation of its floral scents. Here, in previous transcription matrix during scent formation period, we recognized thaumatin-like proteins from the core co-expression members. Thus, we performed the identification of thaumatin-like proteins in the Rosaceae genomes, characterized by conserved cysteine residues and tag sequences to explain the relationship between abiotic stress and floral metabolism. The numbers of TLPs ranged from 22 to 34. Most of the TLP members in Group 9 displayed congregated and expanded. A total of seven tandem duplication events occurred in 27 PmTLPs, which could be the primary driving force behind PmTLP gene expansion. The promoters of the PmTLPs contained various types of cis-elements. Additionally, there existed several miRNAs for certain PmTLPs. As a result, PmTLPs displayed tissue-specific expression trends, and expressions varied across different developmental stages of flowers. For highly activated members, PmTLP19 and 23 increased sharply after 4 h under chilling induction compared with a slow increase by ABA treatment. PmTLPs, PmEOBII, and PmMYB4 owned a positive expression correlation in both responces. Finally, the yeast two-hybrid results also indicated a strong interaction between PmEOBII and PmTLP19. Our results establish the foundation for a comprehensive investigation into the molecular mechanism of PmTLPs involved in the cold-resistant defense response of Prunus mume. Additionally, it will facilitate the identification of genes associated with regulating floral compounds in P. mume.

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.

The naked mole-rat (NMR; Heterocephalus glaber ) is a eusocial subterranean rodent with a highly unusual set of physiological traits that has attracted great interest amongst the scientific community. However, the genetic basis of most of these traits has not been elucidated. To facilitate our understanding of the molecular mechanisms underlying NMR physiology and behaviour, we generated a long-read chromosomal-level genome assembly of the NMR. This genome was subsequently annotated and incorporated into multiple whole genome alignments in the Ensembl database. Our long-read assembly identified thousands of repeats and genes that were previously unassembled in the NMR and improved the results of routinely used short-read sequencing-based experiments such as RNA-seq, snRNA-seq, and ATAC-seq. We identified several spermatozoa related gene losses that may underlie the unique degenerative sperm phenotype in NMRs ( IRGC , FSCB , AKAP3 , MROH2B , CATSPER1 , DCDC2C , ATP1A4 , TEKT5 , and ZAN ), and an additional gene loss related to the established NK-cell absence in NMRs (PILRB). We resolved several tandem duplications in genes related to pathways underlying unique NMR adaptations including hypoxia tolerance, oxidative stress, and nervous system protection ( TINF2 , TCP1 , KYAT1 ). Lastly, we describe our ongoing efforts to generate a reference telomere-to-telomere assembly in the NMR which includes the resolution of complex gene families. This new reference genome should accelerate the discovery of the genetic underpinnings of NMR physiology and adaptation.

Genome-wide survey and expression analysis of JAZ genes in watermelon (Citrullus lanatus).

BACKGROUND JAZ: (Jasmonate ZIM-domain) genes play important roles in plant growth and JA signaling pathway which is correlated with fruit ripening process. However, there have been few reports on the genome-wide identification of JAZ genes in watermelon and its relationship with fruit ripening. METHODS AND RESULTS: In this study, bioinformatics approaches were employed to identify ClaJAZ genes of watermelon at the genome-wide levels. Further exploration delved into the phylogenetic relationships, chromosomal mappings, promoter dynamics, expression, and architectural features of the JAZ genes. The results showed that a total of 9 ClaJAZ genes unevenly distributed across six chromosomes were identified in the watermelon genome, and they all have conserved Jas and TIFY domains. These JAZ genes were divided into four distinct groups with five genes involved in inter-chromosomal tandem duplication events, and members of the same subgroup exhibited a high degree of similarity in their gene structure and protein motif patterns. Analysis of the promoter regions of the ClaJAZ genes indicated the presence of cis-acting elements associated with hormonal responses, stress, and developmental processes. Gene expression analysis through real-time quantitative PCR (qRT-PCR) showed that there were spatiotemporal differences in the expression of ClaJAZ genes at various stages of fruit development. Among them, ClaJAZ7 has the highest level of transcriptional expression and showed strong promoter activity. CONCLUSIONS: This study conducted a comprehensive analysis of the ClaJAZ genes and provided insights into the role of ClaJAZ in the development and ripening of watermelon fruit.

Functional Diversity of A-Type RING Ligases (ATL) Genes: Insights into the Crucial Roles of E3 Ubiquitin Ligases in Plant Biology

AbstractE3 ubiquitin ligases are vital components of the ubiquitin–proteasome system (UPS), responsible for maintaining protein balance and controlling cellular functions. E3 ligases target specific proteins for degradation or modify their activities through ubiquitin attachment. One prominent E3 ligase family is the ATL family, which comprises 100 members in Arabidopsis thaliana and has significantly expanded in plant genomes. All ATLs share a common domain architecture, featuring a transmembrane domain at the amino-terminal region, a distinct RING-H2 finger domain, and the GLD motif. The RING domain facilitates interactions between E3 ligases, E2-conjugating enzymes, and target proteins, enabling the transfer of ubiquitin molecules. The amino-terminal and carboxy-terminal regions introduce sequence diversity and potentially mediate interactions with other components that assist in UPS function or target recognition. ATLs had been classified within groups, each group encompasses specific ATLs with defined roles in various biological processes. For example, group C-ATLs are implicated in drought tolerance, flower development, phosphate homeostasis, and immune signaling. G-ATLs are associated with carbon/nitrogen stress, immune signaling, salt stress, ABA responses, cadmium tolerance, and sugar-mediated plant growth. A-ATLs participate in early elicitor-response, salt and drought responses, and flowering time regulation. Lastly, D-ATLs are involved in the regulation of programmed cell death. This review let perceive ATLs as a cohesive group of E3 ligases, shedding light on their functional diversifity and redundancy, specifically examining their participation in diverse biological processes, explore their evolutionary history shaped by gene duplication events, and appraise their interactions with key proteins and targets of ubiquitination. This comprehensive overview aims to offer insights into the role of ATLs in plant adaptation, defense mechanisms, and stress tolerance, while also underlying molecular and evolutionary mechanisms and regulatory networks that govern these processes.

In silico analysis of L- and G-type lectin receptor kinases in tomato: evolution, diversity, and abiotic responses

Solanum lycopersicum (family: Solanaceae) is a crucial crop and model organism for many phenotypic traits, and its sequenced genome provides valuable insights into plant biology and crop improvement. This study investigated lectin receptor-like kinases (LecRLKs) in tomato, focusing on L-type and G-type families. Mining the tomato genome (ITAG2.4) revealed 161 putative lectin genes across seven families, with GNA-related genes being the most abundant. Gene duplication analysis indicated that tandem and segmental duplications were the primary mechanisms driving LecRLK gene family expansion, particularly for G-type LecRLKs. These duplicated genes showed evidence of both purifying and negative selection, suggesting functional conservation and sub-functionalization. L-type and G-type LecRLKs exhibited diverse domain rearrangement architectures and subcellular localizations, with G-type LecRLKs showing greater expansion and architectural diversity. Differential expression analysis during abiotic stress (drought, heat, and cold stress) revealed key responsive genes. During drought stress, 63.2% of L-type and 18.5% of G-type LecRLK genes were expressed, with L-type Solyc09g005000.1 and G-type Solyc03g078360.1 genes showing significant 2-fold upregulation. Heat stress (42 °C) induced the upregulation of L-type Solyc04g071000.1 and G-type Solyc03g078360.1 and Solyc04g008400.1, particularly after 12–24 h of exposure. Promoter analysis revealed numerous stress-related cis-elements. Transcription factor predictions and miRNA targeting sites suggest complex regulatory mechanisms. This comprehensive in silico characterization of tomato LecRLKs, including their expansion patterns and evolutionary pressures, provides insights into their potential roles in abiotic stress responses and lays the groundwork for enhancing crop resilience through targeted breeding or genetic engineering approaches.

Genome-wide identification and expression analysis of the glutathione transferase gene family and its response to abiotic stress in rye (Secale cereale)

BackgroundGlutathione S-transferases (GSTs) are a crucial class of plant enzymes, playing pivotal roles in plant growth, development, and stress responses. However, studies on the functions and regulatory mechanisms of GSTs in plants remain relatively limited.ResultsThis study aimed to comprehensively identify and analyze GST proteins in rye. A total of 171 rye GST genes were identified and classified into four subfamilies, Tau, Phi, Theta, and Zeta, based on their sequence similarity and structural features. Notably, genes classified under the Tau subfamily were the most abundant at 118, while only one gene was under the Theta subfamily. Subsequent phylogenetic and collinearity analysis revealed 29 tandem duplications and 6 segmental duplication events. There were 13 collinear genes between rye and wheat, maize, and rice, demonstrating the expansion and evolution of the GST gene family. An analysis of the expression profiles of 20 representative ScGST genes in different tissues and under various environmental stresses was performed to further understand the functions and expression patterns of ScGST genes. The results showed that these genes exhibited the highest expression levels in stems, followed by fruits and leaves.ConclusionsThis study provides a comprehensive identity, classification, and analysis of rye GST genes, which offer valuable insights into the functionality and regulatory mechanisms of the GST gene family in rye. Especially, ScGST39 was identified as a candidate gene because it was significantly upregulated under multiple stress conditions, indicating its potential crucial role in plant stress tolerance mechanisms.

Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass

BackgroundArgonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) are essential components of RNA silencing pathways in plants. These components are crucial for the generation and regulatory functions of small RNAs, especially in plant development and response to environmental stresses. Despite their well-characterized functions in other plant species, there is limited information about these genes and their stress responses in centipedegrass (Eremochloa ophiuroides), a key turfgrass species.ResultsUsing genome-wide analysis we identified 20 AGO, 6 DCL, and 10 RDR members in centipedegrass and provided a comprehensive overview of their characteristics. We performed the chromosomal location, gene duplication, syntenic analysis, conserve motif, gene structure, and cis-acting elements analysis. And conducted phylogenetic analyses to clarify the evolutionary relationships among the EoAGO, EoDCL, and EoRDR gene families. Three-dimensional modeling prediction of EoAGO, EoDCL, and EoRDR proteins supported the phylogenetic classification. Furthermore, we examined the expression patterns of these genes in different tissues (spike, stem, leaf, root, and flower) and under different stress conditions (cold, salt, drought, aluminum, and herbicide) using RT-qPCR. The results revealed that most of EoAGO, EoDCL, and EoRDR genes were upregulated in response to multiple abiotic stresses, while some exhibited unique responses, suggesting potential specialized regulatory functions.ConclusionIn this study, we performed a comprehensive genome‑wide identification, and phylogenetic and expression pattern analyses of the EoAGO, EoDCL and EoRDR gene families. Our analysis provides a foundation for future research on the RNA silence elements of turfgrass, and affords scientific basis and insights for clarifying the expression patterns of EoAGO, EoDCL and EoRDR genes under adversity stress. Further functional validation and molecular breeding of these genes can be carried out for enhancing the stress resistance of centipedegrass.

Identification of inhibitors targeting the FLT3-ITD mutation through 4D-QSAR, in vitro, and in silico

The FMS-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) mutation is a key target for acute myeloid leukemia (AML) treatment. The second-generation inhibitors such as Gilteritinib still present off-target effects and associated side effects. Therefore, identifying novel FLT3-ITD inhibitors has become a promising strategy for AML treatment. In this study, a 4D-QSAR model was developed based on Gilteritinib and its analogues, and it was found that introducing hydrophobic bulky groups at the piperazine or piperidine of Gilteritinib would enhance the binding affinity to FLT3-ITD. So, three series of targeted compounds (A1-A5, B1–B5 and C1–C5) were designed and synthesized. The antiproliferative activity against MOLM-13 cells was evaluated in vitro. Compound A1 (IC50 = 25.65 nM), with a cubane group at the piperazine position; Compounds B2 (IC50 = 63.38 nM) and C2 (IC50 = 54.96 nM), with a norbornene group at the piperidine position, showed the strongest inhibition in their series. Their IC50 values were comparable to that of the positive control Gilteritinib (IC50 = 22.37 nM). FLT3-ITD was confirmed as the degradation target through a kinase inhibition assay, where the IC50 values were 2.12 nM (Compound A1), 1.29 nM (Compound B2), and 3.06 nM (Compound C2), which were comparable to that of Gilteritinib (IC50 = 0.43 nM). Additionally, molecular docking and molecular dynamics (MD) simulations showed that Compounds A1, B2, and C2 had similar binding modes to that of Gilteritinib with more stable affinities. Overall, these results demonstrated that Compounds A1, B2, and C2 were promising inhibitors for targeting AML with FLT3-ITD mutation.

Development of Potent and Selective Inhibitors of Methylenetetrahydrofolate Dehydrogenase 2 for Targeting Acute Myeloid Leukemia: SAR, Structural Insights, and Biological Characterization.

Methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2 (MTHFD2), a pivotal mitochondrial enzyme in one-carbon metabolism, is significantly upregulated in various cancers but minimally expressed in normal proliferating cells. In contrast, MTHFD1, which performs similar functions, is predominantly expressed in normal cells. Therefore, targeting MTHFD2 with selective inhibitors holds promise for a broader therapeutic window with reduced toxicity and fewer side effects. This study identified selective 2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl ureido-based derivatives through systematic chemical modifications and SAR studies. Structural biology investigations revealed substitutions in the phenyl ring and tail region modulate potency and selectivity toward MTHFD2. Additionally, a comprehensive cell screening platform revealed acute myeloid leukemia cells with FLT3 internal tandem duplication mutations are particularly sensitive to these inhibitors. Furthermore, synergistic effects were observed when combining potential compounds with Alimta. Compound 16e emerged as a leading candidate, demonstrating superior inhibition and selectivity for MTHFD2, favorable pharmacokinetics, and potent antitumor efficacy in MOLM-14 xenograft models.