Mol. Genet. Genomics [JOURNAL]
Sun
200 papers
A pentatricopeptide repeat protein restores fertility in Moricandia arvensis based cytoplasmic male sterility system in Brassica juncea.
Bisht DS, Kumar N, Watts A … +7 more , Chamola R, Kumar V, Jain P, Kumar M, Adhikari BS, Savadi S, Bhat SR
Mol Genet Genomics · 2025 Sep · PMID 40892256 · Publisher ↗
An introgression from Moricandia arvensis is known to restore male fertility to Brassica juncea cytoplasmic male sterile lines carrying M. arvensis, Diplotaxis berthautii, D. catholica or D. erucoides cytoplasm. We have...
An introgression from Moricandia arvensis is known to restore male fertility to Brassica juncea cytoplasmic male sterile lines carrying M. arvensis, Diplotaxis berthautii, D. catholica or D. erucoides cytoplasm. We have previously mapped the fertility-restorer gene (Rfm) to the distal end of A09 chromosome of B. juncea but the restorer gene remains to be discovered. This study was undertaken to identify and clone the restorer gene(s) using next-generation sequencing approach, leveraging its known chromosomal location and flanking markers. We assembled the draft genome of the B. juncea fertility restorer line (MRS15), carrying the M. arvensis introgression. Alignment of the MRS15 genomic scaffolds to B. juncea reference genome identified six scaffolds aligned to the terminal region of chromosome A09 (between 51 and 58.5 Mb) harbouring the Rfm. The high-density linkage map of Rfm locus confirmed the correct orientation of these scaffolds. Based on segregation of tightly linked flanking markers, namely, the earlier reported BjESSR06 and a newly identified SRB17 marker, the Rfm gene was assigned to Scaffold-547. In silico analysis revealed six pentatricopeptide repeat (PPR)-encoding Restorer-of-Fertility-Like (RFL) genes in the ~ 300 kb region delimited by the above stated markers. Based on the expression profiles of these genes in CMS and fertility restorer lines, and in a segregating population, PPR-640 was identified as the Rfm gene. Further, we designed a gene-based, co-dominant marker perfectly co-segregating with fertility restorer trait through collinearity analysis of the genomic region spanning PPR-640 and the B. juncea genome. The Rfm gene and the marker reported here are critical for utilising this CMS system in hybrid breeding and to clone and study evolution of restorer genes in other Brassicaceae members.
Advanced techniques and applications in fennel (Foeniculum vulgare Mill.) breeding.
Giachino RRA, Boztaş G
Mol Genet Genomics · 2025 Sep · PMID 40892151 · Publisher ↗
Fennel (Foeniculum vulgare Mill.) is a widely cultivated medicinal and aromatic plant valued for its essential oils used in pharmaceutical, culinary, and industrial applications. Breeding activities for fennel have been...
Fennel (Foeniculum vulgare Mill.) is a widely cultivated medicinal and aromatic plant valued for its essential oils used in pharmaceutical, culinary, and industrial applications. Breeding activities for fennel have been historically limited, but recent genomic advances have revealed substantial genetic diversity and variability among its populations, offering new opportunities to improve yield, oil composition, and stress resilience. Studies using molecular markers including RAPD, ISSR, SSR, and SNPs have characterized the genetic structure of fennel germplasm and identified key loci for traits such as seed yield, essential oil profile, and disease tolerance. Quantitative trait locus (QTL) mapping and principal component analysis (PCA) have refined genotype selection. Transcriptomic studies related to t-anethole biosynthesis and expression profiles under stress conditions have enabled functional gene discovery. Biotechnological tools such as callus induction, doubled haploid protocols, and in vitro selection techniques have emerged as adjunct strategies to accelerate breeding outcomes. Integration of classical breeding methods with molecular and biotechnological approaches enables precision breeding of fennel cultivars tailored for modern agricultural needs. Enhancing genetic diversity utilization and targeting key traits will support the development of high-performing, resilient varieties. This direction advances both the sustainability of fennel cultivation and its utility in agro-industrial sectors.
Assessment of DNA damage and expression variation of genes related to DNA damage in salt mine workers.
Mazhar T, Akram Z, Sidiqque A … +3 more , Mahjabeen I, Haroon L, Noor H
Mol Genet Genomics · 2025 Sep · PMID 40892137 · Publisher ↗
Salt mine workers are occupationally exposed to DNA damaging agents at their workplace. The present study estimates the extent of DNA damage and expression deregulation of related genes in mine workers, staff, community...
Salt mine workers are occupationally exposed to DNA damaging agents at their workplace. The present study estimates the extent of DNA damage and expression deregulation of related genes in mine workers, staff, community living nearby and unexposed controls. Blood samples were collected from all groups. Expression analysis of AGT, H2AX and Mre11 genes was done using RT-PCR. DNA damage was detected by comet assay. Relative expression of selected genes was upregulated in mine, staff and community group compared to control. Expression of all three genes increased significantly with increasing age, total exposure time and smoking. DNA damage was higher in mine workers compared to control, staff and community groups. Elevated serum levels of sodium, potassium, chloride and total ROS were observed in mine and staff group compared to control and community group. Positive correlation was observed between gene expression versus total exposure time. Moreover, significant dependable regression was observed between gene expression versus comet parameters. The present study anticipated a negative impact of mine environment on the genomic stability of mine workers and staff group. Moreover, age, exposure time and smoking act synergistically to enhance the extent of DNA damage, ROS production, electrolyte imbalance and expression deregulation of selected genes. In addition, current research will provoke thoughtful insights to rethink the risk assessments for genetic integrity of community living nearby mines.
Shared genetics between metabolic traits and sensorineural hearing loss: a large-scale genome-wide cross-trait analysis.
Wang X, Xia X, Qiu K … +4 more , Shu T, Pang W, Ren J, Zhao Y
Mol Genet Genomics · 2025 Aug · PMID 40886219 · Publisher ↗
Sensorineural hearing loss (SNHL) has been epidemiologically linked to metabolic traits, yet their shared genetic basis remains unclear. We performed the largest genome-wide association study (GWAS) meta-analysis for SNH...
Sensorineural hearing loss (SNHL) has been epidemiologically linked to metabolic traits, yet their shared genetic basis remains unclear. We performed the largest genome-wide association study (GWAS) meta-analysis for SNHL and analyzed GWAS data from 14 metabolic traits to assess genetic correlations and infer causal relationships. Significant genetic correlations were observed between SNHL and high triglyceride (TG) levels and low high-density lipoprotein (HDL) levels. Cross-trait meta-analyses identified dozens of shared loci and pleiotropic genes, especially between SNHL and HDL or TG. Functional analyses revealed enrichment in pathways related to auditory and metabolic processes, with key involvement of outer hair cells. Protein–protein interaction networks highlighted TRIOBP, BUD13, APOA5, APOB, and CETP as central genes. Druggability analysis suggested SOST and CETP as candidate therapeutic targets. These findings provide novel insights into the genetic architecture of SNHL and its connection with lipid metabolism, highlighting opportunities for developing targeted interventions.
Prevalence and spectrum of STRC variants in 1015 sensorineural hearing loss patients: insights from the Chinese population.
Guo L, Yu S, Zhao W … +11 more , Chen L, Cheng G, Li W, Li W, Ji H, Sun S, Yu H, Liu H, Gui C, Li H, Shu Y
Mol Genet Genomics · 2025 Aug · PMID 40886188 · Publisher ↗
Mutations in the STRC gene are a major cause of autosomal recessive mild-to-moderate sensorineural hearing loss (SNHL); however, its prevalence and mutational spectrum in the Chinese population remain largely unexplored....
Mutations in the STRC gene are a major cause of autosomal recessive mild-to-moderate sensorineural hearing loss (SNHL); however, its prevalence and mutational spectrum in the Chinese population remain largely unexplored. To address this, we analyzed 1015 unrelated Chinese patients with bilateral SNHL using whole-exome sequencing (WES), multiplex ligation-dependent probe amplification (MLPA), and Sanger sequencing. Biallelic STRC variants were identified in 2.1% of all patients, with the diagnostic yield significantly rising to 15.6% among mild-to-moderate SNHL cases. Copy number variants (CNVs) were predominant (90.5%, 19/21), which were potentially mediated by non-allelic homologous recombination (NAHR) involving the pseudogene STRCP1. Notably, 26.2% (11/42) of mutant alleles harbored CNVs spanning both STRC and the adjacent CATSPER2 gene, highlighting critical implications for clinical management and genetic counseling due to potential syndromic associations. MLPA detected additional CNVs missed by WES, emphasizing the necessity of combining multiple genetic testing strategies. Audiologically, patients with biallelic STRC variants exhibited a distinctive frequency-dependent hearing loss, characterized by mild impairment at low frequencies (0.125-0.5 kHz) and moderate to moderately severe impairment at higher frequencies (0.5-8 kHz). These findings highlight the critical importance of CNV detection for genetic diagnosis and clinical management of STRC-related SNHL, particularly in mild-to-moderate cases, and provide essential insights for genetic counseling involving co-occurring STRC and CATSPER2 CNVs.
The accuracy and real resolution of karyotyping technique in detecting chromosomal aberrations identified by molecular genetic methods.
Zhang S, He Y, Huang Y … +5 more , Zhang Y, Du Y, Zhang T, Sun Y, Lu Y
Mol Genet Genomics · 2025 Aug · PMID 40879815 · Publisher ↗
Although karyotyping technology has been implemented in genetic diagnosis for a long time, the comprehensive understanding of this technology is still limited. The aim of this study was to investigate the accuracy and re...
Although karyotyping technology has been implemented in genetic diagnosis for a long time, the comprehensive understanding of this technology is still limited. The aim of this study was to investigate the accuracy and resolution of karyotyping method in detecting chromosomal abnormalities by molecular genetic method. In this study, we conducted a retrospective analysis of embryonic molecular karyotypes and peripheral blood cytogenetic karyotypes from patients with balanced chromosomal rearrangements undergoing preimplantation genetic testing at our reproductive center. Blood karyotyping was performed using routine G-banding at the 400-band resolution by two well-trained technicians. The embryonic molecular karyotypes were detected using either high-throughput sequencing or single nucleotide polymorphism microarray method. We compared the breakpoint locations, determined by unbalanced rearrangements, in the embryonic molecular karyotypes with the corresponding rearranged chromosome bands in the peripheral blood karyotypes. A total of 508 cases were enrolled and 2078 embryos were detected, 404 cases were analyzed finally. We found that only 39.32% (289/735) of embryonic molecular breakpoints were located within the rearranged bands identified by peripheral blood karyotyping, while the remaining 60.68% (446/735) fell outside these regions. Our results showed only 73 cases exhibited accurate karyotyping results, indicating an accuracy rate of 18.07%. Furthermore, the average resolution of karyotyping technique was found to be approximately 9.01 megabases (Mb) pairs. These findings provide profound insight into the accuracy and resolution of karyotyping techniques, which can contribute to more precise genetic counseling.
Genome-wide lipidomic profiling reveals causal lipid species as targets for inguinal hernia risk.
Xu X, Luo Z, Xie X
Mol Genet Genomics · 2025 Aug · PMID 40839010 · Full text
Inguinal hernia (IH) is a common condition with a substantial health burden and emerging evidence suggests that lipid metabolism-related indicators may contribute to its risk. However, the exact role of specific lipid ty...
Inguinal hernia (IH) is a common condition with a substantial health burden and emerging evidence suggests that lipid metabolism-related indicators may contribute to its risk. However, the exact role of specific lipid types in causing IH is still unclear. This study aims to investigate whether any of 179 distinct lipid species have a causal impact on IH risk using causal inference. We applied a two-sample Mendelian randomization (MR) framework, integrating lipidomic genome-wide association studies (GWAS) data from 7,174 Finnish individuals with IH summary statistics from the UK Biobank (16,749 cases and 439,599 controls). Linkage disequilibrium pruning and genome-wide significance (P < 5E-8) were used to choose genetic instruments. Primary causal estimates were derived with inverse-variance weighted (IVW) method, and further supported by weighted median (WM) and robust adjusted profile score (RAPS). We employed sensitivity tests, like Cochran's Q for heterogeneity, MR-Egger for directional pleiotropy, Radial MR for outlier detection, and leave-one-out analysis to measure the impact of individual variants. Among 179 lipid species, 162 had valid IVs, and 94 met the criteria for causal inference. IVW analysis identified 25 lipid species with nominal significance, 24 of which were supported by WM and RAPS. Sensitivity analyses consistently provided robust evidence supporting a causal relationship between four lipid species and increased IH risk: diacylglycerol (18:1_18:1) (OR = 1.16, P = 0.005), diacylglycerol (18:1_18:2) (OR = 1.12, P = 0.006), phosphatidylinositol (18:0_20:4) (OR = 1.10, P = 1.47E-04), and triacylglycerol (54:6) (OR = 1.21, P = 0.001). Our findings provides genetic molecular evidence that four lipid species are causally linked to an increased IH susceptibility, offering novel insights into lipid-centered interventions for disease prevention and highlighting the importance of metabolic health in hernia pathogenesis.
Role of Php domain and related enzymes in the enzymatic degradation of G-series nerve agents.
Ramamoorthy D, Iyer R
Mol Genet Genomics · 2025 Aug · PMID 40839030 · Publisher ↗
The enzymatic breakdown of organophosphate (OP) nerve agents marks a pivotal advancement in both bioremediation and biodefense. This review explores the genetic diversity and evolutionary lineage of phosphotriesterase-re...
The enzymatic breakdown of organophosphate (OP) nerve agents marks a pivotal advancement in both bioremediation and biodefense. This review explores the genetic diversity and evolutionary lineage of phosphotriesterase-related proteins across multiple species, with a particular focus on the Php domain, key to substrate recognition and hydrolysis. The study underscores the functional importance of Php-containing enzymes in neutralizing G-series nerve agents, highlighting their promise for environmental detoxification and defense applications. By laying the groundwork for enzyme-based OP degradation strategies, this work emphasizes the need for continued research and optimization of these enzymes and their microbial hosts to support sustainable remediation efforts.
Exploring the genetic footprints of the gotra system in the Koṅkaṇī Sārasvata Brahmins.
Sequeira JJ, Shastri S, Shrivastava P … +5 more , Yadav R, Yadav B, Sharma S, van Driem G, Mustak MS
Mol Genet Genomics · 2025 Aug · PMID 40794136 · Publisher ↗
The gotra system of exogamy is followed by the Brahmin caste group in India. This system restricts the marriage of individuals who belong to the same gotra. In genetic terms, each gotra forms an exogamous group within a...
The gotra system of exogamy is followed by the Brahmin caste group in India. This system restricts the marriage of individuals who belong to the same gotra. In genetic terms, each gotra forms an exogamous group within a population and thereby maintains a lineage. In Koṅkaṇī Sārasvata Brahmins, the gotras are patrilineal. To understand the genetic footprints of the gotras in this population, we reconstructed the maternal and paternal ancestry of 95 individuals using single nucleotide polymorphism (SNP) markers and Y-chromosomal short tandem repeats (Y-STR). The haplogroup distribution in the gotras showed a significant association with the paternal lineage (p < 0.005) as compared with the maternal lineage. We observed a similar significant association of the gotras with the Y-STR haplotypes. Our findings provide scientific evidence for an actively existing gotra system followed by the caste groups of India. Comparative analysis of 334 Indian Brahmins and over 1300 Eurasian Y-STR profiles showed that all Brahmin groups share a common R1a ancestor with Western Iranian males likely predating the Indo-Iranian split in northern Afghanistan. Whilst North Indian Brahmins shared the lineage with Afghanistan groups, the Koṅkaṇī and southern Brahmins may represent an earlier divergence. The persistence of common gotras throughout India implies the gotra system originated before Brahmin dispersal from north to south. These findings provide genetic evidence for the role of gotra system in shaping Brahmin population structure.
Multi-trait GWAS for growth under contrasting thermal rearing conditions in rainbow trout (Oncorhynchus mykiss).
Gallardo-Hidalgo J, Tapia DA, Garcia BF … +6 more , Marin-Nahuelpi R, Cáceres P, Bassini LN, Mastrochirico-Filho VA, Araya C, Yáñez JM
Mol Genet Genomics · 2025 Aug · PMID 40788500 · Publisher ↗
Thermal variability significantly impacts fish performance, and current breeding objectives may soon be suboptimal due to climate change. Growth is a critical trait for aquaculture profitability. Understanding the genomi...
Thermal variability significantly impacts fish performance, and current breeding objectives may soon be suboptimal due to climate change. Growth is a critical trait for aquaculture profitability. Understanding the genomic differences in growth under varying water temperatures is essential to predict climate change's impact on cold water species production. This study examined a rainbow trout population grown under low (~ 7 °C) and high (~ 22 °C) non-lethal temperatures. The objectives were to: (i) explore the genetic architecture of growth under upper and lower temperature (UT and LT) conditions using multi-trait genome-wide association, and (ii) identify candidate genes and biological processes related to growth in these conditions through a gene-based meta-analysis approach. The results revealed: (i) significant genetic variation for body weight, body length, and average daily gain at both LT and UT conditions, with genomic heritabilities ranging from 0.19 ± 0.06 to 0.32 ± 0.05 and 0.16 ± 0.05 to 0.39 ± 0.08, respectively; (ii) distinct genetic architectures and genes associated with UT and LT growth, with SNP effect correlations from r = 0.06 to 0.22; (iii) shared biological functions for growth at UT and LT, involving cardiovascular function maintenance and cell communication. Cytoskeleton-related functions were predominant in growth at LT, while DNA repair functions were more significant at UT. Notably, sema6ba emerges as a potential candidate gene involved in growth-related traits across contrasting thermal environments in rainbow trout, given its strong association under both low and high temperature conditions.
DNA methylation biomarkers in diabetic kidney disease: insights and implications.
Feng Z, Kong X, Ma L
Mol Genet Genomics · 2025 Jul · PMID 40736706 · Publisher ↗
Diabetic kidney disease (DKD) is a significant consequence of diabetes, markedly contributing to the global burden of end-stage renal disease (ESRD). DKD, a substantial public health challenge, is characterized by elevat...
Diabetic kidney disease (DKD) is a significant consequence of diabetes, markedly contributing to the global burden of end-stage renal disease (ESRD). DKD, a substantial public health challenge, is characterized by elevated urinary albumin excretion and/or reduced glomerular filtration rate. As the primary cause of end-stage renal disease (ESRD), comprehending the prevalence of DKD and investigating relevant biomarkers for diagnosis is imperative. The pathogenesis of DKD is intricate, involving both genetic and epigenetic factors. Among these factors, DNA methylation has surfaced as a pivotal element, offering insights into the progression of DKD and potential therapeutic targets. This review endeavors to synthesize current research on DNA methylation biomarkers in DKD, emphasizing advances and potential clinical applications.
Loss of dcst2 expression in male zebrafish is not associated with muscle hypertrophy.
Allard-Chamard X, Rodríguez EC, Brais B … +1 more , Armstrong GAB
Mol Genet Genomics · 2025 Jul · PMID 40736578 · Publisher ↗
Recently, a large family of French-Canadians was found to possess above-average strength and muscle hypertrophy that segregated with a single variant in the gene encoding Dendritic Cell-specific Six Transmembrane domain...
Recently, a large family of French-Canadians was found to possess above-average strength and muscle hypertrophy that segregated with a single variant in the gene encoding Dendritic Cell-specific Six Transmembrane domain containing protein 2 (DCST2). To investigate the potential role DCST2 has in muscle cell biology we used the CRISPR/Cas9 mutagenic system and generated a 2-nucleotide deletion in exon 3 of zebrafish dcst2 resulting in a frameshift mutation. Homozygous carriers of the mutation displayed reduced transcriptional expression of dcst2 suggesting that our mutation disrupted gene expression. Homozygous mutant dcst2 zebrafish developed normally to adulthood and displayed no differences in motor function using a free-swim and swim tunnel assays. Furthermore, histological examination of muscle cells revealed no differences in slow-twitch or fast-twitch muscle cell cross-sectional area in our mutants. We did observe that male dcst2 zebrafish were infertile. The data collected here, suggest that dcst2 does not play a role in zebrafish muscle cell biology.
A missense mutation in TCFL5 is associated with male infertility due to oligoasthenoteratozoospermia.
Yu K, Zhang W, Wang Y … +8 more , Xiang M, Zheng N, Zhang J, Zha X, Duan Z, Wang F, Cao Y, Zhu F
Mol Genet Genomics · 2025 Jul · PMID 40711600 · Publisher ↗
Oligoasthenoteratozoospermia (OAT) is a prevalent situation of male infertility partly caused by genetic defects with largely undiscovered. To further unravel the genetic etiology of OAT, we recruited cases for whole-exo...
Oligoasthenoteratozoospermia (OAT) is a prevalent situation of male infertility partly caused by genetic defects with largely undiscovered. To further unravel the genetic etiology of OAT, we recruited cases for whole-exome sequencing (WES) to screen candidate pathogenic mutations. Here, we identified a heterozygous missense mutation in transcription factor-like 5 (TCFL5) (NM_006602.4: c.1207G > A: p.E403K) from two infertile brothers born into a non-consanguineous family. TCFL5 was previously linked to male infertility since Tcfl5 male mice manifested infertile due to OAT, while Tcfl5 mice could not be generated. Sperm morphological analysis of these brothers exhibited a similar OAT phenotype to Tcfl5 mice. In vitro functional analysis performed to explore the pathogenicity of TCFL5 mutation. Regardless of no significant effect on the expression of mutant TCFL5 detected by western blotting and immunofluorescence, dual-luciferase reporter assay revealed a serious impact on its transcriptional regulatory function. Many crucial genes involved in spermatogenesis, such as DMRT1, DAZL, SYCE1, SPACA1, CNTROB, IFT88, HOOK1 and SPATA6, occurred transcriptional abnormalities after TCFL5 mutated. Our results showed that TCFL5 mutation disrupted the normal transcription of spermatogenesis genes, finally resulting in male infertility raised by OAT. Our work firstly linked TCFL5 mutation to male infertility in human, which provides a new perspective on the genetic underpinnings of OAT and a theoretical basis for clinic genetic counseling and treatment strategies selection.
Unraveling genetic diversity and population structure of pineapple germplasm using genome-wide SNP markers.
Lyu H, Matsumoto T, Yu Q
Mol Genet Genomics · 2025 Jul · PMID 40682678 · Full text
Pineapple (Ananas comosus (L.) Merr.) is one of the most important tropical fruits worldwide. It is primarily propagated clonally and exhibits high heterozygosity which can mask deleterious mutations, potentially leading...
Pineapple (Ananas comosus (L.) Merr.) is one of the most important tropical fruits worldwide. It is primarily propagated clonally and exhibits high heterozygosity which can mask deleterious mutations, potentially leading to inbreeding depression and hindering breeding efforts. To address this, we conducted a comprehensive genome-wide analysis of 91 pineapple accessions and identified over 7.9 million high-quality SNPs. We utilized these SNPs to investigate the genetic structure and reproductive patterns of diverse cultivars and related varieties. Population structure analysis revealed a unique genetic makeup of A. comosus var. microstachys accessions and unidirectional gene flow from A. comosus var. microstachys into A. comosus var. comosus, A. comosus var. bracteatus, and A. comosus var. erectifolius. Among the cultivated pineapples, 'Mordilona-related' and 'Smooth Cayenne' cultivars showed unidirectional gene flow from 'Singapore Spanish', 'Queen', and the wild A. comosus var. microstachys. Heterozygosity patterns suggested predominantly asexual reproduction in 'Queen', 'Singapore Spanish', 'Smooth Cayenne', and A. comosus var. microstachys populations, while 'Mordilona-related' and A. comosus var. bracteatus populations might have experienced increased sexual reproduction or population expansion. We developed two SNP panels: one for germplasm identification and the other one for pedigree analysis. These resources will facilitate pineapple germplasm evaluation, diversity analysis, and informed breeding decisions for cultivar improvement.
Deciphering gonadal transcriptome reveals circRNA-miRNA-mRNA regulatory network involved in sex differentiation and gametogenesis of Apostichopus japonicus.
Li Z, Tang X, Liu X … +3 more , Huo J, Guo Y, Yang Y
Mol Genet Genomics · 2025 Jul · PMID 40682658 · Publisher ↗
As stable and conserved non-coding RNAs, circular RNAs (circRNAs) play vital roles in gene regulation, particularly in reproductive development. However, their functions in marine invertebrate gonadal differentiation rem...
As stable and conserved non-coding RNAs, circular RNAs (circRNAs) play vital roles in gene regulation, particularly in reproductive development. However, their functions in marine invertebrate gonadal differentiation remain largely unexplored. Understanding the molecular mechanisms of sexual differentiation and gonadal development is essential for advancing reproductive biology in marine invertebrates. The sea cucumber Apostichopus japonicus is a vital species in economic aquaculture. Before the breeding season, A. japonicus exhibits minimal sexual dimorphism, significantly impeding breeding efficiency and posing challenges for the development of superior germplasm resources. Investigating the role of circRNAs in mature A. japonicus will enhance our understanding of its specific molecular mechanism during sexual differentiation and gonadal reproduction. In this study, we constructed differential expression profiles of circRNAs. A total of 18,121 circRNAs were identified, distributed across the 23 chromosomes of A. japonicus. 584 circRNAs exhibited significant expression differences, with 296 up-regulated and 288 down-regulated. Through GO enrichment and KEGG pathway analysis of these circRNAs, two pathways related to sexual differentiation were identified: the AMPK signaling pathway and the TGF-β signaling pathway, which may regulate sexual differentiation by influencing sex hormone synthesis. Additionally, several genes, such as smad3, smoc2, and ppp2r1a may play critical regulatory roles in the development and activity of germ cells. Our study elucidates the molecular regulatory roles of circRNAs in the sexual differentiation and gonadal development of A. japonicus. Given its evolutionary position as the closest phylum to chordates, the present study on A. japonicus provides valuable insights into the non-coding RNA resource for marine invertebrates.
Molecular breeding for stress tolerance in sesame.
Weldemichael MY, Gebremedhn HM, Runo S … +1 more , Gandhi H
Mol Genet Genomics · 2025 Jul · PMID 40668473 · Publisher ↗
Sesame (Sesamum indicum L.) is a vital oilseed crop known for its high-quality edible oil, proteins, minerals, and vitamins. It is primarily cultivated in arid and semi-arid regions, where unpredictable drought poses a m...
Sesame (Sesamum indicum L.) is a vital oilseed crop known for its high-quality edible oil, proteins, minerals, and vitamins. It is primarily cultivated in arid and semi-arid regions, where unpredictable drought poses a major constraint to its production. Sesame is a valuable source of healthy vegetable oil, attracting growing interest worldwide. However, its cultivation in dry regions makes it vulnerable to various biotic and abiotic stresses. Sesame is grown for food, pharmaceutical, medicinal, and industrial uses, which is cultivated as a main cash crop by African and Asian smallholder farmers. Despite its importance, sesame production and productivity remain low due to numerous challenges such as; drought, salinity, diseases, insect pests, inherent genetic problems, and poor agronomic and postharvest practices. Fortunately, the crop's extensive genetic diversity offers potential for enhancing stress resilience. Our understanding of sesame molecular responses will be facilitated by ongoing attempts to develop methods for quantifying biotic and abiotic stresses. We review recent advances in the molecular mechanisms underlying sesame's tolerance to biotic and abiotic stresses focusing on stress-related genes and key agronomic traits. Additionally, we review recent advancements in functional genomics and transcriptomics, specifically in deciphering sesame's responses to drought, water-logging, temperature fluctuations, osmotic stress, and salinity as well as biotic stressors. To accelerate the development of stress-resistant sesame varieties, we propose advancing research in genomics-assisted breeding. Approaches such as genome-wide association studies (GWAS) and high-density linkage mapping can help identify key genetic markers associated with stress tolerance. These markers can then be applied in marker-assisted selection to develop resilient cultivars, ensuring stable yields under changing climate conditions.
Unravelling the genomic landscape of Acinetobacter baumannii: deep dive into virulence factors, resistance elements, and evolutionary adaptations.
Sholeh M, Hamidieh F, Beig M … +1 more , Badmasti F
Mol Genet Genomics · 2025 Jul · PMID 40650755 · Publisher ↗
The increasing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Acinetobacter baumannii presents a major global health threat, particularly in hospital settings. Understanding the genomic land...
The increasing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Acinetobacter baumannii presents a major global health threat, particularly in hospital settings. Understanding the genomic landscape of A. baumannii is essential to elucidate its virulence mechanisms, resistance profiles, and evolutionary adaptations, which are critical for developing novel therapeutic strategies. This study aims to comprehensively analyze the pan-genome, antimicrobial resistance (AMR) genes, virulence factors, and clonal relationships of A. baumannii, with the goal of uncovering insights into its pathogenicity and genomic evolution. A total of 27,884 A. baumannii genomes were retrieved from GenBank for analysis. Genome annotation was carried out using Prokka, and pan-genome analysis was performed with Roary. AMR genes and virulence factors were identified through AMRFinderPlus and the Virulence Factor Database via Abricate. Temporal trends in AMR and virulence were analyzed statistically to assess changes over time. The study found that A. baumannii possesses a stable core genome and a highly diverse accessory genome, suggesting an open pan-genome structure. Temporal analysis revealed a significant increase in AMR genes, including bla, bla, and pmrCAB. Virulence genes were widely distributed across strains, with the sequence types (ST) like ST2 clone exhibiting global dissemination, highlighting the strain's potential for widespread pathogenicity. This comprehensive genomic analysis of A. baumannii reveals its significant genomic diversity and adaptability, underscoring the critical role of both core and accessory genomes in shaping its pathogenicity and resistance mechanisms. The increasing prevalence of key AMR genes, alongside the widespread dissemination of virulent clones, highlights the urgent need for enhanced surveillance and novel therapeutic strategies to control the spread of this global pathogen. Future research should focus on the functional characterization of resistance and virulence factors to better understand their roles in pathogenicity and to facilitate the development of targeted interventions against A. baumannii.
A reference genome for Plinia edulis: expanding the pharmacological and nutraceutical potential of a neglected brazilian tree species.
Stefenon VM, Ornellas TS, Fritsche Y … +4 more , Guterres SM, Brand ILD, de Sousa Silva AK, Joner F
Mol Genet Genomics · 2025 Jun · PMID 40583094 · Publisher ↗
Widely distributed in tropical and subtropical regions, the Myrtaceae family includes several species with vast nutraceutical potential due to their rich composition of bioactive compounds with pharmacological and nutrac...
Widely distributed in tropical and subtropical regions, the Myrtaceae family includes several species with vast nutraceutical potential due to their rich composition of bioactive compounds with pharmacological and nutraceutical importance. Plinia edulis is a neglected and endangered Myrtaceae species of the Brazilian Atlantic Forest, with tasteful nutraceutical fruits and potential use in the pharmacological industry. Here we report the sequencing, assembling, and annotation of a reference genome for this species, towards stimulating its conservation, cultivation, domestication, and genetic improvement. The reference genome presented 98.5% BUSCO completeness, N50 = 21.2 Mb, and 37.428 gene models predicted. These gene models are related to 327 pathways of secondary metabolites biosynthesis, including 59 of terpenoids and polyketides and 40 of propanoids and flavonoids metabolism. The KEGG mapping revealed key genes for producing 20 important secondary metabolites with pharmacological significance, enlarging the opportunities for nutraceutical and pharmacological uses of the species. The prospection of SSR markers allowed primer design for 30,897 loci, of which about 75% are potentially informative for SSR and SSRseq analysis. This reference genome will assist conservation and genetic breeding programs, and the annotation will support studies on secondary metabolite production. Genetic conservation and breeding projects for P. edulis may also consider the revealed genomic potential of this species to react to environmental stresses.
Genomic analysis of terpene synthase family and characterization of ent-kaurene synthase in Chenopodium quinoa.
Tian S, Wang L, Liu L … +4 more , Sha X, Wu J, Fu J, Wang Q
Mol Genet Genomics · 2025 Jun · PMID 40583067 · Publisher ↗
Terpenoids produced in plants play important roles in growth, development and response to environmental stimuli. Terpene synthases are responsible for the terpene backbone formation of terpenoid metabolites. In this stud...
Terpenoids produced in plants play important roles in growth, development and response to environmental stimuli. Terpene synthases are responsible for the terpene backbone formation of terpenoid metabolites. In this study, fifty-one terpene synthase genes were identified in the quinoa genome and categorized into seven sub-families through bioinformatics and phylogenetic analysis. Gene structures, conserved motifs and cis-elements in promoters were also analyzed for these CqTPSs, as well as prediction of secondary and tertiary protein structure. Four terpene synthase genes in the TPS-e sub-family were further cloned for functional characterization. Among which, CqTPS49 and CqTPS51 were detected to react with ent-CPP to generate ent-kaurene, the intermediate of gibberellin biosynthesis, subsequently name as CqTPS49/KS1 and CqTPS51/KS2, respectively. CqTPS47 and CqTPS48 reacted with syn-CPP to form diterpene products, which needs to be identified with chemical structure characterization. All four tested CqTPSs were found to be localized in the chloroplast, consistent with their functions as diterpene synthease. Expression patterns analysis in different tissues revealed that CqTPS49/KS1 and CqTPS51/KS2 are mainly expressed in the active growing buds, suggesting involvement in gibberellic acid metabolism. This study identified the terpene synthase gene family in quinoa and provided the basis for further functional characterization of terpenoid metabolism.
Kenaf cyclic nucleotide-gated channel gene HcCNGC27 confers plant drought stress tolerance and involved in flowering regulation.
Chen C, Xiao H, Yue J … +5 more , Wang X, Wang C, Wei R, Luo D, Chen P
Mol Genet Genomics · 2025 Jun · PMID 40579568 · Publisher ↗
Cyclic Nucleotide-Gated Channel (CNGC) gene consists a large family and plays an important role in plant growth and development, biotic and abiotic stresses, yet their functions in non-model crops like kenaf (Hibiscus ca...
Cyclic Nucleotide-Gated Channel (CNGC) gene consists a large family and plays an important role in plant growth and development, biotic and abiotic stresses, yet their functions in non-model crops like kenaf (Hibiscus cannabinus L.), a highly stress-resistant bast fiber crop, remain poorly understood. To investigate the role in kenaf abiotic stress response and plant development regulation, we characterized the HcCNGC27 gene in kenaf. Our study aimed to elucidate the role of HcCNGC27 in drought stress response and its impact on plant development. HcCNGC27 was identified subcellularly localized to the plasma membrane. Expression analysis showed that HcCNGC27 is ubiquitously expressed across various tissues including roots, stems, leaves, flowers, and seeds, with the highest expression observed in flowers. Importantly, HcCNGC27 was significantly induced under drought stress conditions. To investigate the function of HcCNGC27, we performed virus-induced gene silencing (VIGS) in kenaf and overexpression in Arabidopsis thaliana. Silencing of HcCNGC27 in kenaf resulted in a dwarf phenotype and reduced drought stress tolerance, evidenced by decreased antioxidant enzyme activities, increased reactive oxygen species (ROS) accumulation, and decreased osmoregulatory substances content. Additionally, the expression levels of antioxidant enzyme-related genes and stress-responsive genes were markedly down-regulated in the silenced lines. Conversely, overexpression of HcCNGC27 in Arabidopsis thaliana enhanced drought stress tolerance, characterized by stronger protective enzyme activity, better ROS scavenging capacity, improved osmotic adjustment, higher total chlorophyll content, lower death rate, and significant up-regulation of stress-responsive genes. Moreover, overexpression of HcCNGC27 delayed flowering in Arabidopsis thaliana, as indicated by qRT-PCR analysis showing significant down-regulation of AtFT and AtSOC1 and up-regulation of AtFLC in the overexpression lines compared to wild-type controls. In summary, HcCNGC27 emerges as a dual-function regulator enhancing drought tolerance via ROS scavenging and osmotic adjustment while delaying flowering may through modulation of the FT/SOC1/FLC pathway.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe