Journal of Genetics最新文献

{"title":"Full-length transcriptome sequencing and identification of skin colour-associated genes in red tilapia.","authors":"Zhao Chen, Suprita Kalra, Cailin Huang, Huaping Zhu, Shan Xiao, Dayan Zhou, Huanhuan Su, Yumei Xiang, Zigui Chen, Shouou Wen, Heyong Zhao, Dongmei Ma, Zongwei Yuan, Hongfei Xu","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Red tilapia has gained increasing popularity worldwide in the commercial aquaculture production due to its rapid growth and delightful taste. However, the occurrence of skin colour variation poses a significant challenge to the advancement of commercial culture. Furthermore, the molecular regulatory mechanism and genetic basis for the distinct skin colouration in red tilapia remain undisclosed. In this study, a comprehensive transcriptome analysis was conducted on red tilapia with different skin colour by integrating PacBio Iso-seq technology with Illumina short-read sequencing methods. A total of 41.38 Gb of clean data was generated, resulting in the acquisition of 30,970 transcripts. Among them, 10,829 transcripts were successfully annotated in at least one public database. In addition, 10,827 coding sequences, 452 transcription factors, and 781 lncRNAs were identified in new transcripts. Furthermore, we performed RNA-seq analysis to identify skin colour-associated genes in red tilapia with three colour spots (white spots, W; black spots, B; red spots, R). The results revealed the identification of 278 differentially expressed genes (DEGs) between the comparison groups, which included B vs R, B vs W, and WvsR.Amongthem, some known genes were found to be involved in regulating the skin pigment synthesis, including PMEL, Wnt-4, melanoregulin and ALK in red tilapia with different skin colour. In addition, some pathways, including melanogenesis (ko04916), ECM receptor interaction (ko04512), Hedgehog signaling pathway (ko04340) and steroid hormone biosynthesis (ko00140), were associated with the skin pigment synthesis in red tilapia. Furthermore, the quantitative real-time PCR analysis confirmed a moderate correlation (coefficient of 0.68) between the results obtained from the qPCR and RNA-seq methodologies. In summary, our findings will significantly contribute to the enhanced comprehension of the molecular regulatory mechanisms underlying the variation in skin colour observed in red tilapia..</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitotic karyotyping and FISH mapping of the gender-specific locus indicate an advanced XY system in <i>Hippophae rhamnoidesa</i>.","authors":"Manisha Jhajhariya, Yash Mangla, Sachin Singh Sorokhaibam, Shailendra Goel, Rajesh Tandon","doi":"","DOIUrl":"","url":null,"abstract":"<p><p><i>Hippophae rhamnoides</i> ssp. <i>turkestanica</i>, a subdioecious plant inhabiting the cold desert of the Indian Himalaya, has gained immense recognition for its nutritional and medicinal values. In recent years, the plant species has proven to be a suitable system to understand the evolution of dioecy. Despite its biological significance, the cytogenetics of this dioecious plant is unclear due to various conflicting accounts of its X-Y chromosome system, particularly the length of Y-chromosome. In this study, we resolved these ambiguities through comprehensive cytogenetic analyses across diverse western Himalayan populations. Using morphometric analysis and fluorescence <i>in situ</i> hybridization (FISH) with a gender-specific marker (HRMSSR), we confirmed homomorphic XX chromosomes in females and heteromorphic sex-chromosomes in males with a notably smaller Y-chromosome. The investigation also revealed a predominant somatic chromosome number of 2<i>n</i> = 24, although minor deviations (2<i>n</i> = 18, 20, 22) appeared at the seed level. These findings highlight an evolutionarily advanced sex-chromosome system. This first detailed cytogenetic investigation of Himalayan Seabuckthorn provides critical insights into the chromosomal architecture, laying a crucial foundation for future evolutionary, genomic, and conservation studies in the species.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization of individuals with RASopathies: Spectrum of genetic variants in a large Indian cohort.","authors":"Ambika Srikanth, Tejashwini Vittal Kumar, Jeevana Praharsha Athota, Monisha Morris, Meenakshi Bhat, Sanjeeva Ghanti Narayanachar, Sheela Nampoothiri, Dhanya Yeshodharan, Kalpana Gowrishankar, Gautham Arunachal, Swathi Shetty","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>RASopathies are a group of developmental disorders caused by variations in genes of the RAS/mitogen activated protein kinase (MAPK) pathway and affect 1 in 1000 individuals worldwide. Due to overlapping clinical features, accurate diagnosis is challenging and therefore we used next-generation sequencing (NGS) panels as an effective molecular diagnostic tool. Targeted sequencing was performed on 130 samples using a multigene panel comprising of 21 RASopathy genes. Molecular analysis revealed variations in 74 individuals (57%). Pathogenic or likely pathogenic variations were observed in 60/74 (81%) of the cases, 13 (17.5%) had variant(s) of uncertain significance (VUS), and one novel variant was identified in RASA2 whose pathogenicity has not yet been established. In individuals with Noonan Syndrome, pathogenic variants were identified in eight different genes mainly <i>PTPN11, SOS1, RAF1</i> and <i>LZTR1</i>. Nine clinically diagnosed Cardio-facio-cutaneous syndrome cases harboured variations in <i>BRAF, MAP2K2</i> and <i>MAP2K1</i> The c.34G>A variant in <i>HRAS</i> was seen in all nine individuals diagnosed with Costello syndrome. This study provides a comprehensive molecular and clinical profile of the largest Indian RASopathy cohort. The use of targeted gene panel has increased the variation detection rate in affected individuals.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148218113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Craniometaphyseal dysplasia with severe maxillary hypoplasia due to <i>ANKH</i> gene mutation: A case report.","authors":"Umesh Kumar, Saugat Ray, Amrit Thapa, Baljinder Singh Walia, Barun Kumar Chakrabarty","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Craniometaphyseal dysplasia (CMD) is characterized by metaphyseal dysplasia, sclerosis of the skull base, and craniofacial bone overgrowth. The autosomal dominant form of CMD (OMIM: 123000) is associated with features such as mandibular prognathism, dental misalignment, and bony paranasal bossing. In contrast, the autosomal recessive form (OMIM: 218400) can result in severe distortion of the craniofacial structure, accompanied by complications such as cranial nerve compression, facial palsy, deafness, and visual impairment. Mutations causing CMD have been linked to the <i>ANKH</i> gene sequence variants. This case report describes a 11-year-old male diagnosed with CMD based on clinical and genetic findings. The patient presented with facial asymmetry, mandibular prognathism, delayed intellectual response, and gradual visual impairment, culminating in optic nerve compression and partial blindness. Radiographic evaluation revealed mixed dentition, thickened skull bones, cranial suture fusion, and Chiari I malformation. Biochemical analysis indicated hyperdense bone with normal serum calcium and phosphorus levels. Genetic testing confirmed an autosomal dominant pathogenic variant of a heterozygous nonframeshift deletion mutation of the <i>ANKH</i> gene (c.1124_1126del, p.Ser375del).</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and demographic history of the invasive mussel <i>Mytella strigata</i> in Indian coastal waters.","authors":"T Raahavishree, B Agalya, A Pavan-Kumar, S Sangeetha, A Kathirvelpandian, M Srihari, Asha T Landge, B B Nayak","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The American brackish water mussel, <i>Mytella strigata</i> (Hanley, 1843), is an invasive species with a growing global footprint, recently recorded in the Indian coastal ecosystems. Despite its rapid spread and potential ecological impact, no genetic data are available for Indian populations. We assessed the genetic diversity and population structure of <i>M. strigata</i> with a 683 bp fragment of the mitochondrial cytochrome <i>b</i> (cyt <i>b</i>) gene from 71 individuals collected from six locations along the Arabian Sea and the Bay of Bengal. Sixteen haplotypes were identified. The Vembanad lake and Ennore creek populations on the Kerala/West Coast and Tamil Nadu/East Coast, respectively, had the highest haplotype and nucleotide diversity, whereas otherWest and East Coast populations had very low diversity. AMOVA indicated that 16.7% of the genetic variance occurs among populations, which contrasts with the expectation for a species with a high dispersal of planktonic larvae. The haplotype network includes both shared and population-specific haplotypes, consistent with multiple introduction events and restricted gene flow rather than range expansion from a single source. Neutrality and mismatch analyses showed no significant evidence of demographic expansion, which likely reflects the limited resolution of the short cyt <i>b</i> fragment. The invasion history of <i>M. strigata</i> in India is complex, and is characterized by independent introductions, local diversification, and constrained post-settlement dispersal.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomewide signatures revealing new evidence for selection of important traits in indigenous cattle breeds of Tamil Nadu, India.","authors":"S Vani, D Balasubramanyam, Karanbir Singh, S M K Karthickeyan, K G Tirumurugan, A Gopinathan, P Hepsibha, B Jaya Madhuri","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Scanning genomes for selection signals could illuminate the impact of domestication, natural, and artificial selection on the phenotypic traits of cattle breeds. The present study investigated the diverse genomic selection signatures using whole genome sequencing data from 15 pooled samples of five indigenous cattle breeds of Tamil Nadu: Alambadi, Bargur, Kangayam, Pulikulam, and Umblachery. Two approaches, namely composite likelihood ratio (CLR) and fixation index (<i>F_ST</i>), were employed to detect selection signatures from the 1,390,449 filtered single-nucleotide polymorphisms. The analysis identified 7250 and 806 genomic regions containing selective sweeps in 1238 and 101 candidate genes using CLR and <i>F_ST</i> methods, respectively. These regions were predominantly associated with production traits (<i>PAIPI, NNT</i> and <i>OCIAD1</i>), coat colour (<i>MC1R, KIT, KDR</i> and <i>PDGFRA</i>), disease resistance (<i>TCF25, CDH15</i> and <i>SPIRE2</i>), and adaptation to tropical climates (<i>SLC22A31</i> and <i>SPG7</i>). Particularly, six regions were shared across all the five cattle breeds, of which, five were intergenic regions and one had a candidate gene, <i>GALNTL6</i>, associated with susceptibility to bovine tuberculosis. A total of 12 candidate genes were common between CLR and <i>F_ST</i> methods, relating to production, disease resistance, and behavioural traits. NETWORK analysis revealed six candidate genes allied with calving ease (<i>JAK1</i> and <i>DOCK1</i>), milk fat yield (<i>ITGA1</i>), bovine respiratory disease susceptibility (<i>ITGA3</i> and <i>ITGAL</i>), and meat and carcass traits (<i>EPS15L1</i>). This study presents the first genomewide map of selective sweeps in Tamil Nadu cattle breeds, providing insights into selection signatures and candidate genes that could enhance genomeassisted breeding for improved production and health.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First draft genome and genetic diversity analysis of the economically important and vulnerable tree species Saraca asoca (Roxb.) W.J. de Wilde.","authors":"P Mahalakshmi, Santhosh N Hegde, Malali Gowda, Abdul Kareem, M Anbarashan, Noorunnisa Begum, Subrahmanya Kumar Kukkupuni, Pavithra Narendran","doi":"","DOIUrl":"","url":null,"abstract":"<p><p><i>Saraca asoca</i>(Roxb.) Wilde. (Ashoka tree), a culturally revered and pharmaceutically valuable species endemic to the Indian subcontinent, is currently listed as vulnerable on the IUCN Red List due to habitat loss and overharvesting. Saraca asoca is known for its extensive pharmacological properties. In particular, its bark is widely used in the treatment of menorrhagia, dysfunctional uterine bleeding, hemorrhagic dysentery, and other gynecological disorders, and it holds a prominent place in Ayurvedic medicine. Despite its longstanding use in traditional medicine, no genomic resources are available for this species. Here, we present the first draft genome of S. asoca, assembled using Illumina paired-end reads into a genome of 1.6 Gb, covering 76% of the estimated genome size. A total of 63,913 proteincoding genes were predicted. Pathway analysis identified key enzymes and regulators in flavonoid and phenylpropanoid biosynthesis pathways, including chalcone synthases, flavanone 3-hydroxylase, and UDP-glucosyltransferases. We analyzed the genetic diversity of 49 Saraca asoca samples from Kolluru and other locations in southern India using genotyping by sequencing (GBS). Analysis of 49 samples established genetic diversity relationships using a distance matrix. Population structure analysis revealed three distinct genetic clusters corresponding to geographic origin. A survey of simple sequence repeats (SSRs) identified 584,615 SSRs, with 236,123 sequences containing SSRs. This comprehensive genomic analysis of Saraca asoca provides critical insights for conservation efforts aimed at preserving this vulnerable species.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148404912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide CRISPR/Cas9 screening reveals lipid metabolism and inflammatory signalling as modulators of ganoderic acid DM cytotoxicity.","authors":"Nimo Abdullah, Jacqueline Lewis, Prakash Arumugam","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Ganoderic acid DM (GA-DM), a triterpenoid derived from Ganoderma lucidum, exhibits anti-cancer and anti-diabetic activities, but the underlying mechanisms of action remain unclear. To identify genetic modulators of the GA-DM response, we conducted a genome-wide CRISPR/Cas9 knockout screen in human melanoma cells. The screen revealed key roles for genes regulating lipid metabolism and inflammatory signalling, particularly those involved in the SREBP (sterol regulatory element-binding protein) and NF-jB (nuclear factor kappa-light-chain-enhancer of activated B cells) pathways, in the cellular response to GA-DM. While loss of genes involved in the regulation of cholesterol biosynthesis conferred resistance to GA-DM, disruption of genes involved in ubiquitin-mediated proteolysis and the Hippo pathway sensitised cells to GA-DM. Inflammatory genes enriched at later time points suggests that a delayed cellular response contributes to cytotoxicity. Our findings propose a mechanistic model wherein GA-DM perturbs lipid and inflammatory pathways to exert cytotoxic effects and highlight potential targets to enhance its therapeutic efficacy. This work demonstrates the utility of functional genomics in elucidating the mechanisms of action of natural products and guiding rational drug development.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148404111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting signals of selection at the <i>EDAR</i> gene in global and Latin American populations.","authors":"Jorge Briceño Moya, Alejandro Díaz Muñoz, Germán Manríquez-Soto, Sergio Flores-Carrasco","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The <i>EDAR</i> gene is a classic target of positive selection in humans, mainly through the nonsynonymous variant rs3827760 (EDARV370A) associated with ectodermal traits. Using high-resolution data from the 1000 Genomes Project, we combined sliding-window F_ST, BayeScan, and extended haplotype homozygosity (EHH) analyses to examine global and Latin American patterns of differentiation. Globally, a strong signal of positive selection was confirmed at <i>EDAR</i>, dominated by the rs3827760 haplotype background and its extended linkage disequilibrium structure. In contrast, within Latin America, differentiation reflected admixture-driven haplotype persistence rather than contemporary selection. A genome-wide FST scan comparing individuals from the upper and lower quartiles of Native American ancestry showed that EDAR lies among the most highly differentiated regions in this contrast, consistent with ancestry-driven haplotype structure rather than post-admixture adaptive evolution. These results indicate that <i>EDAR</i> retains its evolutionary signature globally but not within recently admixed populations, where demographic history rather than selection shapes its genetic landscape.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148880841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and functional insights from detailed computational analysis of <i>Plasmodium</i> repetome.","authors":"Satinder Kaur, Vikash Kumar, Karanbir Singh, Ankita Beh, Arpna A, Prakash Chandra Mishra, Rachna Hora","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Eukaryotic proteomes harbour tandem repeats (TRs) of amino acids that may play critical roles in the biology of organisms. While a few TRs have been shown to contribute to protein structure and function, information about the vast majority of repeat regions remains obscure. This article reports a detailed computational analysis of the repeat content of different <i>Plasmodium</i> species proteomes, identifying <i>P. falciparum</i> (Pf) and <i>P. vivax</i> to be exceptionally rich in TR regions. <i>P. falciparum</i> 'repetome' was found to carry longer TRs, which were majorly present in exported parasite proteins, important for pathogen survival and immune evasion. Short and intermediate TRs of <i>P. falciparum</i> showed a bias towards Asparagine usage, suggesting an evolutionary outcome influenced by replication slippage and positive selection. Gene ontology analysis revealed the largest proportion of TR containing Pf proteins to be involved in binding nucleic acids, proteins and other small molecules. Surprisingly, the <i>Plasmodium</i> specific variable surface antigen (VSA) families known to have roles in immune evasion and cytoadherence were found to contain low repeat content. Our analysis also revealed that all the TR containing VSAs were sero-reactive, where several antigenic peptides were present within the repeats. Three-dimensional structure predictions of TR regions showed several repeats to form ordered super-secondary conformations, which are often reported to facilitate intermolecular interactions. Overall, this comprehensive study provides glimpses into the probable roles of TRs in <i>Plasmodium</i> biology and also suggests a novel method for understanding protein function via characterization of repetitive sequences.</p>","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"105 ","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146213210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}