Genome最新文献 - Book学术

Genotype dependent microbial community restructuring under salinity stress outweighs direct benefits of native microbe inoculation in Hordeum vulgare. 盐胁迫下基因型依赖的微生物群落重组超过了原生微生物接种的直接效益。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-06 DOI: 10.1139/gen-2025-0095

Jack Walter Lewis Royle, Soudeh Farzadfar, John Paul Wasan, Jonathan Bennett

{"title":"Genotype dependent microbial community restructuring under salinity stress outweighs direct benefits of native microbe inoculation in Hordeum vulgare.","authors":"Jack Walter Lewis Royle, Soudeh Farzadfar, John Paul Wasan, Jonathan Bennett","doi":"10.1139/gen-2025-0095","DOIUrl":"https://doi.org/10.1139/gen-2025-0095","url":null,"abstract":"Soil salinization is an escalating threat to global food security under climate change, necessitating innovative strategies to enhance crop resilience. Native microbial inoculants, sourced from salinity-adapted soils, offer a potential avenue for sustainable agricultural adaptation. Here, we evaluated the effects of saline prairie-derived, AMF-enriched microbial inoculants on the growth of barley (Hordeum vulgare) cultivars under a salinity gradient. Greenhouse trials demonstrated that salinity was the dominant constraint on biomass production, but inoculant identity and genotype significantly influenced plant performance and microbial assembly. Inoculant effects on shoot biomass were heterogeneous, with neutral or negative outcomes predominating under saline conditions. Amplicon sequencing of bacterial, fungal, oomycete, and arbuscular mycorrhizal (AMF) communities revealed that salinity strongly restructured microbial diversity and composition, reducing bacterial and fungal evenness. Genotype and inoculant identity shaped fungal communities, while oomycete responses depended on specific plant-microbe pairings. Model selection confirmed that shoot biomass was primarily explained by salinity, with additional contributions from barley genotype, inoculant identity, and fungal evenness. These results demonstrate that microbial community restructuring under salinity stress outweighs direct benefits of native microbial inoculation, and emphasize that successful microbial interventions in salt-affected soils must account for genotype-specific compatibility and stress-driven community dynamics, rather than assuming universal benefits.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145910813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome Mining Algorithm for Identifying Identical Repeat Sequences to Enhance DNA-Based Diagnostic Assays. 识别相同重复序列的基因组挖掘算法以增强基于dna的诊断分析。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-05 DOI: 10.1139/gen-2025-0027

Kalepu Rajeswari, Raksha Poojary, Padival Shruptha, Rajesh Muliyar Krishna, Kapaettu Satyamoorthy, Bobby Paul

{"title":"Genome Mining Algorithm for Identifying Identical Repeat Sequences to Enhance DNA-Based Diagnostic Assays.","authors":"Kalepu Rajeswari, Raksha Poojary, Padival Shruptha, Rajesh Muliyar Krishna, Kapaettu Satyamoorthy, Bobby Paul","doi":"10.1139/gen-2025-0027","DOIUrl":"https://doi.org/10.1139/gen-2025-0027","url":null,"abstract":"A pair of primers that can bind at multiple loci across the genome and randomly amplify multiple copies increases the analytical sensitivity of the currently used diagnostic assays. We developed a novel genome mining algorithm to identify short identical repeat sequences (IRSs) dispersed across the genome. The genome mining algorithm for IRS identification can be accessed from the GitHub portal (https://github.com/BPaul-bioinfoLAB/IRS-Finder). Using this algorithm, we have identified the IRS from five pathogens, namely, gammaherpesvirus, vaccinia virus, Mycobacterium tuberculosis, Plasmodium falciparum, and Phytophthora palmivora. In-silico PCR revealed that these IRSs can amplify multiple nonhomologous regions of variable amplicon sizes via three priming combinations. We further performed a polymerase chain reaction assay with an IRS pair identified from M. tuberculosis. Interestingly, the PCR with single IRS amplified multiple non-homologous copies and even more variable sized copies in pair. These results indicate that the IRS-based diagnostic assays can detect pathogens in case of low-concentration DNA during disease progression. The genome mining algorithm can be used as a translation technology platform for developing highly sensitive varieties of PCR, microarray, loop-mediated isothermal amplification, fluorescence in-situ hybridization based diagnostic assays.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Revealing gene-metabolite interactions in wheat defenses against Pyrenophora tritici-repentis in resistant and susceptible genotypes. 揭示抗性和易感基因型小麦抗小麦焦裂菌的基因-代谢物相互作用。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0026

Larissa Carvalho Ferreira, Flavio Martins Santana, Manfred Beckmann, Luis A J Mur

{"title":"Revealing gene-metabolite interactions in wheat defenses against Pyrenophora tritici-repentis in resistant and susceptible genotypes.","authors":"Larissa Carvalho Ferreira, Flavio Martins Santana, Manfred Beckmann, Luis A J Mur","doi":"10.1139/gen-2025-0026","DOIUrl":"10.1139/gen-2025-0026","url":null,"abstract":"Wheat defenses against Pyrenophora tritici-repentis (Ptr), the cause of tan spot disease, are complex and require further characterization. We previously identified two wheat genotypes, Robigus (resistant) and Hereward (susceptible), and characterized their differentially expressed genes (DEGs) and accumulated metabolites (DAMs) following challenge with Ptr. In this study we uncover coordinated shifts in gene expression and metabolism triggered by Ptr. The DEGs and DAMs from each genotype were integrated using regularized canonical correlation analysis, yielding scale-free networks with 69 745 edges in Robigus and 760 433 in Hereward. In Robigus, hub genes were upregulated at 48 and 96 h post-inoculation and included hst2 (encoding hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2), located within a QTL for Ptr resistance (QTs.fcu-5D locus), a receptor-like kinase, and a late embryogenesis abundant protein (which play roles in cell wall organization). Pathway enrichment showed significant involvement of catalytic activity, chitinase activity, and cell wall metabolic processes. In contrast, Hereward hub genes were mostly downregulated, except for a hexosyltransferase, with enriched pathways related to energy metabolism, such as ATP binding and phosphorylation. These results suggest that cell wall modifications and chitinase activity are part of an effective defense response against Ptr, whereas costly energetic processes may contribute to tan spot susceptibility.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Utilitarian selection signatures co-localized with copy number variation regions in Indian goat breeds revealed through whole-genome re-sequencing. 通过全基因组重测序发现印度山羊品种的功利选择特征与拷贝数变异区共定位。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0029

Nidhi Sukhija, Indrajit Ganguly, K K Kanaka, S P Dixit, Sanjeev Singh, Avnish Bhatia, Rangasai Chandra Goli, Pallavi Rathi

{"title":"Utilitarian selection signatures co-localized with copy number variation regions in Indian goat breeds revealed through whole-genome re-sequencing.","authors":"Nidhi Sukhija, Indrajit Ganguly, K K Kanaka, S P Dixit, Sanjeev Singh, Avnish Bhatia, Rangasai Chandra Goli, Pallavi Rathi","doi":"10.1139/gen-2025-0029","DOIUrl":"10.1139/gen-2025-0029","url":null,"abstract":"This study investigates the selection signatures of 11 Indigenous goat breeds from diverse eco-topographies of India, using whole-genome re-sequencing data from 103 individuals. We identified population-wide copy number variation regions (as well as selection signatures through a variance-stabilizing transformation approach for utility traits. A total of 32 711 polymorphic sites were analyzed, revealing 327 significant and 32 highly significant signatures under selection. Key genes identified in selection signatures include GHR, PLAG1, and MTOR, which play crucial roles in growth, development, and reproductive traits across different utility groups. Notable reproduction-related genes such as ITPR3, ESRRG, and SOX6 were found to be associated with fertility, hormone regulation, and reproductive system. Network analysis revealed ESR1 as a central hub gene forming significant interactions with RUNX2, HDAC2, and BCL2, indicating its vital role in muscle development and metabolism. The MTOR signaling pathway emerged as another crucial hub, connecting with DEPDC5 and SESN1, suggesting its importance in nutrient sensing and metabolic regulation for production traits. Gene ontology analysis of the selection signatures revealed pathways for functional categories between meat, milk, and fiber-producing breeds, reflecting the genetic architecture underlying their specialized phenotypes. Identified selection signatures and hub genes can be used in marker-assisted and genomic selection to improve growth, reproduction, and adaptability in indigenous goats, aiding precision breeding and conservation programs.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145307740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Classical and molecular cytogenetics of Ponerinae ants reveal evolutionary and taxonomic insights. 蚂蚁的经典和分子细胞遗传学揭示了进化和分类学的见解。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0056

Emilly Camila Soares Nobre, Gisele Amaro Teixeira, Linda Inês Silveira, Natália Martins Travenzoli, Luísa Antônia Campos Barros, Hilton Jeferson Alves Cardoso de Aguiar

{"title":"Classical and molecular cytogenetics of Ponerinae ants reveal evolutionary and taxonomic insights.","authors":"Emilly Camila Soares Nobre, Gisele Amaro Teixeira, Linda Inês Silveira, Natália Martins Travenzoli, Luísa Antônia Campos Barros, Hilton Jeferson Alves Cardoso de Aguiar","doi":"10.1139/gen-2025-0056","DOIUrl":"10.1139/gen-2025-0056","url":null,"abstract":"Eleven species of Ponerinae ants belonging to six distinct genera from the Amazon and Atlantic rainforests were characterized by karyotype, distribution of ribosomal genes, microsatellites (GA)n, and telomeric sequences (TTAGG)n. This is the first study mapping microsatellites in Ponerinae ants. The karyotypes ranged from 2n = 12 to 2n = 94. Colonies of Neoponera verenae from the Amazon (n = 31) and Atlantic (2n = 40) rainforests reinforce the hypothesis of a species complex within this taxon. Neoponera globularia workers had a 2n = 21 karyotype, including an unpaired, large metacentric chromosome. Neoponera unidentata workers had 2n = 12 chromosomes, all metacentric, or 2n = 13 chromosomes, with two acrocentric and one unpaired metacentric chromosome. The rearrangements involved are discussed using telomeric (TTAGG)n data. All the analyzed species had a single pair of rDNA clusters mostly located in the pericentromeric region. The distribution of (GA)n microsatellites contrasted with that of AT-rich chromatin and supported the occurrence of chromosome fissions and the subsequent expansion of constitutive heterochromatin in Ponerinae, in addition to inversions in some species. The chromosomal rearrangements discussed herein contribute to our understanding of the mechanisms underlying the karyotypic evolution of Ponerinae. This study underscores the importance of cytogenetics in unraveling the taxonomic characteristics of complex groups.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-16"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification and functional validation of key enzymes related to polysaccharide biosynthesis in Platycodon grandiflorus. 桔梗多糖生物合成关键酶的鉴定及功能验证。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0086

Hui Wang, Sijia Wang, Hanwen Yu, Xiao Liang, Liangping Zha, Shuangying Gui

{"title":"Identification and functional validation of key enzymes related to polysaccharide biosynthesis in Platycodon grandiflorus.","authors":"Hui Wang, Sijia Wang, Hanwen Yu, Xiao Liang, Liangping Zha, Shuangying Gui","doi":"10.1139/gen-2025-0086","DOIUrl":"10.1139/gen-2025-0086","url":null,"abstract":"Platycodon grandiflorus (Jacq.) A. DC., a herbaceous plant belonging to the Campanulaceae family, is recognized for its substantial medicinal properties, attributed to its rich composition of bioactive compounds, including polysaccharides, saponins, and flavonoids. The polysaccharide components have been shown to exhibit significant anti-obesity effects. However, there is a notable lack of research on the biosynthesis of polysaccharides in P. grandiflorus. This study aimed to identify and functionally validate key enzymes involved in the polysaccharide biosynthetic pathway of P. grandiflorus. Based on transcriptomic data, the researchers identified four genes associated with the polysaccharide biosynthetic pathway in P. grandiflorus, specifically including one phosphomannose isomerase gene (PgPMI), one phosphoglucose isomerase gene (PgGPI1), and two phosphomannose mutase genes (PgPMM1 and PgPMM2). The enzymatic activity of genes was verified in Escherichia coli, demonstrating that the recombinant PgPMI protein catalyzes the interconversion of mannose-6-phosphate and fructose-6-phosphate. Additionally, the recombinant PgPMM1 and PgPMM2 proteins were shown to catalyze the interconversion of mannose-1-phosphate and mannose-6-phosphate, while the recombinant PgGPI1 protein is capable of catalyzing the conversion of glucose-6-phosphate to fructose-6-phosphate. This study enhances knowledge of the polysaccharide biosynthetic pathway and underpins subsequent molecular research on polysaccharide metabolism and related physiology.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-11"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146029407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sex and genetic variation interact to modify the response of Drosophila melanogaster to metal stress. 性别和遗传变异相互作用，改变果蝇对金属应激的反应。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0099

Allie K Hutchings, Mitchell R Slobodian, Joshua W R Keeping, Jesse D Petahtegoose, Athena L Wallis, Thomas J S Merritt

{"title":"Sex and genetic variation interact to modify the response of Drosophila melanogaster to metal stress.","authors":"Allie K Hutchings, Mitchell R Slobodian, Joshua W R Keeping, Jesse D Petahtegoose, Athena L Wallis, Thomas J S Merritt","doi":"10.1139/gen-2025-0099","DOIUrl":"10.1139/gen-2025-0099","url":null,"abstract":"Organisms are under nearly continuous stress from anthropogenic contaminants, but the molecular response mechanisms, particularly the variation in these responses, are not well understood. Nickel (Ni) contamination, often associated with mining activity, is known to cause a series of health effects, but surprisingly little is known about individual variation in Ni response. In this study, we quantified the mortality response of Drosophila melanogaster to environmental Ni across a series of lines and both sexes and compared it with that of copper (Cu), a well-characterized metal contaminant. Ni exposure had substantial negative effects that were significantly modified by sex, line, and interactions between the two. Strikingly, these trends in differential responses between the sexes and lines were mirrored in both Ni and Cu. Variation in Ni-driven mortality was correlated with starvation resistance, but not with Ni body burden. This contrast suggests a possible role of starvation resistance, but not body burden, in differential mortality. Across all experiments, sex and line effects were not independent; the level of sexual dimorphism varied significantly and substantially across lines, and line effects differed between the sexes. Overall, the results of this study highlight the fact that an understanding of biology requires examination of both sexes and multiple lines.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-8"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Highly conserved complete organellar genomes of Bangia atropurpurea (Bangiales, Rhodophyta) revealed by refined annotation. 通过精细注释揭示了Bangia atropurpurea （Bangiales, Rhodophyta）高度保守的完整细胞器基因组。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0067

Jie Wang, Yan-De Wang, Yu-Lian Li, Chuan-Ming Hu, Jing Chen, Li-En Yang

{"title":"Highly conserved complete organellar genomes of Bangia atropurpurea (Bangiales, Rhodophyta) revealed by refined annotation.","authors":"Jie Wang, Yan-De Wang, Yu-Lian Li, Chuan-Ming Hu, Jing Chen, Li-En Yang","doi":"10.1139/gen-2025-0067","DOIUrl":"10.1139/gen-2025-0067","url":null,"abstract":"Bangia atropurpurea is the only freshwater species in the ancient order Bangiales, which dates back to approximately 1047 Mya. It was speculated that B. atropurpurea originated from a marine ancestor. However, the timing and mechanism by which this species transitioned from the marine to the freshwater environment remain unclear. Genomic data could shed light on these problems. We provided the complete organellar genomes of a sample of B. atropurpurea from China in the present study. The gene content, genomic organization, tRNA secondary structures and codon usage of the organellar genomes were analyzed. The gene annotations were manually refined. Comparative genomics revealed that the chloroplast genomes in Bangiaceae are highly conserved, whereas the mitochondrial genomes are relatively less conserved. The factors and probable mechanisms that affect the genome were discussed. Genes unique to freshwater or filamentous species could be interesting candidates for the next step of adaptive evolution research. The phylogeny based on genomic data provides solid evidence to split Pyropia into four genera.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosomal dynamics and evidence of differentiation of the proto-sex chromosomes XY in Farlowella oxyrryncha (Loricariidae; Loricariinae). 法罗蝇科原性染色体XY的染色体动力学和分化证据。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0079

Leandro Marajó, Patrik Ferreira Viana, Alex Matheus Viana Ferreira, Victoria Tura, Eliana Feldberg

{"title":"Chromosomal dynamics and evidence of differentiation of the proto-sex chromosomes XY in Farlowella oxyrryncha (Loricariidae; Loricariinae).","authors":"Leandro Marajó, Patrik Ferreira Viana, Alex Matheus Viana Ferreira, Victoria Tura, Eliana Feldberg","doi":"10.1139/gen-2025-0079","DOIUrl":"10.1139/gen-2025-0079","url":null,"abstract":"Farlowella is the second most species-rich genus within Loricariinae; however, cytogenetic data for its species remain scarce. In this study, we employed conventional and molecular cytogenetic procedures on Farlowella oxyrryncha, a species widely distributed across the Amazon and Orinoco River basins. Karyotypic analysis revealed a conserved diploid number (2n = 58), with 12m+22sm+18st+6a, in addition to notable structural variation compared to other species of the genus. The pattern of constitutive heterochromatin (CH) facilitated the characterization of chromosome pairs. Furthermore, a conspicuous sex-linked heteromorphism was detected in chromosome pair 27, suggesting the presence of an XY sex chromosome system. Fluorescence in situ hybridization identified single site of 18S and 5S ribosomal DNA, with 18S colocalizing with U2 small nuclear DNA, simple sequence repeats, and CH. Interstitial telomeric sequences (ITSs) were found in five pairs, with dimorphic ITS patterns in pair 27, suggesting its role as a proto-sexual pair. The colocalization of repetitive sequences in pair 27 suggests that repetitive DNA plays a key role in the early differentiation of sex chromosomes. These findings indicate that F. oxyrryncha is a structurally dynamic lineage and provide new insights into karyotype evolution and sex chromosome differentiation in Loricariidae.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146040859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development and application of new chromosome-specific oligonucleotide probes for Thinopyrum elongatum. 一种新的染色体特异寡核苷酸探针的研制与应用。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0009

Jianing Zhao, Xiangqian Chen, Hao Wang, Xiaofang Cheng, Zi Wang, Yue Guan, Fantao Liu, Zuchun Li, Tingdong Li, Chunhuan Chen, Jixin Zhao, Changyou Wang, Xinlun Liu, TingTing Li, Pingchuan Deng, Wanquan Ji

{"title":"Development and application of new chromosome-specific oligonucleotide probes for Thinopyrum elongatum.","authors":"Jianing Zhao, Xiangqian Chen, Hao Wang, Xiaofang Cheng, Zi Wang, Yue Guan, Fantao Liu, Zuchun Li, Tingdong Li, Chunhuan Chen, Jixin Zhao, Changyou Wang, Xinlun Liu, TingTing Li, Pingchuan Deng, Wanquan Ji","doi":"10.1139/gen-2025-0009","DOIUrl":"10.1139/gen-2025-0009","url":null,"abstract":"The E genome of Thinopyrum elongatum is an important alien genetic resource for the breeding of Triticum aestivum. The purpose of this study was to develop chromosome-specific oligonucleotide probes for Th. elongatum. Based on the Th. elongatum reference genome, 1 522 611 tandem repeats were identified using bioinformatics methods. By further merging tandem repeats using bedtools in sliding windows of 10 kb, we obtained 15 500 high-copy sequences with a copy number exceeding 100. We identified 1609 unique high-copy tandem repeats of Th. elongatum as candidate sequences by comparing them with the wheat reference genome. Based on their chromosome specificity and distribution sites, 19 Th. elongatum oligonucleotide probes were developed and applied to material identification. The results showed that the Oligo-7ES-2 probe produced a clear and stable in situ hybridization signal on the chromosome of the CS-7E addition line material, located on the long arm of 7E chromosome. The Oligo-7ES-2 probe developed in this study can help the traditional E genome GISH probe for mapping chromosomes or chromosome fragments of 7E and 7EL derived lines of wheat and Th. elongatum. This lays a foundation for the efficient identification of exogenous chromosomes of Th. elongatum in wheat genetic improvement.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146018296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0