IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0011

Utsav Surati, Saket K Niranjan, Rakesh Kumar Pundir, Ymberzal Koul, Vikas Vohra, Ravi Kumar Gandham, Amod Kumar

{"title":"Comprehensive whole genome sequence analysis unravels QTLs and genes under selection in Indian native riverine buffalo.","authors":"Utsav Surati, Saket K Niranjan, Rakesh Kumar Pundir, Ymberzal Koul, Vikas Vohra, Ravi Kumar Gandham, Amod Kumar","doi":"10.1139/gen-2025-0011","DOIUrl":"https://doi.org/10.1139/gen-2025-0011","url":null,"abstract":"During evolution, organisms evolve mainly through natural and artificial selection, leaving distinctive signatures on genomic coordinates. Such genomic regions offer valuable insights into the molecular mechanisms that influence quantitative traits. India harbours a diverse buffalo population with Murrah breed exhibiting exceptional milk production and quality, notably a high fat and solids-not-fat content. Therefore, the present investigation focused on exploring selection signatures within the genome of the Murrah buffalo through whole-genome resequencing. A total of 17 472 799 SNPs were identified, which were further utilized for identification of selection signatures using site frequency spectrum-based Tajima's D and Nucleotide Diversity; and linkage disequilibrium-based iHS approaches. A total of 248 regions under selection overlapped with 64 QTLs across various traits (milk, production, reproduction, meat and carcass, health, and exterior) on chromosomes 5, 9, and 17. A majority of the identified QTLs (39) were associated with milk-related traits, with 27 QTLs specifically linked to milk fat content. Notably, genes such as ARHGAP26, ADGRL3, and SUCLG2 mapped within the QTLs under selection are implicated in milk traits, while XPR1 is associated with growth. Hub genes included RPL23A, ADGRL3 (milk); AP3B1, TXN2 (reproduction); CDK6, IGF2R (body confirmation), and HSPA9 (heat tolerance). This study lays the groundwork for targeted breeding efforts aimed at enhancing milk production in buffalo.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","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":"145988705","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

The Cucumis sativus kinome: identification, annotation, and expression patterns in response to powdery mildew infection. 黄瓜激酶：白粉病感染的鉴定、注释和表达模式。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0044

Francisco Cleilson Lopes Costa, Welison Andrade Pereira

{"title":"The Cucumis sativus kinome: identification, annotation, and expression patterns in response to powdery mildew infection.","authors":"Francisco Cleilson Lopes Costa, Welison Andrade Pereira","doi":"10.1139/gen-2025-0044","DOIUrl":"10.1139/gen-2025-0044","url":null,"abstract":"Protein kinases (PKs) are key regulators of plant development and responses to biotic and abiotic stresses. However, a comprehensive characterization of this superfamily remains lacking in cucumber (Cucumis sativus), particularly regarding its role in powdery mildew resistance caused by Podosphaera xanthii. Here, we identified and characterized the cucumber kinome using Hidden Markov Models (HMMs), revealing 835 PKs distributed across seven chromosomes and classified into 20 groups and 123 families, with RLKs being the most abundant. Gene structure, domain composition, and subcellular localization analyses highlighted substantial structural and functional diversity. Tandem and whole-genome duplication events contributed significantly to PK expansion. Transcriptomic analyses using RNA-seq data from resistant and susceptible cultivars inoculated with P. xanthii revealed between 8 and 105 differentially expressed PK genes (DEGs), depending on the comparison. A greater number of PK DEGs were detected in susceptible genotypes, many of which are putatively associated with signaling pathways and cell cycle regulation. The expression of specific RLKs, MAPKs, CAMKs, and cyclin-dependent kinases suggests their role in defense responses. These findings enhance our understanding of the cucumber kinome and signal the potential of specific PKs in plant-pathogen interactions, providing a foundation for future functional studies and resistance-focused breeding strategies.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-15"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289785","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

Integrating behaviour and microbiomes into considerations of bee health. 将行为和微生物组纳入蜜蜂健康考虑。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0047

Phuong N Nguyen, Sandra M Rehan

引用次数: 0

DESeq2-MultiBatch: batch correction for multi-factorial RNA-seq experiments. DESeq2-MultiBatch：多因子RNA-seq实验的批量校正。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0049

Julien Roy, Adrian S Monthony, Davoud Torkamaneh

引用次数: 0

Technological advances in trait development: from conventional breeding and untargeted mutagenesis to precision genome editing. 性状发育的技术进展：从传统育种和非靶向诱变到精确基因组编辑。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0020

Ladan Ajdanian, Sylvain Villot, Benjamin Karikari, Davoud Torkamaneh

{"title":"Technological advances in trait development: from conventional breeding and untargeted mutagenesis to precision genome editing.","authors":"Ladan Ajdanian, Sylvain Villot, Benjamin Karikari, Davoud Torkamaneh","doi":"10.1139/gen-2025-0020","DOIUrl":"10.1139/gen-2025-0020","url":null,"abstract":"Plant biotechnology has revolutionized modern agriculture by enabling precise and efficient crop improvement strategies. This review explores the evolution of selective breeding, mutation breeding, and precision breeding, highlighting their applications in Canada's agricultural sector. Conventional selective breeding has been instrumental in developing high-yielding and disease-resistant cultivars, while mutation breeding, through physical and chemical mutagenesis, has introduced valuable genetic diversity. The advent of transgenic breeding allowed for the direct insertion of foreign genes, leading to the development of crops with herbicide tolerance, pest resistance, and improved nutritional content. However, concerns over regulatory restrictions and public acceptance have driven the rapid adoption of genome editing tools, which enable precise modifications without introducing foreign DNA. Canada has played a key role in applying these biotechnological innovations, successfully developing genetically modified canola, CRISPR-edited wheat, stress-resistant soybean, and barley and oat cultivars improved for stress resistance and yield. While each breeding approach presents distinct advantages and limitations, integrating conventional and molecular techniques is essential for maximizing genetic potential, ensuring agriculture, and effectively food security challenges.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145488205","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

Low complexity (A/C)GG repeats and m¹A methylation sites in 5' UTRs regulate gene expression. 低复杂度（A/C）GG重复序列和5 ' UTRs中的m1 A甲基化位点调控基因表达。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0071

Zachery W Dickson, Megan Bilodeau, Daniel L Ruiz, G Brian Golding

{"title":"Low complexity (A/C)GG repeats and m1A methylation sites in 5' UTRs regulate gene expression.","authors":"Zachery W Dickson, Megan Bilodeau, Daniel L Ruiz, G Brian Golding","doi":"10.1139/gen-2025-0071","DOIUrl":"10.1139/gen-2025-0071","url":null,"abstract":"Repetitive and compositionally biased low-complexity (LC) motifs appear in biological sequences where they interact with the machinery controlling the abundance of their host molecules. They can have significant impacts on physiological function, and act as raw material for evolution of regulatory motifs. The extent to which LC motifs affect abundance is not known. Even definitions of LC sequences are not well established, let alone which motifs exists in LC sequences, and which of those are abundance associated. To fill these knowledge gaps for post-transcriptional impacts of LC motifs, we integrated data from the GTEx project, PaxDb, and the IGSR. We establish definitions for LC motifs in both RNA and protein sequences. We observed that the presence of LC motifs in the 5' untranslated regions (UTRs) were positively associated with transcript abundance. We present a method to de novo identify abundance associated motifs and identified trinucleotide repeats of (A/C)GG as most strongly abundance associated. We observed that m1A methylation sites were strongly associated with both LC motifs and abundance, an effect which is amplified as methylation signatures from unspecialized RNA-seq increased. Together, our results demonstrate that LC motifs play important roles in regulating gene expression.","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":"145943335","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

Resistance genes against yellow rust pathogen in Triticum spelta: a possible new Yr resistance gene in accession IARI276 and Yr5 presence confirmed in PI348764. 小麦黄锈病的抗性基因：在PI348764中发现了可能的新抗病基因IARI276和Yr5。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0171

Lovely Arya, Malavika N Shal, M Niranjana, S K Jha, Madhu Patial, M S Saharan, N Mallick, K Raghunandan, A Priyanka, D P Walia, S M S Tomar, Vinod

{"title":"Resistance genes against yellow rust pathogen in Triticum spelta: a possible new Yr resistance gene in accession IARI276 and Yr5 presence confirmed in PI348764.","authors":"Lovely Arya, Malavika N Shal, M Niranjana, S K Jha, Madhu Patial, M S Saharan, N Mallick, K Raghunandan, A Priyanka, D P Walia, S M S Tomar, Vinod","doi":"10.1139/gen-2024-0171","DOIUrl":"10.1139/gen-2024-0171","url":null,"abstract":"Yellow/stripe rust caused by Puccinia striiformis f. sp. tritici is a major biotic stress in global wheat production. Introgression lines derived from the Triticum spelta accessions PI348764 and IARI276 showed high levels of yellow rust resistance at seedling and adult plant stage. The Yr5 gene located on 2B chromosome was previously the only stripe rust resistance gene described in T. spelta gene pool. By genotyping parental and introgressed material with markers linked with the Yr5 gene, we demonstrate that PI348764 likely carries Yr5, and that it appears to be absent from IARI276. By employing a combination of methods, including screening for adult plant resistance and seedling resistance at multiple field trials, bulked segregant analysis (BSA) on F5 families, and genotyping using wheat Breeders' 35K array, we show that YrIARI276 is a novel stripe rust resistance gene with putative chromosomal locations on 1BL, 1DL, 5AL, or 7BL. Furthermore, genetic analysis revealed that YrIARI276 showed a goodness of fit to Mendelian ratios for a single dominant gene. As the gene is distinct from Yr5 and the chromosomal location is unique from earlier reported Yr genes, it will be useful in improving diversity of Yr gene repertoire in disease resistance breeding programmes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-11"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604688","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

Satellitome analysis on Microtus thomasi (Arvicolinae) genome, a mammal species with high karyotype and sex chromosome variations. 对具有高度核型和性染色体变异的哺乳动物--Microtus thomasi（Arvicolinae）基因组进行卫星组分析。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0141

Gaël Aleix-Mata, Eugenia E Montiel, Pablo Mora, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez

{"title":"Satellitome analysis on Microtus thomasi (Arvicolinae) genome, a mammal species with high karyotype and sex chromosome variations.","authors":"Gaël Aleix-Mata, Eugenia E Montiel, Pablo Mora, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez","doi":"10.1139/gen-2024-0141","DOIUrl":"10.1139/gen-2024-0141","url":null,"abstract":"The voles of the Microtus thomasi/Microtus atticus species complex (Arvicolinae) display extensive karyotypic variation, in the number of autosomes and the morphology of sex chromosomes. We analyzed the satellitome of Microtus thomasi and identified 17 satellite DNA (satDNA) families, corresponding to 6.704% of the genome. Homogenization and divergence analyses showed that some satDNA families are more homogeneous, indicative of recent amplification, while others displayed higher variation, suggesting ancient amplification. Twelve of the satDNA families are conserved across Arvicolinae with a substantial variation in the abundance and the composition. These results support the \"library\" hypothesis, where a shared collection of satDNAs exists across related species, with differential amplification driving species-specific genomic profiles. Localization analysis demonstrated that an increased number of satDNA families are localized in the pericentromeric and the heterochromatic regions of autosomes and sex chromosomes. Our results suggest that the heterochromatin of the X and Y chromosomes co-evolved and that satDNA families might have contributed to the chromosomal rearrangements involved in the karyotypic variation and sex chromosome polymorphism of the chromosomal races. Our study contributes to a deeper understanding of the evolutionary mechanisms underlying karyotype diversification in Microtus species, which exhibit some of the highest rates of karyotypic variation among mammals.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398732","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

The filamins of Drosophila. 果蝇的典型和非典型丝状结构。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0159

Tiara Mulder, Jennifer Johnson, Nicanor González-Morales

引用次数: 0

Peroxisome inter-organelle cooperation in Drosophila. 果蝇的过氧物酶体细胞器间合作

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0082

Andy Y Cheng, Andrew J Simmonds

{"title":"Peroxisome inter-organelle cooperation in Drosophila.","authors":"Andy Y Cheng, Andrew J Simmonds","doi":"10.1139/gen-2024-0082","DOIUrl":"10.1139/gen-2024-0082","url":null,"abstract":"Many cellular functions are compartmentalized within the optimized environments of organelles. However, processing or storage of metabolites from the same pathway can occur in multiple organelles. Thus, spatially separated organelles need to cooperate functionally. Coordination between organelles in different specialized cells is also needed, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Peroxisomes coordinate with other organelles including mitochondria, endoplasmic reticulum, lysosomes, and lipid droplets. This functional coordination requires, or is at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545118","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

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