IF 1.9 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":"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":1.9,"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 1.9 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":1.9,"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

The genomic impacts of rapid range expansions. 快速范围扩展对基因组的影响。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0065

Zach S Balzer, Amanda D Roe, Catherine I Cullingham, David W Coltman

{"title":"The genomic impacts of rapid range expansions.","authors":"Zach S Balzer, Amanda D Roe, Catherine I Cullingham, David W Coltman","doi":"10.1139/gen-2025-0065","DOIUrl":"10.1139/gen-2025-0065","url":null,"abstract":"Human-mediated change has resulted in the expansion of many species into novel habitats. Range expansions have been described demographically as either pulled or pushed, depending on the number of individuals on the leading front, and can leave distinct genomic signatures within the genome. The recent expansions of Agrilus planipennis, Lycorma delicatula, and Dendroctonus ponderosae represent different types of range expansion which can be analyzed by coupling rigorous monitoring of recent expansions with whole-genome assemblies to provide a strong comparative framework with which to study the genomic signatures of expansion type. Here, we synthesize range expansion theory in the context of these recent expansions and generate hypotheses on the expected patterns of genomic change. We then outline statistical and genome-structural methods that can be used to identify putatively adaptive loci, leveraging the increased genomic resolution provided by whole-genome assemblies. Finally, we complement the overarching expansion hypotheses with a discussion of using a top-down approach to identify loci under selection, using cold tolerance traits as an example. With these methods we can better understand the risk of further spread and persistence of these expanding insect populations, as well as establish a framework for quantifying the adaptive potential of other expanding species.","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":"147941235","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

Diacylglycerol kinase promotes forgetting of aversive olfactory memory in Drosophila. 二酰基甘油激酶促进果蝇厌恶嗅觉记忆的遗忘。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0030

Olivia Kim, Dana C Guhle, Jacob A Berry

{"title":"Diacylglycerol kinase promotes forgetting of aversive olfactory memory in Drosophila.","authors":"Olivia Kim, Dana C Guhle, Jacob A Berry","doi":"10.1139/gen-2026-0030","DOIUrl":"10.1139/gen-2026-0030","url":null,"abstract":"Decades of neuroscience research utilizing Drosophila has led to enormous strides in uncovering genes that positively support the ability to form new memories or consolidate them for the long-term. However, recent research has revealed the existence of more rare but equally important memory suppressor genes whose normal function is to limit memory formation or even promote active forgetting. Here we report that RNAi targeting of diacylglycerol kinase (dgk), a regulator of lipid signaling, within the mushroom body memory circuitry, specifically enhances aversive olfactory memory retention while leaving learning and sensory-motor behavioural controls unaffected. Furthermore, memory retention is enhanced when targeting dgk in these circuits with two additional RNAi lines. Finally, using in vivo functional imaging, we offer evidence that dgk plays a role in regulating baseline synaptic transmission of memory circuits. While the exact mechanism for Dgk's synaptic effects and the implications for memory storage remain unclear, our findings implicate lipid signaling via Dgk as an important regulator of active-forgetting pathways. This work builds on our prior understanding of the importance of lipids in cognition by extended their role to memory suppression and active forgetting.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-7"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257828","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

Transposable element dynamics in Drosophila suzukii: characterization and implications for food consumption-related genes. 铃木果蝇的转座因子动力学：表征及其对食物消费相关基因的影响。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0096

Simón Gaviria-Orrego, Juan A Gallego-Romero, Doris Vela, Romain Guyot, Gustavo Isaza, Simon Orozco-Arias

{"title":"Transposable element dynamics in Drosophila suzukii: characterization and implications for food consumption-related genes.","authors":"Simón Gaviria-Orrego, Juan A Gallego-Romero, Doris Vela, Romain Guyot, Gustavo Isaza, Simon Orozco-Arias","doi":"10.1139/gen-2025-0096","DOIUrl":"10.1139/gen-2025-0096","url":null,"abstract":"Drosophila suzukii, a species native to southeast Asia, is a major pest of berry and stone fruit crops. This species has invaded Europe and the Americas in just a few decades, becoming a global concern to agriculture. In contrast to other flies, D. suzukii infests ripening fruits, causing substantial economic losses worldwide. Nevertheless, genomic studies on this species remain insufficient, especially in transposable elements (TEs), which constitute nearly half of its genome and represent a substantially larger genomic fraction than in most other Drosophila species. Given their ability to reshape genome structure and influence gene regulation, TEs have been implicated in adaptive and invasive processes across diverse organisms. Therefore, this study characterized the dynamics of TEs in the genome of D. suzukii by developing a new manually curated reference TE library and generating a comprehensive genome-wide TE annotation employing bioinformatics techniques. Our analysis of TE dynamics highlights key associations between TEs and food consumption-related genes that are unique to the D. suzukii genome and absent in the model species Drosophila melanogaster, which infests rotten fruits. These findings provide new insights about food selection in this species, offering potential targets for developing improved pest management strategies in fruit production.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-16"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148792286","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

Insights on the vegetal diet of Blue-and-yellow Macaw (Ara ararauna (Linnaeus, 1758)) in an urban area from Central-West Brazil, by DNA metabarcoding. 利用DNA元条形码研究巴西中西部城市地区蓝黄金刚鹦鹉（Ara ararauna; Linnaeus, 1758）的植物性饮食。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0124

Frederico N Ferreira, Jeferson V Ramos, Larissa Tinoco, Kamilla M Almeida, Maria Eduarda M Nascimento, Neiva M R Guedes, Leila S Ullmann, Aline P Lorenz, Gecele M Paggi

{"title":"Insights on the vegetal diet of Blue-and-yellow Macaw (Ara ararauna (Linnaeus, 1758)) in an urban area from Central-West Brazil, by DNA metabarcoding.","authors":"Frederico N Ferreira, Jeferson V Ramos, Larissa Tinoco, Kamilla M Almeida, Maria Eduarda M Nascimento, Neiva M R Guedes, Leila S Ullmann, Aline P Lorenz, Gecele M Paggi","doi":"10.1139/gen-2025-0124","DOIUrl":"10.1139/gen-2025-0124","url":null,"abstract":"Studying animal diets can be of great value to conservation biology; however, identifying diet items by observation can be challenging, constrained by factors like habitat structure, observer distance, and climatic conditions. Our aim was to evaluate the diet of the free-living Blue-and-yellow Macaw in an urban area of Central-West Brazil, using DNA metabarcoding. Cloacal swab samples were collected in nests during the nestlings' monitoring season. After eDNA extractions, the nuclear internal transcribed spacer (ITS) and the chloroplast psbA-trnH intergenic regions were amplified and sequenced using the Oxford Nanopore Technologies MinION. Blastn was performed using a local database to analyze our sequences. The most abundant taxa detected included pink ipê (Handroanthus impetiginosus), amate (Ficus obtusifolia), and mango (Mangifera indica) at central nest; and queen's crape myrtle (Lagerstroemia speciosa), java plum (Syzygium cumini), pequi (Caryocar brasiliense), peterebi (Cordia trichotoma), and mango at peripheral nest. Our findings showed that DNA metabarcoding provides a more comprehensive and detailed assessment of the diet of Blue-and-yellow Macaw, complementing traditional methods and underscoring its value as a powerful and sensitive tool for advancing ecological and conservation studies.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-7"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148850454","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

Unraveling evolutionary relationships in the Sida generic alliance (Malvaceae, Malvoideae): a phylogenetic and cytotaxonomic overview. 揭示西达属联盟（malvacae, Malvoideae）的进化关系：系统发育和细胞分类学综述。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0118

Harrison Luiz Santos Rocha, Jefferson Carvalho-Sobrinho, Matheus Colli-Silva, Gustavo Souza

{"title":"Unraveling evolutionary relationships in the Sida generic alliance (Malvaceae, Malvoideae): a phylogenetic and cytotaxonomic overview.","authors":"Harrison Luiz Santos Rocha, Jefferson Carvalho-Sobrinho, Matheus Colli-Silva, Gustavo Souza","doi":"10.1139/gen-2025-0118","DOIUrl":"https://doi.org/10.1139/gen-2025-0118","url":null,"abstract":"Sida (Malvaceae), the largest Malveae-Abutilinae member, has poorly defined morphological limits which overlaps with 11 phylogenetically closely related genera that comprises the \"Sida generic alliance\". The 12 genera are distributed in the tropics especially in Brazil where one third of its species diversity is found. Evolutionary relationships within Sida generic alliance remain unresolved due to morphological convergence, limited taxon sampling, and lack of integrative approaches including cytogenetic data. We reconstructed the phylogeny of Sida and allied genera using a multilocus dataset (nuclear ITS and seven plastid loci) including 193 species classified in 19 genera and analyzed chromosome evolution using cytogenetic data (chromosome number) for 79 species of the 19 genera. The phylogeny recovered seven clades-Abutilon, Bakeridesia, Callianthe, Gaya, and three Sida clades (I-III)-and confirmed the polyphyly of Sida, the largest genera. We detected reticulate evolution, with incongruence between nuclear and plastid topologies. Chromosome number ranged from 2n = 12 to 60 and represented synapomorphies for most clades. Ancestral character reconstruction indicated that ascending dysploidy and polyploidy predominated in karyotype evolution of Sida and allied genera. Our results reveal taxonomic incongruence in current classifications probably related to reticulate evolution. A generic-level taxonomic revision is necessary and should rely on integrated phylogenetic and karyotypic evidence. This study provides a framework for phylogenetic systematics and emphasizes the role of Brazil as a hotspot for plant genomic research.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","pages":"1-15"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148976670","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 1.9 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

A Drosophila teissieri I-element retrotransposon's ORF1p shows RNA binding cis-preference in the D. melanogaster female germline. 果蝇i -元件反转录转座子ORF1p在黑腹果蝇雌性种系中显示RNA结合顺式偏好。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0028

Lauren M Miller, Denise V Clark

{"title":"A Drosophila teissieri I-element retrotransposon's ORF1p shows RNA binding cis-preference in the D. melanogaster female germline.","authors":"Lauren M Miller, Denise V Clark","doi":"10.1139/gen-2026-0028","DOIUrl":"10.1139/gen-2026-0028","url":null,"abstract":"The transposable I-element from Drosophila melanogaster encodes an RNA-binding protein ORF1p required for its retroansposition. ORF1p binds single-stranded DNA and RNA in vitro nonspecifically. If this nonspecific RNA binding occurs in the germline, then we hypothesize that it plays a role in the production of heritable retrocopies of genes other than the I-element. The goal of this study was to test this hypothesis by investigating the specificity of ORF1p RNA binding in the female germline. To this end, we cloned a D. teissieri I-element. We first tested D. melanogaster strains transgenic for this element for its RNA and protein expression, and its transposition, and demonstrated that it has similar properties to those reported for previously isolated D. teissieri and D. melanogaster I-elements. Then, using RNA immunoprecipitation of epitope-tagged HAORF1p from ovary extracts, followed by high-throughput sequencing (RIP-seq), we found that HAORF1p binds RNA in cis with high specificity. Therefore, the I-element ORF1p does not appear to play a role in generating retrocopies by binding host cellular RNAs in trans in the female germline, unless it binds these RNAs rarely or with low affinity.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148381990","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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