IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0003

Arash Mohammadi Matak, Yizhu Mu, Seyedeh Mahdiye Mohati, Stephanie Makdissi, Francesca Di Cara

{"title":"Circadian rhythm and immunity: decoding chrono-immunology using the model organism Drosophila melanogaster.","authors":"Arash Mohammadi Matak, Yizhu Mu, Seyedeh Mahdiye Mohati, Stephanie Makdissi, Francesca Di Cara","doi":"10.1139/gen-2025-0003","DOIUrl":"10.1139/gen-2025-0003","url":null,"abstract":"Circadian rhythms are important cellular pathways first described for their essential role in helping organisms adjust to the 24 h day-night cycle and synchronize physiological and behavioral functions. Most organisms have evolved a circadian central clock to anticipate daily environmental changes in light, temperature, and mate availability. It is now understood that multiple clocks exist in organisms to regulate the functions of specific organs. Epidemiological studies in humans reported that disruption of the circadian rhythms caused by sleep deprivation is linked to the onset of immune-related conditions, suggesting the importance of circadian regulation of immunity. Mechanistic studies to define how circadian clocks and immune responses interact have profound implications for human health. However, elucidating the clocks and their tissue-specific functions has been challenging in mammals. Many studies using simple model organisms such as Drosophila melanogaster have been pioneering in discovering that the clock controls innate immune responses and immune challenges can impact circadian rhythms and/or their outcomes. In this review, we will report genetic studies using the humble fruit fly that identified the existence of reciprocal interactions between the circadian pathway and innate immune signaling, contributing to elucidate mechanisms in the growing field of chrono-immunology.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-18"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763889","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 diversity in Crematogaster Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest. 亚马逊雨林中 Crematogaster Lund, 1831 (Formicidae: Myrmicinae) 的染色体多样性。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-09-03 DOI: 10.1139/gen-2023-0130

Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar

{"title":"Chromosomal diversity in Crematogaster Lund, 1831 (Formicidae: Myrmicinae) from the Amazon rainforest.","authors":"Linda Inês Silveira, Gisele Amaro Teixeira, Luísa Antônia Campos Barros, Jorge Abdala Dergam, Hilton Jeferson Alves Cardoso de Aguiar","doi":"10.1139/gen-2023-0130","DOIUrl":"10.1139/gen-2023-0130","url":null,"abstract":"Crematogaster Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical Crematogaster, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five Crematogaster species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2n = 22 chromosomes were observed in Crematogaster erecta Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. Crematogaster aff. erecta had 2n = 28, while Crematogaster limata Smith, 1858, Crematogaster tenuicula Forel, 1904, and Crematogaster sp. had 2n = 38. The telomeric motif (TTAGG) n was found in all five species, and the (TCAGG) n motif was detected in the telomeres of C. limata. This peculiar motif was also detected in the centromeric regions of C. erecta cytotype I. The microsatellite (GA) n was dispersed in the chromosomes of all species studied, which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on Crematogaster.","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":"142125506","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 evolution of genomic organization through chromosomal rearrangements in Arctic charr (Salvelinus alpinus). 北极鲑（Salvelinus alpinus）基因组组织的染色体重排进化。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0180

Christine L Ouellet-Fagg, Anne A Easton, Kevin J Parsons, Cameron M Nugent, Roy G Danzmann, Moira M Ferguson

{"title":"The evolution of genomic organization through chromosomal rearrangements in Arctic charr (Salvelinus alpinus).","authors":"Christine L Ouellet-Fagg, Anne A Easton, Kevin J Parsons, Cameron M Nugent, Roy G Danzmann, Moira M Ferguson","doi":"10.1139/gen-2024-0180","DOIUrl":"https://doi.org/10.1139/gen-2024-0180","url":null,"abstract":"Chromosomal rearrangements (CRs) can play an important role in evolutionary diversification by preserving linkage among favourable alleles through reduced recombination and/or by reducing hybrid fitness due to genomic incompatibilities. Our goal was to determine to what extent CRs contribute to known patterns of genetic variation in Arctic charr (Salvelinus alpinus). To address this goal, we compared genetic linkage maps to identify whole arm CRs and smaller scale structural variants (SVs) such as translocations/transpositions and inversions found in groups of populations that reflect the temporal sequence of geographic isolation events. If CRs contribute to genetic differentiation, we expected that CRs would be specific to glacial lineages, geographic clusters of populations within lineages, and sympatric morphs. We detected fusions and fissions of whole chromosome arms and SV involving translocations/transpositions of the sex-determining gene (sdY) and inversions. Several CRs were shared across populations from the Arctic and Atlantic glacial lineages, Canadian and Icelandic populations within the Atlantic lineage, between two Icelandic populations and sympatric morphs within Icelandic populations, suggesting that their origin predates geographic isolation in glacial refugia. Other CRs were specific to single populations, which suggests a more recent origin of these variants in refugia, during post-glacial recolonization and/or in contemporary populations. Thus, CRs contribute relatively little to known patterns of genetic differentiation at different geographic scales but represent a pool of standing genetic variation for evolution.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-19"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011729","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

Cryptic diversity identified by DNA barcoding reveals the impact of pleistocene climate oscillations on a forest interior spider. DNA条形码鉴定的隐蔽性多样性揭示了更新世气候振荡对森林内部蜘蛛的影响。

IF 1.7 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0028

Mariana Costa Terra, Antonio Domingos Brescovit, Ana Lúcia Dias, Matheus Pires Rincão, Renata da Rosa

{"title":"Cryptic diversity identified by DNA barcoding reveals the impact of pleistocene climate oscillations on a forest interior spider.","authors":"Mariana Costa Terra, Antonio Domingos Brescovit, Ana Lúcia Dias, Matheus Pires Rincão, Renata da Rosa","doi":"10.1139/gen-2025-0028","DOIUrl":"https://doi.org/10.1139/gen-2025-0028","url":null,"abstract":"Quaternary climate oscillations significantly influenced the configuration of the Brazilian Atlantic Forest. In this study, mitochondrial DNA analysis of Enoploctenus cyclothorax (Bertkau, 1880) was conducted to investigate potential cryptic diversity within populations across the state of Paraná, Brazil. Two divergent genetic lineages were identified based on genetic distances, haplotype network, and phylogenetic inference. A phylogeographical break separates the lineages into two geographic regions; one lineage is found exclusively in the eastern region and the other is found mainly in the northern and western regions of the state. The coalescence tree estimates the divergence time between 1.8 million years and 500 000 years ago, period marked by glaciation, suggesting historical forest fragmentation as a potential isolating mechanism. These findings support the hypothesis of independently evolving units within E. cyclothorax, possibly representing cryptic species, though broader sampling and integrative approaches are necessary for taxonomic validation.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145563620","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

Sequence-based identification of polyamine oxidase genes in Sorghum bicolor L. 高粱多胺氧化酶基因的序列鉴定。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0143

Heba T Ebeed, Mohamed El-Zonkorany, Eman Habib, Esraa Ali, Ahmed Zahran, Aya Hamdy Ragab

引用次数: 0

Mining and identification of solitary long terminal repeat (Solo-LTR) presence polymorphisms in the sheep genomes. 绵羊基因组中孤长末端重复序列（Solo-LTR）存在多态性的挖掘与鉴定

IF 1.7 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0012

Ahmed A Saleh, Naisu Yang, Fengxu Wang, Amr M A Rashad, Ali Shoaib Moawad, Cai Chen, Xiaoyan Wang, Bo Gao, Chengyi Song

{"title":"Mining and identification of solitary long terminal repeat (Solo-LTR) presence polymorphisms in the sheep genomes.","authors":"Ahmed A Saleh, Naisu Yang, Fengxu Wang, Amr M A Rashad, Ali Shoaib Moawad, Cai Chen, Xiaoyan Wang, Bo Gao, Chengyi Song","doi":"10.1139/gen-2025-0012","DOIUrl":"10.1139/gen-2025-0012","url":null,"abstract":"The analysis of 51 sheep genomes led to the identification of 3624 high-confidence Solitary Long Terminal Repeats (Solo-LTRs), remnants of Long Terminal Repeat retrotransposons (LTR-RTns). These elements, comprising 3308 absence-type and 316 presence-type sites, are integrated into functional regions of the genome, where they can influence gene structures and regulation. Approximately 4.39% of protein-coding genes and 0.54% of long noncoding RNA genes contain sequences derived from these Solo-LTRs. Analysis across 12 diverse sheep breeds revealed that 83.63% of the tested Solo-LTR sites were polymorphic, demonstrating substantial genetic diversity and highlighting their utility as genetic markers. Furthermore, these elements were linked to key genes governing economically important traits such as growth, immunity, and milk production. Notable genes identified include PAG3, ANXA5, KCNJ6, MX2, and XKR4. The findings confirm that Solo-LTRs are major contributors to genomic diversity and breed-specific adaptation in sheep, providing essential insights for future genetic research and breeding programs.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-16"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145488152","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 degradation strategy of aniline blue by Lysinibacillus sp. 38-6 via genomic analysis. 通过基因组分析揭示Lysinibacillus sp. 38-6降解苯胺蓝的策略。

IF 1.7 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0066

Dai Di Chen, Xiao Na Liu, Liu Lian Zhang, Jiu Hua Zhang, Wen Ting Ban, Qing Hua Lu, Qingxin Li, Jin Chuan Wu

{"title":"Revealing degradation strategy of aniline blue by Lysinibacillus sp. 38-6 via genomic analysis.","authors":"Dai Di Chen, Xiao Na Liu, Liu Lian Zhang, Jiu Hua Zhang, Wen Ting Ban, Qing Hua Lu, Qingxin Li, Jin Chuan Wu","doi":"10.1139/gen-2025-0066","DOIUrl":"10.1139/gen-2025-0066","url":null,"abstract":"Aniline blue, a triphenylmethane dye, has been widely used in industrial and medical fields, leading to its gradual enrichment in environmental water. Its removal and degradation from the water is essential but very challenging. A bacterium Lysinibacillus sp. 38-6, which is able to efficiently degrade aniline blue, was isolated from the surface soil samples under withered leaves. The strain exhibited excellent decolorization capacity at high concentrations of aniline blue (91% at 1000 mg/L) and salt (90% at 75 g/L) as well as high temperature (92% at 45 °C). To investigate the dye degradation strategies of Lysinibacillus sp. 38-6 at the genomic level, its genome was sequenced and analyzed. The isolate possesses abundant genomic features responsible for degrading dyes. In particular, several genes encoding laccase, iron-dependent peroxidase, NAD(P)H-dependent FMN reductase, and short-chain dehydrogenase/reductases might contribute to the cleavage of chromophore groups and aromatic rings in aniline blue. In addition, a number of genes required for heat, salt, and oxidative stress responses were found, indicating that Lysinibacillus sp. 38-6 is able to efficiently degrade dyes at higher temperature, salty and oxidative environments. It is thus inferred that isolate 38-6 has the potential for applications in efficient degradation of aniline blue in wastewater treatment.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145556783","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

Asp/ASPM phospho-regulation throughout the cell cycle. Asp/ASPM在整个细胞周期中的磷酸化调控。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0111

Maria C Burns, Lori Borgal

{"title":"Asp/ASPM phospho-regulation throughout the cell cycle.","authors":"Maria C Burns, Lori Borgal","doi":"10.1139/gen-2024-0111","DOIUrl":"10.1139/gen-2024-0111","url":null,"abstract":"In mammals and Drosophila melanogaster, Asp/ASPM proteins contribute to cell proliferation and spindle formation. Recent evidence also suggests interphase roles for Asp/ASPM proteins, but little is known about the regulation allowing distinct roles in different cell cycle phases. In this review, we consider a cross-species comparison of Asp/ASPM protein sequences in light of cyclin-CDK literature, and suggest Asp/ASPM proteins to be prime candidates for cyclin-CDK regulation. Conserved regulatory features include an N-terminal proline directed serine/threonine (S/T-P) \"supershift\" phosphorylation domain common to proteins with bistable interphase and mitotic roles, as well as putative cyclin-binding sites positioned to allow multisite phosphorylation by cyclin-CDK complexes. Human, mouse, and Drosophila Asp/ASPM protein structural predictions show that multisite phosphorylation of the N-term supershift domain could alter the availability of CH-domains and HEAT-motifs, which can contribute to microtubule binding and protein aggregation likely required for spindle formation. Structural predictions of the smallest reported microcephaly patient truncation also emphasize the importance of the arrangement of these motifs. We position this in silico analysis within recent literature to build new hypotheses for Asp/ASPM regulation in interphase and mitosis, as well as de-regulation in microcephaly and cancer. We also highlight the utility of comparing structural/functional differences between human ASPM and Drosophila Asp to gain further insight.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545115","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

First insights into the satellitomes and new evidence for the absence of canonical insect telomere in the Neuroptera order. 首次深入了解卫星组和神经翅目昆虫端粒缺失的新证据。

IF 1.7 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0018

Diogo C Cabral-de-Mello, Ana Elisa Gasparotto, José M Rico-Porras, Ana Beatriz S M Ferretti, Pablo Mora, Rhavenna Thais Alves-Gomes, Vitória Lourejan, Elton L Scudeler, Pedro Lorite, Vanessa B Bardella

{"title":"First insights into the satellitomes and new evidence for the absence of canonical insect telomere in the Neuroptera order.","authors":"Diogo C Cabral-de-Mello, Ana Elisa Gasparotto, José M Rico-Porras, Ana Beatriz S M Ferretti, Pablo Mora, Rhavenna Thais Alves-Gomes, Vitória Lourejan, Elton L Scudeler, Pedro Lorite, Vanessa B Bardella","doi":"10.1139/gen-2025-0018","DOIUrl":"10.1139/gen-2025-0018","url":null,"abstract":"Repetitive DNA is a major component of eukaryotic genomes, playing structural, and evolutionary roles. However, in Neuroptera, its characterization remains unexplored. To address this, we analyzed the satellitomes of two Chrysopini (Chrysopidae) species using cytogenomic tools, also investigating telomeric and ribosomal DNA (rDNA). The canonical insect telomeric motif was absent, and rDNA clusters showed variation compared to other neuropterans, despite karyotype stasis (2n = 12, XY). Satellite DNA (satDNA) abundance varied between Ceraeochrysa cincta and Chrysopa pallens, representing a minor fraction of their repetitive DNA content. Notably, no satDNA sequences were shared between species, suggesting a rapid turnover. Exceptionally, the second-most abundant satDNA in each species showed low sequence similarity and a putative common origin. A relationship between satDNAs and transposable elements was also observed. Chromosome mapping revealed that abundant satDNAs accumulated in euchromatin, providing insights into their genomic distribution. These findings enhance our understanding of satDNA organization in Neuroptera, offering a foundation for future genome assembly efforts and evolutionary studies in these insects.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186865","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 Pathway to Increase Standards and Competency of eDNA Surveys (PISCeS) 2023 conference-Towards standardization and data management in the field of eDNA. 提高eDNA调查标准和能力的途径（双鱼）2023会议-迈向eDNA领域的标准化和数据管理。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0158

Morgan R H Humphrey, Tzitziki Loeza-Quintana, Kate Lindsay, Margaret F Docker, Caren C Helbing, Robert H Hanner

引用次数: 0

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