Genome最新文献

{"title":"Sequence-based identification of polyamine oxidase genes in <i>Sorghum bicolor</i> L.","authors":"Heba T Ebeed, Mohamed El-Zonkorany, Eman Habib, Esraa Ali, Ahmed Zahran, Aya Hamdy Ragab","doi":"10.1139/gen-2024-0143","DOIUrl":"10.1139/gen-2024-0143","url":null,"abstract":"<p><p>Polyamine oxidases (PAOs) are enzymes associated with polyamine catabolism and play important roles in growth and development and stress tolerance of plants. In the present study, genome-wide discovery and analysis of the PAO family in sorghum was done utilizing model PAO of Arabidopsis. Six PAO genes were found using publicly available genomic data. Sorghum has the PAO gene representatives distributed throughout four chromosomes (chr1, chr3, chr6, and chr7), and most members have eight to nine exons. The molecular weights of PAO proteins range from 53 to 63 kDa. PAO proteins have a theoretical PI between 5.2 and 8.1. The identification and characterization of PAO gene members in sorghum lay the foundation for further experimental studies elucidating their roles in growth, development, and stress responses, ultimately contributing to our understanding of plant biology, with significant implications for plant breeding by providing valuable insights into potential targets for enhancing stress tolerance and improving crop performance.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-5"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064946","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}

{"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":"<p><p>In mammals and <i>Drosophila melanogaster</i>, 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 <i>Drosophila</i> 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 <i>in silico</i> 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 <i>Drosophila</i> Asp to gain further insight.</p>","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}

{"title":"Chromosome homologies and polymorphisms in a Neotropical species complex of frogs revealed by the U2 snRNA gene.","authors":"Lucas Henrique Bonfim Souza, Bruno Cansanção Silva, Jennifer Nunes Pompeo, Kaleb Pretto Gatto, Luciana Bolsoni Lourenço","doi":"10.1139/gen-2024-0131","DOIUrl":"10.1139/gen-2024-0131","url":null,"abstract":"<p><p>The <i>Physalaemus cuvieri-Physalaemus ephippifer</i> species complex is a Neotropical frog group that encompasses seven well-supported major clades. Although very similar morphologically, the five lineages previously karyotyped show notorious cytogenetic signatures. There is also evidence of ancient secondary contact between <i>P. ephippifer</i>, which has heteromorphic sex chromosomes, and the lineage known as L1B, which lacks sex chromosome heteromorphism. Here, to aid comparative analysis within this complex, we mapped the U2 small nuclear RNA (snRNA) gene using fluorescent in situ hybridization (FISH). All samples presented a U2 snRNA gene cluster terminally in the short arm of chromosome 6. Additional small FISH signals were also revealed, particularly in one lineage with previously noted polymorphism of nucleolar organizer regions. Moreover, one additional site contributed for the analysis of sex chromosomes, since the Z chromosome of <i>P. ephippifer</i> harbors a small FISH signal, which is absent in the W chromosome. In lineage L1B, chromosome 9-which is homologous to the sex chromosomes of <i>P. ephippifer-</i>is polymorphic for a small FISH signal, as did the Z chromosome in the group derived from the contact between these lineages. Finally, nucleotide sequence analysis revealed some truncated gene sequences, suggesting the presence of pseudogenes of the U2 snRNA gene in these frogs.</p>","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":"143482787","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}

{"title":"Reducing the regulatory burden of plant biotechnology regulations in Canada.","authors":"Simona Lubieniechi, Savannah Gleim, Stuart J Smyth","doi":"10.1139/gen-2024-0164","DOIUrl":"10.1139/gen-2024-0164","url":null,"abstract":"<p><p>Regulations within the crop agriculture industry exist to ensure that products undergoing risk assessment prior to commercialization are safe for the environment and human consumption. Since 1995, these regulations have provided safe crops and foods for Canadians to consume, as no commercialized innovative product has caused any post-commercialization health or environmental problems. However, Canada suffers from a gap in its innovation pipeline in that far more investments go into the innovation pipeline than products come out. Canada is a global top ten nation in terms of innovation investments yet drops over ten positions when it comes to outputs. Additionally, Canada is one of the lowest ranked on the G30 list of countries in terms of regulatory burden on the economy. This article describes updates to the regulatory framework for plant biotechnology, highlighting recent changes regarding regulation of gene editing technologies and how these changes respond to previously identified innovation barriers.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-9"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763890","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}

{"title":"Differential expression analysis of soybean pod tissue between Canadian environments identifies differences in sulfur-containing amino acid-related gene expression.","authors":"Julia C Hooker, Martin Charette, François Lefebvre, Gerardo Zapata, Ramona M Mohr, Ketema A Daba, Aaron J Glenn, Frédéric Marsolais, Mehri Hadinezhad, Tom Warkentin, Anfu Hou, Ashkan Golshani, Elroy R Cober, Bahram Samanfar","doi":"10.1139/gen-2024-0106","DOIUrl":"https://doi.org/10.1139/gen-2024-0106","url":null,"abstract":"<p><p>Soybean seeds are rich in oil and protein; however, the seed composition is influenced by genotype and environment. For years, it has been observed that soybeans grown in western Canada have lower seed protein concentration (by ∼1%-5% total seed weight) than those grown in eastern Canada. In this study, soybean seeds harvested from five varieties were grown in four different locations in Canada (east and west growing regions) and analyzed using RNA-sequencing. Using gene ontology and biological pathway mapping, we identified a difference in cysteine and methionine metabolism between soybeans grown in eastern and western Canada that may attribute to the difference in seed protein concentration. Further, we identified differential gene expression within the oil biosynthesis pathway, specifically upregulation of lipoxygenases in western-grown soybeans, which may also influence seed composition and/or membrane fluidity. The information gained in this study is useful for marker assisted selection in soybean breeding programs across Canada and globally.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","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":"144011199","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}

{"title":"The Pathway to Increase Standards and Competency of eDNA Surveys (PISCeS) 2023 conference-Towards standardization and data management in the field of eDNA.","authors":"Morgan R H Humphrey, Tzitziki Loeza-Quintana, Kate Lindsay, Margaret F Docker, Caren C Helbing, Robert H Hanner","doi":"10.1139/gen-2024-0158","DOIUrl":"10.1139/gen-2024-0158","url":null,"abstract":"<p><p>The second iteration of the international conference \"Pathway to Increase Standards and Competency of eDNA Surveys\" was held at the University of Guelph, Guelph, Ontario, Canada from 18 June to 20 June 2023. During this environmental DNA (eDNA) conference, 60 oral and 25 poster presentations from academia, government, industry, NGOs, and Indigenous partners discussed the latest developments in eDNA research, explored strategies to inform public policy, and presented future directions in the field. The conference also included three panel discussions focused on prominent themes in the eDNA space, and five workshops dedicated to practical eDNA tools and methods. Recordings of presentations at the conference have been made available on YouTube. Here we summarize the major themes covered during the conference, provide our concluding remarks, and share the conference abstracts.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","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":"143624312","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}

{"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":"<p><p>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 <i>Ceraeochrysa cincta</i> and <i>Chrysopa pallens</i>, 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.</p>","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}

{"title":"Museum insights for conservation: unraveling the extinction factors in the Jambato Harlequin frog, <i>Atelopus ignescens</i>.","authors":"Mónica A Guerra, Chengchen Gao, Samuel Crickenberger, Michelle Vélez, Luis A Coloma, Silu Wang","doi":"10.1139/gen-2024-0032","DOIUrl":"10.1139/gen-2024-0032","url":null,"abstract":"<p><p>Natural history museums harbor invaluable resources for conserving endangered species by providing insights into the mechanism of historical population declines. We conducted data synthesis to better understand the extinction factors of the iconic Jambato Harlequin frog, <i>Atelopus ignescens</i>, which was widespread in the Ecuadorian Andes before 1985 but vanished in 1988. We synthesized historical data from natural history museums, the global biodiversity information facility, and mtDNA sequences to examine whether <i>Batrachochytrium dendrobatidis</i> (<i>Bd</i>) fungus infection, climate change, and/or their interaction contributed to the rapid population decline. We found excessive rare alleles reflected in the negative Tajima's D estimated from the mtDNA samples from 1984, indicating a selective sweep or population bottleneck. Sex and geography showed stronger effects on adult body sizes than <i>Bd</i> epizootic timing. The body sizes of adult males formed a geographic cline. Species distribution modeling based on temperature and precipitation accurately predicted the occupancy of <i>A. ignescens</i> in 1960-69, which further projected a rapid decline in species distribution between 1970 and 2020. This investigation revealed strong climate effect and weak epizootics effect on <i>A. ignescens</i> extinction, and inspires future museum genomic studies to dissect the potential climatic maladaptation behind dramatic historical extinctions.</p>","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":"143572794","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}

{"title":"Candidate genes validation for intramuscular fat content of Nellore Cattle.","authors":"Bruna M Salatta, Larissa F S Fonseca, Gabriela B Frezarim, Natalia A Marín-Garzón, Danielly B S Silva, Lucio F M Mota, Marta Serna-García, Sindy L C Nasner, Leonardo M Arikawa, Patricia I Schmidt, Tiago Bresolin, Luis A L Chardulo, Jesus A Ferro, Alexeia Barufatti, Lucia G Albuquerque","doi":"10.1139/gen-2024-0176","DOIUrl":"10.1139/gen-2024-0176","url":null,"abstract":"<p><p>Intramuscular fat is an important factor for the sensory quality and value of meat. However, in tropical breeds such as Nellore, the lower marbling capacity represents a challenge for its positioning in premium markets. Marbling score (MS) and the total lipid (TL) determination methods are complementary methodologies for measuring beef intramuscular fat. <i>Longissimus thoracis</i> samples from the 24 most extreme steers (out of 189 steers) for MS (high = 12 and low = 12) and TL (high = 12 and low = 12) traits were collected to (1) validate in Nellore cattle differentially expressed genes for MS and TL traits found in the literature in other populations using real-time PCR, and (2) verify if differentially expressed genes were translated into differentially expressed proteins through advanced mass spectrometry (LC-MS/MS). Significant differences in the expression levels of the genes <i>FABP4</i>, <i>DGAT1</i>, <i>DGAT2</i>, <i>BARX2</i>, <i>STAT5A</i>, and <i>SDC</i> were observed in the group with high intramuscular fat content. These genes play important roles in lipid metabolism, adipogenesis, and muscle development. Proteins encoded by genes (<i>PRDM1</i> and <i>COL1A2</i>) regulated by the transcription factor <i>STAT5A</i> were differentially expressed and probably play a key role during intramuscular fat deposition. Our results confirm that the genes <i>FABP4, DGAT1, DGAT2</i>, <i>STAT5A</i>, and <i>BARX2</i> validated here can potentially be used as biomarkers for intramuscular fat in Nellore cattle.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173104","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}

{"title":"Chromosomal evolution and evidence of a putative multiple sex chromosome system in the Amazonian northeastern pepper frog (<i>Leptodactylus vastus</i>, Lutz 1930).","authors":"David Santos da Silva, Rodrigo Petry Corrêa de Sousa, Wallax Augusto Silva Ferreira, Anderson José Baia Gomes, Edivaldo Herculano Corrêa de Oliveira","doi":"10.1139/gen-2025-0014","DOIUrl":"https://doi.org/10.1139/gen-2025-0014","url":null,"abstract":"<p><p>The genus <i>Leptodactylus</i> is among the most studied anurans in cytogenetics. Despite exhibiting chromosomal conservatism with 2n = 22, microstructural studies (here defined as investigations of subchromosomal features such as DNA repetitive elements, chromatin organization, and sequence-level structural arrangements) have revealed significant karyotypic diversity within the genus, primarily associated with the distribution of repetitive sequences. Additionally, complex sex chromosome systems have been identified, underscoring the importance of further studies on these species. In this context, we performed a karyotypic characterization of <i>Leptodactylus vastus</i> from the Amazonian region. Using conventional cytogenetics, FISH with repetitive sequences, and phylogenetic analyses, we identified extensive chromosomal rearrangements, evidenced by the distribution of heterochromatin and repetitive sequences, including microsatellites, 18S rDNA, and U2 snDNA. Meiotic analyses in males revealed the presence of multivalent chromosomal chains involving eight chromosomes, a pattern consistent with a multiple sex chromosome system (X₁Y₁X₂Y₂X₃Y₃X₄Y₄). Concerning the clusters of repetitive sequences, we observed in specific chromosome pairs underscores the potential cytotaxonomic relevance of these markers. Phylogenetically, <i>Leptodactylus vastus</i> belongs to the <i>Leptodactylus pentadactylus</i> group, which includes other species known to possess multiple sex chromosome systems, although the absence of female data prevents definitive confirmation of this system in this species. Our results suggest that chromosomal rearrangements may have contributed to the genomic diversification of the species, supporting previous hypotheses on the role of structural variation in <i>Leptodactylus</i> species while highlighting the need for further comparative studies involving both sexes to fully clarify the nature of the multivalent chromosomal chains observed in <i>Leptodactylus vastus</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-11"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145137300","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}