Genome最新文献

{"title":"<i>Cenchrus purpureus</i> and <i>Cenchrus americanus</i> repeatome provide chromosomal markers to distinguish subgenomes.","authors":"Alex Junior Aparecido Silvestrini, Magdalena Vaio, Karla Carvalho Azevedo, Giovana Augusta Torres","doi":"10.1139/gen-2025-0052","DOIUrl":"10.1139/gen-2025-0052","url":null,"abstract":"<p><p><i>Cenchrus</i> L. is an important genus within the family Poaceae, comprising species of agronomic importance, such as <i>Cenchrus purpureus</i> and <i>Cenchrus americanus</i>. <i>Cenchrus americanus</i> is a diploid species (2<i>n</i> = 2<i>x</i> = 14, AA genome), while <i>C. purpureus</i> is an allotetraploid (2<i>n</i> = 4<i>x</i> = 28, A'A'BB genome). The A' subgenome is proposed to be homeologous to and possibly derived from the A subgenome, while the origin of the B subgenome remains undefined. Despite their distinct subgenomic compositions, both species exhibit a high level of genome homology. This study aimed to characterize and compare the repetitive genome fraction of <i>C. purpureus</i> and <i>C. americanus</i> using genome skimming and a graph-based clustering approach, as well as in situ hybridization. The repetitive genome fraction of <i>C. purpureus</i> and <i>C. americanus</i> corresponds to 52.23% and 76.82%, respectively. The most abundant repetitive elements in both species are the LTR retrotransposons. Satellite DNA sequences correspond to 2.55% and 4.17% of the species' genome, respectively. Four new satellite sequences were identified as A, A', and B subgenome-specific sequences, along with new centromeric variants. The ancestral relationship and the polyploidization-diploidization cycles played a fundamental role in the composition of their repetitive fraction.</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":"145312716","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":"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}

{"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":"Strains of <i>Apis mellifera ligustica</i> honey bees artificially bred for apicultural traits are not consistently differentiated by mitochondrial DNA genome markers.","authors":"Steven M Carr","doi":"10.1139/gen-2025-0033","DOIUrl":"10.1139/gen-2025-0033","url":null,"abstract":"<p><p>Strains of the Italian honey bee <i>Apis mellifera ligustica</i> Spinola, 1806 are selectively bred for desirable apiculture traits. Ma et al. compared SNP differences in mtDNA genomes between a strain bred for enhanced royal jelly production (RJB) and an unselected strain (ITB). Kim et al. compared SNP and intergenic repeats differences between a <i>Varroa</i> mite resistant strain bred for high-hygienic behavior (HHB) and an unselected low-hygienic strain (LHB). Phylogenetic comparison of 23 complete <i>A. m. ligustica</i> mtDNA sequences, including the HHB and LHB strains and 14 RJB and ITB haplotypes, shows significant intrasubspecific clade structure for SNP differences and amino acid substitutions; however, this structure is not diagnostic of the strains under selection. RJB strains occur in three separate clades, and along with HHB are frequently identical or near-identical to other haplotypes. Differences between the selected and unselected strains appear to arise from coincidental fixation of alternative SNPs in different clades. Numbers of repeats show little or no phylogenetic signal: similarities are symplesiomorphic and differences convergent. Evaluation of the diagnostic and (or) adaptive significance of mtDNA markers requires broad knowledge of within-subspecies polymorphism.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-9"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803962","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":"Single-locus species delimitation of Pronophilina butterflies (Nymphalidae: Satyrini) in the Colombian Andes: congruence between morphology and MOTUs.","authors":"Keyner Moreno-Torres, Carlos Prieto, Tomasz W Pyrcz","doi":"10.1139/gen-2025-0041","DOIUrl":"10.1139/gen-2025-0041","url":null,"abstract":"<p><p>The subtribe Pronophilina (Nymphalidae: Satyrinae: Satyrini) is one of the most diverse subtribes within the Lepidoptera. In Colombia, these butterflies are distributed throughout the Andes, where they play a key role in montane ecosystems and exhibit high levels of endemism. Despite their complex genital morphology, species within the same genus often exhibit highly similar wing patterns, complicating taxonomic identification. In this study, we analyzed the concordance between DNA barcode-based species delimitation and morphological identifications using 334 <i>cytochrome c oxidase subunit I</i> barcodes from 94 a priori identified morphospecies in Colombia. We applied four molecular species delimitation methods (Automatic Barcode Gap Discovery, Refined Single Linkage, Poisson Tree Processes, and Assemble Species by Automatic Partitioning), delimitating between 98 and 108 molecular operational taxonomic units. Overall, the methods showed high consistency, with high congruence between morphological and molecular delimitations (81%). Additionally, 96.8% of the morphospecies exhibited a barcode gap, indicating clear genetic differentiation. However, we found some inconsistencies, including 6 cases of species merging and 12 cases of species splitting. Our findings underscore the utility of DNA barcoding for species delimitation in Pronophilina, while highlighting the need for integrative approaches to resolve taxonomic uncertainties in this diverse group.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","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":"144591123","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":"Environmental DNA detection of the male mitochondrial genome of freshwater mussels (Unionidae).","authors":"Nathaniel T Marshall, Daniel E Symonds, W Cody Fleece","doi":"10.1139/gen-2024-0031","DOIUrl":"https://doi.org/10.1139/gen-2024-0031","url":null,"abstract":"<p><p>Environmental DNA (eDNA) has shown promise for the detection of threatened and endangered species and has been implemented for monitoring aquatic spawning events. Freshwater unionid mussels exhibit a rare form of mitochondrial inheritance, in which males possess a unique mitochondrial mitotype that is divergent from the female mitotype. As freshwater mussels are spermcasters, the detection of male mitotype eDNA may provide critical conservation information related to timing of sperm release. This study re-purposed an existing eDNA metabarcoding dataset to detail the unique detection of eDNA pertaining to the male mitotype. Water samples collected alongside an extensive mussel salvage within the Walhonding River, Ohio, detected 16 distinct male mitotypes. However, several constraints limit the proper interpretation of these detections. There is currently a lack of reporting on assay compatibility with the male mitotype within freshwater mussel eDNA literature. Reference genetic databases are critically lacking, with only four of the 16 male eDNA sequences in this study able to be discerned to a species. This study highlights the importance of detailing these detections as the unique inheritance system provides opportunities to document difficult to record spawning behaviors, and eDNA may be employed as a survey tool to evaluate patterns of metapopulation geneflow.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-17"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144011200","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}