IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2025-0010

S E Weber, L Roscher-Ehrig, S Zanini, G Yildiz, A Abbadi, T Kox, A A Golicz, R J Snowdon

{"title":"Single-cross prediction with imputed multiomic data: a case study in rapeseed.","authors":"S E Weber, L Roscher-Ehrig, S Zanini, G Yildiz, A Abbadi, T Kox, A A Golicz, R J Snowdon","doi":"10.1139/gen-2025-0010","DOIUrl":"10.1139/gen-2025-0010","url":null,"abstract":"Advancements in sequencing technologies enabled the assembly and characterization of plant genomes with high resolution. In breeding programs, these data are combined with phenotypic information in genomic prediction to select genotypes based on their genetic profiles. Although single nucleotide polymorphism (SNP) arrays are commonly used for genotyping, they capture only a fraction of the genomewide diversity. To address this, one approach involves genotyping the entire population with arrays, sequence a subset using whole-genome sequencing (WGS), or assessing gene expression profiles, followed by imputing the data across the entire population. This study evaluates the effect of imputed WGS markers (SNPs and structural variants) and expression data on genomic prediction in a rapeseed hybrid breeding population. A combination of SNP arrays, WGS, and RNA sequencing was employed, followed by imputation of marker and expression data. Genomic prediction was utilized to estimate general and specific combining ability effects in untested hybrids. However, while adding imputed whole-genome and expression data increased marker density and linkage disequilibrium, it did not enhance prediction accuracy compared to SNP array data. This is attributed to redundancy in relationship, imputation errors, or environmental influences on gene expressions. This suggests that SNP arrays continue to be reliable for genomic prediction in rapeseed hybrid breeding.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","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":"144009011","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

Reducing the regulatory burden of plant biotechnology regulations in Canada. 减轻加拿大植物生物技术法规的监管负担。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0164

Simona Lubieniechi, Savannah Gleim, Stuart J Smyth

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

Chromosome homologies and polymorphisms in a Neotropical species complex of frogs revealed by the U2 snRNA gene. 由U2 snRNA基因揭示的新热带蛙种复合体的染色体同源性和多态性。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0131

Lucas Henrique Bonfim Souza, Bruno Cansanção Silva, Jennifer Nunes Pompeo, Kaleb Pretto Gatto, Luciana Bolsoni Lourenço

{"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":"The Physalaemus cuvieri-Physalaemus ephippifer 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 P. ephippifer, 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 P. ephippifer 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 P. ephippifer-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.","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}

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

Differential expression analysis of soybean pod tissue between Canadian environments identifies differences in sulfur-containing amino acid-related gene expression. 加拿大大豆豆荚组织在不同环境下的差异表达分析确定了含硫氨基酸相关基因表达的差异。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0106

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

{"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":"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.","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}

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

Museum insights for conservation: unraveling the extinction factors in the Jambato Harlequin frog, Atelopus ignescens. 博物馆对保护的见解：解开Jambato Harlequin Frog， Atelopus ignescens的灭绝因素。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0032

Mónica A Guerra, Chengchen Gao, Samuel Crickenberger, Michelle Vélez, Luis A Coloma, Silu Wang

{"title":"Museum insights for conservation: unraveling the extinction factors in the Jambato Harlequin frog, Atelopus ignescens.","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":"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, Atelopus ignescens, 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 Batrachochytrium dendrobatidis (Bd) 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 Bd 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 A. ignescens 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 A. ignescens extinction, and inspires future museum genomic studies to dissect the potential climatic maladaptation behind dramatic historical extinctions.","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}

引用次数: 0

Environmental DNA detection of the male mitochondrial genome of freshwater mussels (Unionidae). 淡水贻贝雄性线粒体基因组的环境DNA检测。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0031

Nathaniel T Marshall, Daniel E Symonds, W Cody Fleece

{"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":"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.","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}

引用次数: 0

Chromosome identification of Medicago polymorpha by oligonucleotide-based FISH. 多形紫花苜蓿染色体的寡核苷酸FISH鉴定。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0136

Min Cheng, Jia Xu, Ying Li, Yaling Jian, Feng Yu

{"title":"Chromosome identification of Medicago polymorpha by oligonucleotide-based FISH.","authors":"Min Cheng, Jia Xu, Ying Li, Yaling Jian, Feng Yu","doi":"10.1139/gen-2024-0136","DOIUrl":"10.1139/gen-2024-0136","url":null,"abstract":"Medicago polymorpha (2n = 2x = 14) is a valuable forage legume, but the identification of its somatic chromosomes has been challenging due to a lack of distinctive chromosome morphological features. With appropriate probes, oligonucleotide-based FISH is a highly effective method for chromosome identification. However, there are no available probes for M. polymorpha. In this study, we isolated five tandem repeats from the M. polymorpha genome, named Mp51, Mp139, Mp167, Mp179, and Mp497. Mp51 showed two pairs of signals located at the pericentromere. Mp139 exhibited four pairs of signals, located at the pericentromere and short arm of chromosomes. Mp167 and Mp179 showed seven pairs of signals, respectively, concentrated in the pericentromere. Mp497 exhibited three pairs of signals, distributed across the pericentromere and proximal position of the chromosomes. The combined FISH results of Mp51 and Mp139 oligo probes with 5S rDNA and 18S-26S rDNA probes demonstrated distinct signal patterns for each chromosome, enabling the precise identification of all chromosome pairs. Finally, the visual identification of M. polymorpha chromosomes was resolved. This will provide useful cytological information for studying the chromosomal structure and behavior of M. polymorpha.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-8"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143515477","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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