IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0055

Benilson Silva Rodrigues, Ivanete de Oliveira Furo, Ricardo José Gunski, Analía Del Valle Garnero, Patrícia O'Brien, Malcolm Ferguson-Smith, Rafael Kretschmer, Edivaldo Herculano Correa de Oliveira

{"title":"Cytogenetic characterization and phylogenetic analysis in two Tyranninae species (Aves: Passeriformes): the leading edge of chromosome evolution in Passeriformes.","authors":"Benilson Silva Rodrigues, Ivanete de Oliveira Furo, Ricardo José Gunski, Analía Del Valle Garnero, Patrícia O'Brien, Malcolm Ferguson-Smith, Rafael Kretschmer, Edivaldo Herculano Correa de Oliveira","doi":"10.1139/gen-2025-0055","DOIUrl":"10.1139/gen-2025-0055","url":null,"abstract":"Chromosome painting has proven to be an essential tool for elucidating the evolutionary mechanisms underlying avian karyotype diversification and for identifying key synapomorphies that enhance our understanding of avian phylogenetic relationships. In the Neotropical region, the family Tyrannidae exhibits the greatest species diversity, providing valuable opportunities to investigate chromosomal evolution among closely related taxa. To contribute to our understanding of chromosomal evolution within Tyrannidae, we analyzed the karyotypes of two representative species, Myiozetetes cayanensis and Lathrotriccus euleri, combining classical cytogenetic techniques with fluorescence in situ hybridization. We employed whole-chromosome probes from Gallus gallus (GGA) and Leucopternis albicollis (LAL), as well as 18S rDNA and telomeric repeats (TTAGGG)n probes. Our results revealed the conserved karyotypic structure characteristic of Passeriformes (approximately 80 chromosomes), with M. cayanensis exhibiting 2n = 80 and Lathrotriccus euleri 2n = 78. In both species, the karyotypes are predominantly composed of acrocentric chromosomes. Telomeric probes produced signals restricted to terminal chromosomal regions, while 18S rDNA probes hybridized to a single pair of microchromosomes. Probes from GGA and LAL revealed chromosomal fissions and inversions in both species. Similar rearrangements have been observed in other tyrannid species from the subfamilies Fluvicolinae, Tyranninae, and Elaeniinae, suggesting a possible shared evolutionary pattern within Tyrannidae.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-14"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289575","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

Detecting bumble bees in the wild using environmental DNA: development and validation of a qPCR assay for the endangered Franklin's bumble bee (Bombus franklini). 利用环境DNA检测野生大黄蜂：濒危富兰克林大黄蜂（Bombus franklini） qPCR检测的开发和验证。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0006

Michaela R Grossklaus, David S Pilliod, Stephen F Spear, Matthew B Laramie, Akhil Kholwadwala, Amanda J Boone, Yer Lor, Marissa Kaminski, Jeffrey G Everett

{"title":"Detecting bumble bees in the wild using environmental DNA: development and validation of a qPCR assay for the endangered Franklin's bumble bee (Bombus franklini).","authors":"Michaela R Grossklaus, David S Pilliod, Stephen F Spear, Matthew B Laramie, Akhil Kholwadwala, Amanda J Boone, Yer Lor, Marissa Kaminski, Jeffrey G Everett","doi":"10.1139/gen-2025-0006","DOIUrl":"https://doi.org/10.1139/gen-2025-0006","url":null,"abstract":"Environmental DNA (eDNA) sampling is a noninvasive alternative to conventional methods of surveying insects that may be particularly useful for detecting pollinators. We developed a quantitative polymerase chain reaction (qPCR) assay to detect the DNA of Franklin's bumble bee (Bombus franklini) from flower samples and conducted an initial test of the assay using samples collected within and around the historical range of the species. We further analyzed all samples using metabarcoding. Our qPCR assay successfully amplified B. franklini DNA and exhibited no cross-reactivity with nontarget bumble bee DNA during in silico and in vitro testing. We did not detect B. franklini DNA from field-collected flower samples using either qPCR or metabarcoding. However, metabarcoding analysis revealed DNA of at least 16 other bumble bee species. This finding underscores the potential utility of eDNA sampling for surveying bumble bees. Nondetection of B. franklini from field-collected flower samples may be due to the extreme rarity of the species; B. franklini is endangered and has not been observed in the wild since 2006. Our B. franklini assay is among the first bee-specific qPCR assays ever developed and provides proof of concept for additional assays that may improve detection rates of rare and endangered bees.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","pages":"1-13"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147638545","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 the environmental regulation of soybean seed protein through WGCNA and multiWGCNA. 通过WGCNA和多WGCNA揭示大豆种子蛋白的环境调控。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0090

Julia C Wozny, Mohamad Elian, Martin Charette, François Lefebvre, Gerardo Zapata, Ramona M Mohr, Ketema A Daba, Aaron J Glenn, Mehri Hadinezhad, Tom Warkentin, Anfu Hou, Ashkan Golshani, Elroy R Cober, Bahram Samanfar

{"title":"Unraveling the environmental regulation of soybean seed protein through WGCNA and multiWGCNA.","authors":"Julia C Wozny, Mohamad Elian, Martin Charette, François Lefebvre, Gerardo Zapata, Ramona M Mohr, Ketema A Daba, Aaron J Glenn, Mehri Hadinezhad, Tom Warkentin, Anfu Hou, Ashkan Golshani, Elroy R Cober, Bahram Samanfar","doi":"10.1139/gen-2025-0090","DOIUrl":"https://doi.org/10.1139/gen-2025-0090","url":null,"abstract":"Soybean is an agronomically important crop due to protein- and oil-rich seeds. Soybeans in Western Canada have lower seed protein content by ∼1%-5% than those from Eastern Canada, as observed over the past two decades. To elucidate the environmental influence on seed protein accumulation, 10 soybean genotypes ranging in seed protein content were planted in four locations (one east, three west) from 2018 to 2021. Multi weighted gene co-expression network analysis (multiWGCNA) identified differentially co-expressed modules with protein × region trait association from two different networks from soybeans grown in 2019 and 2021. Two protein × region modules were assessed by intramodular connectivity, eigengene expression, and functional roles. The results identified differential co-expression of genes with key roles in epigenetic regulation of gene expression, translational modulation, photosynthetic capacity, seed protein storage vacuole filling, and carbon metabolism are environmentally regulated and likely influence seed composition. In this work, WGCNA and multiWGCNA untangled complex expression and trait data, providing valuable information on environmentally influenced genetic mechanisms influencing seed protein content.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","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":"146212990","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

Modeling the impact of unequal recombination on multigene family copy number variation in apomictic lineages. 不平等重组对无融合谱系中多基因家族拷贝数变异影响的建模。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0070

Abir Elguweidi, Emhimad A Abdalla, Teresa J Crease

引用次数: 0

A versatile high-density customized SNP array for augmenting genomic analysis in sheep. 一种多功能高密度定制SNP阵列，用于增强绵羊基因组分析。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0078

Reena Arora, Upasna Sharma, R K Vijh, Pooja Chhabra, D K Yadav, R K Nachiappan, Rekha Sharma, Sonika Ahlawat, Syed Shanaz, Mohsin Ayoub Mir, Ashish Kumar, Mandeep Kaur

引用次数: 0

The first DNA barcode survey of insects from Lebanon. 黎巴嫩昆虫首次DNA条形码调查。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0134

Carole Saliba, Rhea Kahale, Jean Paul Maalouf, Muhammad Ashfaq, Laure El Chamy, Paul D N Hebert, Magda Bou Dagher Kharrat

{"title":"The first DNA barcode survey of insects from Lebanon.","authors":"Carole Saliba, Rhea Kahale, Jean Paul Maalouf, Muhammad Ashfaq, Laure El Chamy, Paul D N Hebert, Magda Bou Dagher Kharrat","doi":"10.1139/gen-2025-0134","DOIUrl":"10.1139/gen-2025-0134","url":null,"abstract":"Lebanon's diverse landscapes and rich ecological zones support a high diversity of insect species, many of which remain taxonomically unresolved. To address this knowledge gap, we conducted the first comprehensive DNA barcoding survey of Lebanese insect diversity. Specimens collected using Malaise traps deployed at four sites between 2019 and 2021 were analyzed for sequence variation in the 658 bp barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. The 58 123 insect specimens included representatives of 5747 Barcode Index Numbers (BINs), and 56% of them are unique to Lebanon. By integrating DNA barcoding with morphological taxonomy, we assigned each BIN to one of 20 insect orders and identified 1224 species. Most specimens (95%) belonged to five dominant orders: Diptera, Hymenoptera, Hemiptera, Coleoptera, and Lepidoptera. The high proportion of unique BINs suggests high endemism within Lebanon and the broader Levant region. By generating a foundational inventory for Lebanon's insect fauna, this study has provided baseline data critical for future biodiversity monitoring and conservation planning in the Eastern Mediterranean while also making a substantial contribution to the global DNA barcode reference library.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147633225","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

Note of appreciation. 表示感谢。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0117

引用次数: 0

The role of CRISPR in modern plant breeding: overcoming breeding barriers and legislative challenges through transgene-free genome editing. CRISPR在现代植物育种中的作用：通过无转基因基因组编辑克服育种障碍和立法挑战。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0063

Kubilay Yıldırım, Musa Kavas

{"title":"The role of CRISPR in modern plant breeding: overcoming breeding barriers and legislative challenges through transgene-free genome editing.","authors":"Kubilay Yıldırım, Musa Kavas","doi":"10.1139/gen-2025-0063","DOIUrl":"10.1139/gen-2025-0063","url":null,"abstract":"Traditional plant breeding techniques-such as crossbreeding, mutation breeding, and marker-assisted selection-have significantly contributed to crop improvement over the past century. However, these methods are often limited by long breeding cycles, low precision, and the unintended transfer of undesirable traits. To address these challenges, transgenic breeding emerged as a powerful tool, enabling the introduction of specific foreign genes to confer desirable traits such as pest resistance or herbicide tolerance. While highly effective and precise, transgenic approaches face considerable regulatory and public acceptance barriers, particularly in regions with strict GMO legislation. The advent of CRISPR/Cas genome editing has revolutionized plant breeding by enabling precise, efficient, and targeted modification of native genes, significantly accelerating the development of improved crops. Among CRISPR-based methods, transgene-free genome editing has gained prominence for producing enhanced plant varieties without integrating foreign DNA, thus avoiding many regulatory constraints associated with GMOs. This review aims to provide a comprehensive overview of CRISPR-mediated genome editing technologies in crop innovation, emphasizing especially the use of transgene-free approaches in modern plant breeding and their transformative potential to overcome the limitations of conventional methods while providing a regulation-friendly pathway for crop improvement.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289833","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

In silico genomic characterization, classification, and expression profiling of the LRR-RLK family in Lactuca sativa under stress and developmental conditions. 逆境和发育条件下芥蓝LRR-RLK家族的基因组特征、分类和表达谱分析。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0085

Welison Andrade Pereira, Elenildo Dos Santos Oliveira, Kelly Aparecida da Cunha Pereira

{"title":"In silico genomic characterization, classification, and expression profiling of the LRR-RLK family in Lactuca sativa under stress and developmental conditions.","authors":"Welison Andrade Pereira, Elenildo Dos Santos Oliveira, Kelly Aparecida da Cunha Pereira","doi":"10.1139/gen-2025-0085","DOIUrl":"10.1139/gen-2025-0085","url":null,"abstract":"Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest receptor kinase family in plants and are involved in diverse processes related to development, environmental perception, and signal transduction. Despite their relevance, the LRR-RLK gene family has not been systematically characterized in Lactuca sativa. In this study, a genome-wide identification and integrative characterization of LsLRR-RLK genes was performed using curated bioinformatic pipelines. Phylogenetic relationships, protein architecture, conserved motifs, biochemical properties, gene structure, chromosomal distribution, duplication patterns, syntenic relationships, cis-regulatory elements, and transcriptomic profiles were comprehensively analyzed. A total of 269 high-confidence LRR-RLK genes were identified and classified into established subfamilies, revealing marked subfamily-specific patterns of structural organization, regulatory architecture, and transcriptional behavior. Expression analyses across developmental stages and multiple environmental conditions demonstrated widespread but heterogeneous transcriptional regulation within the family. Collectively, this work provides a detailed genomic and functional overview of the LRR-RLK gene family in L. sativa, establishing a structured reference for comparative and exploratory studies of receptor-like kinases in plants.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-19"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289678","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

Differential cis-regulatory regions of KS dehydrins of Arctic and temperate Oxytropis spp. 北极和温带棘豆属植物KS脱水剂的不同顺调控区。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0089

J C Camargo-Tavares, Y Zolotarov, S Kawakami, D Praslickova, M V Strömvik

{"title":"Differential cis-regulatory regions of KS dehydrins of Arctic and temperate Oxytropis spp.","authors":"J C Camargo-Tavares, Y Zolotarov, S Kawakami, D Praslickova, M V Strömvik","doi":"10.1139/gen-2025-0089","DOIUrl":"10.1139/gen-2025-0089","url":null,"abstract":"Dehydrins are intrinsically disordered proteins that play central roles in cryoprotection and osmotic stress tolerance in plants. In this study, we investigated orthologous KS dehydrin promoters from the Arctic Oxytropis arctobia (Fabaceae) and the temperate Oxytropis splendens using reporter gene constructs to evaluate transcriptional responses under abiotic stress conditions in transgenic Lotus japonicus. Reporter gene assays in freeze- and heat-exposed Lotus japonicus plantlets showed that a specific region of the Oxytropis splendens promoter functions as a repressor, while both promoters contain temperature-responsive cis-elements. In parallel, we sequenced and analyzed the nuclear genomes of Oxytropis arctobia and Oxytropis splendens, focusing on identifying KS dehydrin orthologs and their regulatory regions. This revealed that the intron in the 3' untranslated region is highly conserved between three Oxytropis species and in close relatives, which may contribute to post-transcriptional regulation and adaptation to harsh environments. Together, these results demonstrate cis-regulatory divergence in dehydrin promoters and provide new insights into the molecular mechanisms and evolutionary trajectories of cold adaptation in Oxytropis.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147289567","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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