IF 1.9 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":"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":1.9,"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

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

IF 1.9 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":1.9,"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

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 1.9 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 1.9 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

Identification and functional analysis of 2,3-dihydroxybenzoic acid and catechol catabolic pathway genes in Aspergillus niger. 黑曲霉2,3-二羟基苯甲酸和儿茶酚分解代谢途径基因的鉴定及功能分析。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0088

Michael Sgro, Ian D Reid, Adrian Tsang

{"title":"Identification and functional analysis of 2,3-dihydroxybenzoic acid and catechol catabolic pathway genes in Aspergillus niger.","authors":"Michael Sgro, Ian D Reid, Adrian Tsang","doi":"10.1139/gen-2026-0088","DOIUrl":"10.1139/gen-2026-0088","url":null,"abstract":"Microorganisms catabolize many plant-derived aromatic compounds through the β-ketoadipate pathway. This pathway has two branches, beginning with protocatechuic acid and catechol, which converge on β-ketoadipate before further catalysis to produce tricarboxylic acid cycle intermediates. The protocatechuic acid branch of the pathway has been characterized in fungi. Here, we characterized the genes of the catechol branch of the β-ketoadipate pathway in the filamentous fungus Aspergillus niger. We predicted the genes involved using comparative transcriptomics and homology to characterized genes. We tested the predictions by constructing knockout mutants lacking candidate genes to observe the growth phenotype on 2,3-dihydroxybenzoic acid (2,3-DHB), which is catabolized through the catechol branch, and by detection of metabolites accumulated in knockout mutants using mass spectrometry. Using these approaches to reconstruct the pathway, we confirmed the reported assignments of dhbA, crcA, kstA, and kctA as encoding 2,3-dihydroxybenzoate decarboxylase, catechol 1,2-dioxygenase, β-ketoadipate:succinyl-CoA transferase, and β-ketoadipyl-CoA thiolase, respectively. We further assigned mciA, mliA, and kelA as encoding muconate cycloisomerase, muconolactone isomerase, and β-ketoadipate enol-lactonase, respectively. Additionally, we identified a transcription regulator involved with the β-ketoadipate pathway in fungi for the first time. This gene, pcaR, is upregulated on 2,3-DHB and deletion of the gene impaired growth on 2,3-DHB.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148968004","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

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 1.9 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":1.9,"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

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 1.9 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":1.9,"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 1.9 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":1.9,"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

Integration of consensus WGCNA and differential expression analysis reveals stable heat shock protein networks in soybean adaptation to Western Canada. 整合共识WGCNA和差异表达分析揭示了大豆适应加拿大西部的稳定热休克蛋白网络。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0058

Jakob Bruggink, Julia Wozny, Ashkan Golshani, Elroy Cober, Bahram Samanfar

{"title":"Integration of consensus WGCNA and differential expression analysis reveals stable heat shock protein networks in soybean adaptation to Western Canada.","authors":"Jakob Bruggink, Julia Wozny, Ashkan Golshani, Elroy Cober, Bahram Samanfar","doi":"10.1139/gen-2026-0058","DOIUrl":"https://doi.org/10.1139/gen-2026-0058","url":null,"abstract":"The expansion of soybean (Glycine max (L.) Merr.) cultivation into Western Canada is constrained by distinct abiotic stressors, including shorter growing seasons and drought. Heat shock proteins (HSPs) are critical regulators of stress adaptation; however, characterizing their expression in field conditions is often confounded by significant annual environmental variability. In this study, we integrated differential expression analysis, consensus Weighted Gene Co-expression Network Analysis (WGCNA), and rigorous protein-protein interactomic modeling across 4 years of field data (2018-2021) involving 10 genotypes grown in Eastern and Western Canada. By filtering temporal noise, we identified a stable, region-specific module that is computationally predicted to resolve into a highly coordinated physical chaperone complex. Subcellular characterization of this network revealed a robust core of chaperones targeting mitochondria and chloroplasts. Crucially, high-confidence predictions identified a physical interaction between a mitochondrial HSP60 hub and a nuclear domains rearranged methyltransferase, suggesting this chaperone complex potentially bridges localized organelle defense with systemic epigenetic regulation to safeguard metabolic capacity. These findings delineate a computationally modeled, geography-dependent stress response machine and provide ideal genetic targets for breeding programs aiming to improve soybean resilience in northern latitudes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","pages":"1-14"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192926","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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