IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0098

Ben Schultz, Elizabeth G Mandeville

引用次数: 0

Genome-wide analysis of lipoxygenase genes in Coffea arabica and its diploid progenitors. 阿拉比卡咖啡及其二倍体祖细胞脂氧合酶基因的全基因组分析。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0016

Paula Oliveira Camargo, Ilara Gabriela Frasson Budzinski, Matheus Oziliero Tagliaferro, Gian Carlos Costa Barros, Salete Aparecida Gaziola, Ricardo Antunes Azevedo, Douglas Silva Domingues

{"title":"Genome-wide analysis of lipoxygenase genes in Coffea arabica and its diploid progenitors.","authors":"Paula Oliveira Camargo, Ilara Gabriela Frasson Budzinski, Matheus Oziliero Tagliaferro, Gian Carlos Costa Barros, Salete Aparecida Gaziola, Ricardo Antunes Azevedo, Douglas Silva Domingues","doi":"10.1139/gen-2026-0016","DOIUrl":"10.1139/gen-2026-0016","url":null,"abstract":"Lipoxygenase proteins (LOXs) play a crucial role in plant growth, development, and defense notably through their involvement in jasmonic acid (JA) biosynthesis. Here, we aimed to identify and characterize genes encoding LOXs in three coffee species, Coffea arabica, Coffea canephora, and Coffea eugenioides, and to evaluate whether LOX genes are differentially expressed following hexanoic acid application in Coffea arabica. We found 18 LOX genes in Coffea arabica and 9 genes each in Coffea eugenioides and Coffea canephora. Chromosomal localization analyses revealed strong correspondence between the LOX genes of tetraploid Coffea arabica and those of its putative diploid progenitors, Coffea eugenioides and Coffea canephora. Transcriptomic and enzymatic analyses showed that hexanoic acid application modulates the expression of specific LOX genes and alters LOX activity in leaves and roots of Coffea arabica cvs. Catuaí Vermelho and Obatã. Notably, three LOX genes displayed strong correlations between transcript abundance and enzymatic activity. Together, these results indicate that a subset of LOX genes in Coffea arabica represents promising candidates for detailed functional analyses, as they likely contribute substantially to LOX activity and elicitor-induced defense responses in Coffea species.","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":"148678245","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

Genomics of tropical forage grasses in Brazil: resources, progress, and future directions. 巴西热带牧草基因组学：资源、进展和未来方向。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0126

Francelly Geralda Campos, Bianca Baccili Zanotto Vigna, Marco Pessoa-Filho, Mauricio de Alvarenga Mudadu, Guilherme Francio Niederauer, Robert Domingues, Jorge Fernando Pereira, Ana Luisa Sousa Azevedo

{"title":"Genomics of tropical forage grasses in Brazil: resources, progress, and future directions.","authors":"Francelly Geralda Campos, Bianca Baccili Zanotto Vigna, Marco Pessoa-Filho, Mauricio de Alvarenga Mudadu, Guilherme Francio Niederauer, Robert Domingues, Jorge Fernando Pereira, Ana Luisa Sousa Azevedo","doi":"10.1139/gen-2025-0126","DOIUrl":"10.1139/gen-2025-0126","url":null,"abstract":"Brazil is the global leader in the production and export of tropical forage seeds. The livestock sector primarily relies on tropical grasses, including species of Urochloa and Megathyrsus maximus, as well as other genera such as Paspalum, Cenchrus, and Setaria. The sustainability and competitiveness of this sector are increasingly threatened by climate change and biotic stresses. While conventional breeding has made progress, enhancing genetic gains requires advanced molecular tools due to the biological complexity of these grasses. Given the growing importance of forage genomics, this paper provides an up-to-date overview of genomic resources available for the main tropical forage species. We synthesized the state-of-the-art applications of genomics, transcriptomics, and functional genetics in forage research, consolidating findings from Brazilian and international institutions. In recent years, significant advances have been made, including the assembly of reference genomes, the development of comprehensive transcriptomic datasets, and the construction of high-density linkage maps. Despite the recent increase in genomic data, we identified significant bottlenecks, including the need for reference pangenomes, standardized phenotyping platforms, and robust functional validation pipelines for novel genes. This review serves as a critical roadmap, emphasizing that collaboration is vital to translate genomic data into resilient, nutritious, and climate-adapted tropical forage cultivars, securing the future of sustainable livestock production.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-16"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535787","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

DNA metabarcoding of Myotis lucifugus guano reveals unexplored arthropod diversity and diet variability in Newfoundland. 纽芬兰节肢动物多样性和食性变异的DNA元条形码分析。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0082

Chadabhorn Insuk, Helen MacDougall-Shackleton, Sophia Bertolo, Holly Lightfoot, Jessica Humber, Jianping Xu

{"title":"DNA metabarcoding of Myotis lucifugus guano reveals unexplored arthropod diversity and diet variability in Newfoundland.","authors":"Chadabhorn Insuk, Helen MacDougall-Shackleton, Sophia Bertolo, Holly Lightfoot, Jessica Humber, Jianping Xu","doi":"10.1139/gen-2025-0082","DOIUrl":"10.1139/gen-2025-0082","url":null,"abstract":"All bats in Newfoundland, Canada are insectivores. While the dietary insects of several bat species have been investigated elsewhere in Canada and North America, little is known about the insect prey of Newfoundland bats. Here, we use DNA metabarcode sequencing of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify insect prey from Myotis lucifugus guano. Among 21 guano samples from six sites in Newfoundland, 346 amplicon sequence variants (ASVs) of arthropods were identified. Among these 346 ASVs, 343 and 330 have not been documented in the barcode of life database from Newfoundland and Canada, respectively. In addition, only 34 and 54 of the 346 ASVs were identified to 19 species and 24 genera, respectively, with high confidence. Overall, Trichoptera had the highest percentage of COI sequences while Coleoptera had the most ASVs. High arthropod variabilities were observed among guano samples from both within and among sites. In eastern Newfoundland, notable difference in prey arthropod compositions was observed between two sampling times. Together, our results show tremendous undiscovered arthropod diversity in Newfoundland and that bat guano DNA metabarcoding can be an effective tool to help reveal this biodiversity. The implications of this research to bat conservation were discussed.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535748","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

Transcriptome sequencing of Phyla nodiflora identifies candidate transcripts associated with the biosynthesis of the anticancer compounds eupafolin and hispidulin. nodiflora门的转录组测序鉴定了与抗癌化合物eupafolin和hispidulin的生物合成相关的候选转录物。

IF 1.9 3区生物学

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

Tanuja, Madasamy Parani

{"title":"Transcriptome sequencing of Phyla nodiflora identifies candidate transcripts associated with the biosynthesis of the anticancer compounds eupafolin and hispidulin.","authors":"Tanuja, Madasamy Parani","doi":"10.1139/gen-2026-0063","DOIUrl":"https://doi.org/10.1139/gen-2026-0063","url":null,"abstract":"Cancer is a serious healthcare issue throughout the world. The rising demand for safe and efficient cancer treatments drives research on phytochemicals. Phyla nodiflora is a perennial species that contains potential anticancer compounds. Eupafolin and hispidulin from P. nodiflora demonstrated significant antitumor efficacy against several cancer types. Nonetheless, the biochemical pathways and genes encoding the enzymes required for the biosynthesis of these compounds remain unknown. Therefore, we sequenced the leaf, root, and flower transcriptomes to identify the transcripts involved in eupafolin and hispidulin biosynthesis. We assembled 113 956 transcripts and assigned 34 876 transcripts to 149 pathways. We associated 102 transcripts in the phenylpropanoid pathway with the biosynthesis of eupafolin and hispidulin. We identified 16 transcripts putatively encoding the enzymes that are associated with the biosynthesis of eupafolin and hispidulin for the first time. Together, these findings provide a transcriptomic framework for Phyla nodiflora that can guide future efforts in metabolic engineering and functional genomics, particularly in optimizing the biosynthesis of the anticancer compounds eupafolin and hispidulin.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","pages":"1-9"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148792309","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

Coffea comparative genomics reveals subgenome-associated expansion and diversification of biosynthetic gene clusters. 咖啡比较基因组学揭示了生物合成基因簇的亚基因组相关扩展和多样化。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0007

Daisy Sotero Chacon, Laura Natalia Gonzalez-Garcia, Vitor Trinca, Alessandro M Varani, Romain Guyot, Douglas Silva Domingues

{"title":"Coffea comparative genomics reveals subgenome-associated expansion and diversification of biosynthetic gene clusters.","authors":"Daisy Sotero Chacon, Laura Natalia Gonzalez-Garcia, Vitor Trinca, Alessandro M Varani, Romain Guyot, Douglas Silva Domingues","doi":"10.1139/gen-2026-0007","DOIUrl":"10.1139/gen-2026-0007","url":null,"abstract":"Biosynthetic gene clusters (BGCs) are important for plant specialized metabolism, but remain poorly characterized in coffee. Given Brazil's importance in coffee production, we performed a comparative genomic analysis of BGCs across the allotetraploid Coffea arabica and its diploid progenitors Coffea eugenioides and Coffea canephora. Using standardized genome filtering, annotation, orthogroup inference, and cluster classification, we identified 472 BGCs comprising 3118 biosynthetic genes, which were grouped into 194 cluster families and integrated with 28 280 orthogroups. Of these, 7091 orthogroups were shared across all species; Coffea canephora and subgenomes shared 10 923, while Coffea eugenioides and subgenomes shared 11 446. Most BGC-associated orthogroups (86.4%) link to a single pathway class. BGC-associated genes form a highly structured yet lineage-dynamic component of the Coffea pangenome. Coffea eugenioides and its derived subgenomes in Arabica contributed disproportionately to 14 BGC-associated orthogroups, including flavonoid-, lipid-, and stress-related functions. In contrast, Coffea canephora derivatives contributed only two terpene-related orthogroups. The parental species showed fewer secondary metabolism-related enriched Gene Ontology terms (3 and 1) than their subgenomes (53 and 56). Species-specific rearrangements, expansions, and subgenome retention indicate that hybridization and polyploidy shaped BGC diversification. These results advance understanding of specialized metabolism in Coffea and identify targets for coffee improvement and climate resilience.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","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":"148792254","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

Technological advances in trait development: from conventional breeding and untargeted mutagenesis to precision genome editing. 性状发育的技术进展：从传统育种和非靶向诱变到精确基因组编辑。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0020

Ladan Ajdanian, Sylvain Villot, Benjamin Karikari, Davoud Torkamaneh

{"title":"Technological advances in trait development: from conventional breeding and untargeted mutagenesis to precision genome editing.","authors":"Ladan Ajdanian, Sylvain Villot, Benjamin Karikari, Davoud Torkamaneh","doi":"10.1139/gen-2025-0020","DOIUrl":"10.1139/gen-2025-0020","url":null,"abstract":"Plant biotechnology has revolutionized modern agriculture by enabling precise and efficient crop improvement strategies. This review explores the evolution of selective breeding, mutation breeding, and precision breeding, highlighting their applications in Canada's agricultural sector. Conventional selective breeding has been instrumental in developing high-yielding and disease-resistant cultivars, while mutation breeding, through physical and chemical mutagenesis, has introduced valuable genetic diversity. The advent of transgenic breeding allowed for the direct insertion of foreign genes, leading to the development of crops with herbicide tolerance, pest resistance, and improved nutritional content. However, concerns over regulatory restrictions and public acceptance have driven the rapid adoption of genome editing tools, which enable precise modifications without introducing foreign DNA. Canada has played a key role in applying these biotechnological innovations, successfully developing genetically modified canola, CRISPR-edited wheat, stress-resistant soybean, and barley and oat cultivars improved for stress resistance and yield. While each breeding approach presents distinct advantages and limitations, integrating conventional and molecular techniques is essential for maximizing genetic potential, ensuring agriculture, and effectively food security challenges.","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":"145488205","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

delimtools: an R package for species delimitation. delimtools：一个用于物种划分的R包。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0119

Pedro S Bittencourt, Rupert A Collins, Tomas Hrbek

引用次数: 0

Large-scale DNA barcoding reveals highly distinct insect distribution patterns across Costa Rican ecosystems. 大规模的DNA条形码揭示了哥斯达黎加生态系统中高度不同的昆虫分布模式。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0128

José A Hernández Ugalde, Daniel H Janzen, Winnie Hallwachs, Bert Kohlmann, Paul D N Hebert, Brian V Brown, James Whitfield, José L Fernández-Triana, Roberto Fernández Ugalde, Eugenie Phillips Rodriguez, Ronald Zúñiga, M Alex Smith, Dirk Steinke, Michael Sharkey, Donald Quicke, Ramya Manjunath, Robert Puschendorf

{"title":"Large-scale DNA barcoding reveals highly distinct insect distribution patterns across Costa Rican ecosystems.","authors":"José A Hernández Ugalde, Daniel H Janzen, Winnie Hallwachs, Bert Kohlmann, Paul D N Hebert, Brian V Brown, James Whitfield, José L Fernández-Triana, Roberto Fernández Ugalde, Eugenie Phillips Rodriguez, Ronald Zúñiga, M Alex Smith, Dirk Steinke, Michael Sharkey, Donald Quicke, Ramya Manjunath, Robert Puschendorf","doi":"10.1139/gen-2025-0128","DOIUrl":"https://doi.org/10.1139/gen-2025-0128","url":null,"abstract":"Although insects are fundamental to understanding and conserving global biodiversity, they are vastly understudied. Here, we present a national inventory of Costa Rican insects based upon 3.78 million DNA barcodes representing 152 891 Barcode Index Numbers (BINs, proxies for species) from 28 localities sampled from 2017 to 2023 through the national BioAlfa program of Costa Rica. Although only 3.6% of BINs are linked to Linnean species, barcode-based community analyses revealed strong, consistent ecogeographic structure. Clustering of BIN data using bootstrapped Jaccard distances revealed seven distinct mainland assemblages and a distinct island cluster, shaped primarily by Costa Rica's mountain ranges, elevation, and slope orientation. Separate analyses for Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera coupled with analyses focused on some of their largest families (e.g., Braconidae, Cecidomyiidae, Cicadellidae, Erebidae, and Staphylinidae) confirmed these patterns and further revealed extremely high species turnover with most BINs being exclusive to a single region or locality. Our results reveal limited overlap of insect communities across ecosystems, implying that each life zone harbors unique taxonomic assemblages. Large-scale DNA barcoding has detected fine-grained spatial structure, providing a genomic framework for biodiversity monitoring and conservation in diverse tropical regions undergoing rapid environmental change.","PeriodicalId":12809,"journal":{"name":"Genome","volume":"69 ","pages":"1-26"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148684418","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

Characterization of the MLO gene family in Glycine max and its role in rust infection. 甘氨酸max MLO基因家族的鉴定及其在锈病中的作用。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0125

Matheus Mertz Ribeiro, Liliane Santana Oliveira, Bruna Barbosa Avelino, Valéria Yukari Abe, Fernanda Machado Castanho, Ivani de Oliveira Negrão Lopes, Adriana Brombini Dos Santos, Danielle C Gregório da Silva, Ricardo V Abdelnoor, Francismar Corrêa Marcelino-Guimarães

{"title":"Characterization of the MLO gene family in Glycine max and its role in rust infection.","authors":"Matheus Mertz Ribeiro, Liliane Santana Oliveira, Bruna Barbosa Avelino, Valéria Yukari Abe, Fernanda Machado Castanho, Ivani de Oliveira Negrão Lopes, Adriana Brombini Dos Santos, Danielle C Gregório da Silva, Ricardo V Abdelnoor, Francismar Corrêa Marcelino-Guimarães","doi":"10.1139/gen-2025-0125","DOIUrl":"https://doi.org/10.1139/gen-2025-0125","url":null,"abstract":"The MLO gene family plays a critical role in plant-pathogen interactions, regulating susceptibility and resistance to fungal diseases. In this study, we performed a genome-wide characterization of the MLO genes in soybean (Glycine max), integrating structural analysis, phylogenetic classification, expression profiling, functional validation by virus-induced gene silencing (VIGS), and SNP mining. We identified 40 MLO genes, including a novel member (GmMLO25) with an unusually small MLO domain (93 aa). Protein length varied from 130 to 600 aa, with differences in the number of transmembrane domains and conserved motifs, including calmodulin-binding domains (CaMBDs). Analysis of SNPs in coding sequences revealed missense substitutions affecting conserved motifs and transmembrane regions, particularly in clade V genes. RNA-seq and RT-qPCR analyses revealed differential regulation of clade V members between resistant (Rpp5) and susceptible (BRS 184) genotypes during Phakopsora pachyrhizi infection. Functional validation by VIGS demonstrated that silencing multiple clade V genes did not reduce the number of uredinia but drastically reduced fungal sporulation. This study identified GmMLO38 as a functional susceptibility gene in soybean and as a prime target for gene editing or RNAi-based strategies to enhance resistance to Asian soybean rust (ASR).","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":"148678268","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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