IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0017

Nayla Zalzalah, Julia C Wozny, Jakob Bruggink, Mohamad Elian, Tim Xing, Elroy R Cober, Bahram Samanfar

{"title":"Molecular network analysis of gene co-expression driving seed oil content in soybean.","authors":"Nayla Zalzalah, Julia C Wozny, Jakob Bruggink, Mohamad Elian, Tim Xing, Elroy R Cober, Bahram Samanfar","doi":"10.1139/gen-2026-0017","DOIUrl":"10.1139/gen-2026-0017","url":null,"abstract":"Soybean seed composition is governed by an inverse correlation between protein and oil, a relationship complicated by environmental factors. In Canada, western grown soybeans consistently have lower seed protein than eastern grown soybeans, a pattern driven by genotype by environment interactions that modulate the protein-oil balance. To uncover the transcriptional networks behind these differences, a multi-year weighted gene co-expression network analysis was performed on leaf transcriptomes from 10 soybean genotypes cultivated in contrasting eastern and western environments. The analysis identified oil-associated co-expression modules preserved across years and environments; their eigengenes showed significant, consistent correlations with seed oil content each year. A core set of recurring hub genes formed the backbone of this network, many of which co-localize with major seed composition quantitative trait loci (QTLs). Notably, a key hub lies adjacent to the protein-oil trade-off regulator on chromosome 20, while additional hubs map within a QTL on chromosome 10 linked to a more favourable protein-oil balance. The relationship between module expression and oil content displayed a genotype by environment interaction, providing a molecular basis for phenotypic differences between eastern and western regions. These hub transcription factors are prime candidates for breeding soybean cultivars with improved seed composition.","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":"148792323","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

Low complexity (A/C)GG repeats and m¹A methylation sites in 5' UTRs regulate gene expression. 低复杂度（A/C）GG重复序列和5 ' UTRs中的m1 A甲基化位点调控基因表达。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0071

Zachery W Dickson, Megan Bilodeau, Daniel L Ruiz, G Brian Golding

{"title":"Low complexity (A/C)GG repeats and m1A methylation sites in 5' UTRs regulate gene expression.","authors":"Zachery W Dickson, Megan Bilodeau, Daniel L Ruiz, G Brian Golding","doi":"10.1139/gen-2025-0071","DOIUrl":"10.1139/gen-2025-0071","url":null,"abstract":"Repetitive and compositionally biased low-complexity (LC) motifs appear in biological sequences where they interact with the machinery controlling the abundance of their host molecules. They can have significant impacts on physiological function, and act as raw material for evolution of regulatory motifs. The extent to which LC motifs affect abundance is not known. Even definitions of LC sequences are not well established, let alone which motifs exists in LC sequences, and which of those are abundance associated. To fill these knowledge gaps for post-transcriptional impacts of LC motifs, we integrated data from the GTEx project, PaxDb, and the IGSR. We establish definitions for LC motifs in both RNA and protein sequences. We observed that the presence of LC motifs in the 5' untranslated regions (UTRs) were positively associated with transcript abundance. We present a method to de novo identify abundance associated motifs and identified trinucleotide repeats of (A/C)GG as most strongly abundance associated. We observed that m1A methylation sites were strongly associated with both LC motifs and abundance, an effect which is amplified as methylation signatures from unspecialized RNA-seq increased. Together, our results demonstrate that LC motifs play important roles in regulating gene expression.","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":"145943335","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

Cytogenetic diversity in maize landraces shaped by long-term cultivation and ecogeographic adaptation. 长期栽培和生态地理适应对玉米地方品种细胞遗传多样性的影响。

IF 1.9 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2026-0002

María Florencia Realini, María Del Pilar Plastine, Lidia Poggio, Graciela E González

{"title":"Cytogenetic diversity in maize landraces shaped by long-term cultivation and ecogeographic adaptation.","authors":"María Florencia Realini, María Del Pilar Plastine, Lidia Poggio, Graciela E González","doi":"10.1139/gen-2026-0002","DOIUrl":"10.1139/gen-2026-0002","url":null,"abstract":"This study characterizes the cytogenetic diversity of maize landraces from Northern Argentina, a region comprising Northwestern Argentina (NWA) and Northeastern Argentina (NEA). New data from four NWA landraces were analyzed using DAPI banding, fluorescence in situ hybridization, and flow cytometry. Intra- and inter-populational variation was detected in heterochromatin content (2.06%-12.6%), as well as in the number (3-15), size, and chromosomal position of knobs. Genome size (2C value) ranged from 5.27 to 5.74 pg, and numerical polymorphism (0-2) of B chromosomes was observed. Consensus idiograms were constructed for each studied landrace. A quantitative analysis combining these data with previously published information on Argentine maize revealed a negative association between knob heterochromatin content and cultivation altitude. In NWA landraces, genome size was also negatively associated with altitude, whereas no such relationship was detected when NWA and NEA data were analyzed together. In NEA landraces, which grow within a narrow altitudinal range, genome size variability may be influenced by local farmers selection practices, whereas in NWA landraces cytogenetic variation may reflect multifactorial anthropogenic and environmental influences. B chromosomes were recorded exclusively at altitudes above 2000 m.a.s.l. The observed cytogenetic patterns are discussed in the context of ecogeographic differentiation among maize landraces.","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":"148850443","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

Resistance genes against yellow rust pathogen in Triticum spelta: a possible new Yr resistance gene in accession IARI276 and Yr5 presence confirmed in PI348764. 小麦黄锈病的抗性基因：在PI348764中发现了可能的新抗病基因IARI276和Yr5。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0171

Lovely Arya, Malavika N Shal, M Niranjana, S K Jha, Madhu Patial, M S Saharan, N Mallick, K Raghunandan, A Priyanka, D P Walia, S M S Tomar, Vinod

{"title":"Resistance genes against yellow rust pathogen in Triticum spelta: a possible new Yr resistance gene in accession IARI276 and Yr5 presence confirmed in PI348764.","authors":"Lovely Arya, Malavika N Shal, M Niranjana, S K Jha, Madhu Patial, M S Saharan, N Mallick, K Raghunandan, A Priyanka, D P Walia, S M S Tomar, Vinod","doi":"10.1139/gen-2024-0171","DOIUrl":"10.1139/gen-2024-0171","url":null,"abstract":"Yellow/stripe rust caused by Puccinia striiformis f. sp. tritici is a major biotic stress in global wheat production. Introgression lines derived from the Triticum spelta accessions PI348764 and IARI276 showed high levels of yellow rust resistance at seedling and adult plant stage. The Yr5 gene located on 2B chromosome was previously the only stripe rust resistance gene described in T. spelta gene pool. By genotyping parental and introgressed material with markers linked with the Yr5 gene, we demonstrate that PI348764 likely carries Yr5, and that it appears to be absent from IARI276. By employing a combination of methods, including screening for adult plant resistance and seedling resistance at multiple field trials, bulked segregant analysis (BSA) on F5 families, and genotyping using wheat Breeders' 35K array, we show that YrIARI276 is a novel stripe rust resistance gene with putative chromosomal locations on 1BL, 1DL, 5AL, or 7BL. Furthermore, genetic analysis revealed that YrIARI276 showed a goodness of fit to Mendelian ratios for a single dominant gene. As the gene is distinct from Yr5 and the chromosomal location is unique from earlier reported Yr genes, it will be useful in improving diversity of Yr gene repertoire in disease resistance breeding programmes.","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":"143604688","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

Satellitome analysis on Microtus thomasi (Arvicolinae) genome, a mammal species with high karyotype and sex chromosome variations. 对具有高度核型和性染色体变异的哺乳动物--Microtus thomasi（Arvicolinae）基因组进行卫星组分析。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0141

Gaël Aleix-Mata, Eugenia E Montiel, Pablo Mora, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez

{"title":"Satellitome analysis on Microtus thomasi (Arvicolinae) genome, a mammal species with high karyotype and sex chromosome variations.","authors":"Gaël Aleix-Mata, Eugenia E Montiel, Pablo Mora, Alona Yurchenko, José M Rico-Porras, Francisco Anguita, Fátima Palomo, Juan Alberto Marchal, Michail Rovatsos, Antonio Sánchez","doi":"10.1139/gen-2024-0141","DOIUrl":"10.1139/gen-2024-0141","url":null,"abstract":"The voles of the Microtus thomasi/Microtus atticus species complex (Arvicolinae) display extensive karyotypic variation, in the number of autosomes and the morphology of sex chromosomes. We analyzed the satellitome of Microtus thomasi and identified 17 satellite DNA (satDNA) families, corresponding to 6.704% of the genome. Homogenization and divergence analyses showed that some satDNA families are more homogeneous, indicative of recent amplification, while others displayed higher variation, suggesting ancient amplification. Twelve of the satDNA families are conserved across Arvicolinae with a substantial variation in the abundance and the composition. These results support the \"library\" hypothesis, where a shared collection of satDNAs exists across related species, with differential amplification driving species-specific genomic profiles. Localization analysis demonstrated that an increased number of satDNA families are localized in the pericentromeric and the heterochromatic regions of autosomes and sex chromosomes. Our results suggest that the heterochromatin of the X and Y chromosomes co-evolved and that satDNA families might have contributed to the chromosomal rearrangements involved in the karyotypic variation and sex chromosome polymorphism of the chromosomal races. Our study contributes to a deeper understanding of the evolutionary mechanisms underlying karyotype diversification in Microtus species, which exhibit some of the highest rates of karyotypic variation among mammals.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-13"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143398732","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 filamins of Drosophila. 果蝇的典型和非典型丝状结构。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0159

Tiara Mulder, Jennifer Johnson, Nicanor González-Morales

引用次数: 0

Peroxisome inter-organelle cooperation in Drosophila. 果蝇的过氧物酶体细胞器间合作

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-10-29 DOI: 10.1139/gen-2024-0082

Andy Y Cheng, Andrew J Simmonds

{"title":"Peroxisome inter-organelle cooperation in Drosophila.","authors":"Andy Y Cheng, Andrew J Simmonds","doi":"10.1139/gen-2024-0082","DOIUrl":"10.1139/gen-2024-0082","url":null,"abstract":"Many cellular functions are compartmentalized within the optimized environments of organelles. However, processing or storage of metabolites from the same pathway can occur in multiple organelles. Thus, spatially separated organelles need to cooperate functionally. Coordination between organelles in different specialized cells is also needed, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Peroxisomes coordinate with other organelles including mitochondria, endoplasmic reticulum, lysosomes, and lipid droplets. This functional coordination requires, or is at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","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":"142545118","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

A quick guide to the calcium-dependent protein kinase family in Brassica napus. 油菜钙依赖性蛋白激酶家族快速指南。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1139/gen-2024-0053

Virginia Natali Miguel, Jacqueline Monaghan

引用次数: 0

AVITI as an alternative to Illumina for low-cost genome-wide genotyping. AVITI作为Illumina低成本全基因组基因分型的替代品。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 DOI: 10.1139/gen-2024-0068

Maxime de Ronne, Brian Boyle, Davoud Torkamaneh

{"title":"AVITI as an alternative to Illumina for low-cost genome-wide genotyping.","authors":"Maxime de Ronne, Brian Boyle, Davoud Torkamaneh","doi":"10.1139/gen-2024-0068","DOIUrl":"10.1139/gen-2024-0068","url":null,"abstract":"Advancements in sequencing technologies have dramatically transformed genomics research by enabling the analysis of genetic information with unprecedented scale and efficiency. Next-generation sequencing, renowned for its high-throughput capabilities, has significantly reduced costs and expanded the scope of sequencing applications. Among these, sequencing by synthesis on Illumina systems is predominant, favored for its accuracy and cost-effectiveness. However, emerging technologies like Element Biosciences' sequencing by Avidity (AVITI) are beginning to challenge this dominance. In this study, we sequenced and genotyped a library of 40 Cannabis samples using both the AVITI and Illumina NovaSeq systems. After filtering out low-quality variants, both technologies showed an 81.2% overlap with 98.9% concordance in genotype calls. AVITI stands out for its flexibility and reduced per-base costs, presenting a viable option particularly for mid-sized laboratories. As the scientific community continues to seek ways to lower genotyping expenses, the combination of the AVITI system with NanoGBS library preparation offers a cost-effective solution adaptable to a wide range of project sizes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-4"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457576","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

A phylogenetic perspective of chromosome evolution in Formicidae. 从系统进化的角度看姬蜂科的染色体进化。

IF 2.3 3区生物学

Genome Pub Date : 2025-01-01 Epub Date: 2024-12-16 DOI: 10.1139/gen-2024-0124

Danon Clemes Cardoso, Maykon Passos Cristiano

{"title":"A phylogenetic perspective of chromosome evolution in Formicidae.","authors":"Danon Clemes Cardoso, Maykon Passos Cristiano","doi":"10.1139/gen-2024-0124","DOIUrl":"10.1139/gen-2024-0124","url":null,"abstract":"Chromosomes, as carriers of genes, are the fundamental units of heredity, with the eukaryotic genome divided into multiple chromosomes. Each species typically has a consistent number of chromosomes within its lineage. Ants, however, display remarkable diversity in chromosome numbers, and previous studies have shown that this variation may correlate with ant diversity. As ants evolved, various karyotypes emerged, primarily through chromosomal fissions, leading to an increase in chromosome number and a decrease in chromosome size. In this study, we investigate chromosome evolution in ants from a phylogenetic perspective using ancestral reconstruction. Our analysis indicates that the most recent common ancestor of ants had an ancestral haploid chromosome number of 11, likely composed of biarmed chromosomes. The bimodal distribution of karyotypes and the trend toward increased chromosome numbers align with previous assumptions. However, both dysploidy and ploidy changes have been indicated as likely mechanisms of chromosome number evolution. Descending dysploidy occurs consistently throughout the phylogeny, while changes in ploidy are believed to occur occasionally within the subfamilies during genus diversification. We propose, based on our results and previous evidence (e.g., genome size in ants), that both fusions and fissions contribute equally to karyotype changes in Formicidae. Additionally, changes in ploidy should not be fully ignored, as they can occur across specific lineages.","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":"142835349","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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