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A second gene for resistance to four pathotypes of Plasmodiophora brassicae identified in the Brassica napus cultivar 'Mendel'. 在甘蓝型油菜栽培品种“孟德尔”中发现了抗四种病型的第二个基因。

IF 2.3 3区生物学

Genome Pub Date : 2025-06-18 DOI: 10.1139/gen-2025-0017

Mizanur Rahamana, Stephen Strelkov, Hao Hu, Fuyou Fu, Fengqun Yu

{"title":"A second gene for resistance to four pathotypes of Plasmodiophora brassicae identified in the Brassica napus cultivar 'Mendel'.","authors":"Mizanur Rahamana, Stephen Strelkov, Hao Hu, Fuyou Fu, Fengqun Yu","doi":"10.1139/gen-2025-0017","DOIUrl":"https://doi.org/10.1139/gen-2025-0017","url":null,"abstract":"Clubroot, caused by the obligate parasite Plasmodiophora brassicae, poses a significant threat to the Canadian canola industry, resulting in substantial yield losses. Genetic resistance is an effective strategy for managing the disease. In this study, 137 doubled haploid (DH) lines derived from the European oilseed rape cultivar 'Mendel' were phenotyped against P. brassicae pathotypes 3D, 5C, and 8J, which are aggressive toward the first-generation clubroot-resistant canola cultivars, and were genotyped using genotyping-by-sequencing. Disease severity indices in the population were highly correlated among the three pathotypes, with correlation coefficients of r ≥ 0.82. In the DH population, 2,642 high-quality SNPs were detected by employing the B. napus 'ZS11' reference genome. A single quantitative trait locus (QTL), Rcr3Mendel, was detected and mapped to a 317 kb region on chromosome A08, flanked by the markers ZS_A08_15999175 and ZS_A08_16316110. Within this region, 43 genes were identified, including a single Toll interleukin-1 receptor (TIR) nucleotide-binding site (NBS)-leucine-rich repeat (LRR) (TNL) gene, BnaA08T0102200ZS. This region is homologous to the 13,415,472 to 15,791,728 bp region of chromosome A08 in B. rapa ECD 04, the donor of clubroot resistance in 'Mendel'. Two TNL genes, BraA08g039211E and BraA08g039212E, were identified in the ECD 04 genome. Kompetitive Allele-Specific PCR analysis identified eight markers that co-segregated with Rcr3Mendel. Resistance to pathotype 3H was also found to co-segregate with resistance to pathotypes 5C, 3D, and 8J.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325301","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 analysis of Brassica napus near-isogenic lines carrying clubroot resistance from turnip (B. rapa var. rapifera). 甘蓝型油菜近等基因系携带芜菁根茎抗性的转录组分析。

IF 2.3 3区生物学

Genome Pub Date : 2025-06-06 DOI: 10.1139/gen-2024-0182

Kawalpreet Kaur, Urmila Basu, Nat N V Kav, Habibur Rahman

{"title":"Transcriptome analysis of Brassica napus near-isogenic lines carrying clubroot resistance from turnip (B. rapa var. rapifera).","authors":"Kawalpreet Kaur, Urmila Basu, Nat N V Kav, Habibur Rahman","doi":"10.1139/gen-2024-0182","DOIUrl":"https://doi.org/10.1139/gen-2024-0182","url":null,"abstract":"Understanding the intricate molecular interplay between Brassica hosts and the pathogen Plasmodiophora brassicae, causative agent of clubroot disease, is pivotal for devising effective resistance to this disease in Brassica crops. While existing transcriptomic studies have elucidated the host responses to pathogen infection, a comprehensive analysis employing near-isogenic lines (NILs) remains imperative for better understanding of the resistance mechanisms. In this study, we conducted a comparative transcriptome profiling utilizing clubroot-susceptible (CS-NILs) and clubroot-resistant (CR-NILs) near-isogenic Brassica napus lines, carrying the clubroot resistance of turnip (B. rapa var. rapifera), at 7 and 14 days after inoculation. We observed the upregulation of the genes governing phytohormone signaling, receptor kinases, transcription factors, calcium fluxes, and glucosinolate metabolism in the CR-NILs. In addition, the novel differentially expressed genes (DEGs) pertaining to jasmonic acid, calcium signaling, receptor kinases, and glucosinolate biosynthesis were also observed to be differentially expressed. Based on our results, we propose a comprehensive model delineating the molecular events potentially contributing to clubroot resistance in B. napus CR-NILs. Our findings have contributed to an enhanced understanding of the potential mechanisms involved in clubroot resistance which may have utility in targeted breeding initiatives to mitigate the threat of clubroot disease in Brassica crops including canola.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247486","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

Diversity and T-cell antigenic potentials of Mycoplasma mycoides subsp. mycoides vaccine candidates. 支原体亚种的多样性和t细胞抗原性。真菌候选疫苗。

IF 2.3 3区生物学

Genome Pub Date : 2025-06-03 DOI: 10.1139/gen-2024-0177

Emily L Wynn, Rohana P Dassanayake, Daniel W Nielsen, Eduardo Casas, Michael Clawson

{"title":"Diversity and T-cell antigenic potentials of Mycoplasma mycoides subsp. mycoides vaccine candidates.","authors":"Emily L Wynn, Rohana P Dassanayake, Daniel W Nielsen, Eduardo Casas, Michael Clawson","doi":"10.1139/gen-2024-0177","DOIUrl":"https://doi.org/10.1139/gen-2024-0177","url":null,"abstract":"Mycoplasma mycoides subsp mycoides (Mmm) is the causative agent of contagious bovine pleuropneumonia (CBPP), a severe respiratory disease affecting cattle mostly in sub-Saharan African countries. CBPP can cause significant economic losses, and there is a need for efficacious vaccines to help bring the disease under control. To that end, all publicly available non-redundant whole genome sequences of Mmm strains isolated from cattle (n=15) were used to identify a 93% core genome of 806 genes, which included 86 of 208 genes encoding outer membrane and extracellular proteins identified from the literature. Many of them and their encoded protein products were found to be highly conserved at the sequence level, including at the sites of predicted epitope binding with bovine major histocompatibility complex (MHC) Class I and II molecules. Despite the high sequence conservation, multiple proteins had large differences in the numbers of MHC Class I and II epitopes and their predicted binding strengths. These results highlight several promising targets supporting the development of new recombinant protein vaccines for CBPP.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215679","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

First insights into the satellitomes and new evidence for the absence of canonical insect telomere in the Neuroptera order. 首次深入了解卫星组和神经翅目昆虫端粒缺失的新证据。

IF 2.3 3区生物学

Genome Pub Date : 2025-05-30 DOI: 10.1139/gen-2025-0018

Diogo C Cabral-de-Mello, Ana Elisa Gasparotto, José M Rico-Porras, Ana Beatriz S M Ferretti, Pablo Mora-Ruiz, Rhavenna Thais Alves-Gomes, Vitória Lourejan, Elton L Scudeler, Pedro Lorite, Vanessa B Bardella

{"title":"First insights into the satellitomes and new evidence for the absence of canonical insect telomere in the Neuroptera order.","authors":"Diogo C Cabral-de-Mello, Ana Elisa Gasparotto, José M Rico-Porras, Ana Beatriz S M Ferretti, Pablo Mora-Ruiz, Rhavenna Thais Alves-Gomes, Vitória Lourejan, Elton L Scudeler, Pedro Lorite, Vanessa B Bardella","doi":"10.1139/gen-2025-0018","DOIUrl":"https://doi.org/10.1139/gen-2025-0018","url":null,"abstract":"Repetitive DNA is a major component of eukaryotic genomes, playing structural and evolutionary roles. However, in Neuroptera, its characterization remains unexplored. To address this, we analyzed the satellitomes of two Chrysopini (Chrysopidae) species using cytogenomic tools, also investigating telomeric and ribosomal DNA (rDNA). The canonical insect telomeric motif was absent, and rDNA clusters showed variation compared to other neuropterans, despite karyotype stasis (2n = 12, XY). Satellite DNA (satDNA) abundance varied between Ceraeochrysa cincta and Chrysopa pallens, representing a minor fraction of their repetitive DNA content. Notably, no satDNA sequences were shared between species, suggesting a rapid turnover. Exceptionally, the second most abundant satDNA in each species showed low sequence similarity and a putative common origin. A relationship between satDNAs and transposable elements (TEs) was also observed. Chromosome mapping revealed that abundant satDNAs accumulated in euchromatin, providing insights into their genomic distribution. These findings enhance our understanding of satDNA organization in Neuroptera, offering a foundation for future genome assembly efforts and evolutionary studies in these insects.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186865","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

Understanding the genomics responses of freshwater zooplanktons to salinization: a research hotspot in a saltier world. 了解淡水浮游动物对盐碱化的基因组反应：盐碱化世界的研究热点。

IF 2.3 3区生物学

Genome Pub Date : 2025-05-30 DOI: 10.1139/gen-2024-0129

Ran Bi, Leyao Xiao, Lei Zhao, Bret L Coggins, Sen Xu, Michael E Pfrender, Mingbo Yin

引用次数: 0

Candidate genes validation for intramuscular fat content of Nellore Cattle. 内洛牛肌内脂肪含量候选基因验证。

IF 2.3 3区生物学

Genome Pub Date : 2025-05-28 DOI: 10.1139/gen-2024-0176

Bruna Maria Salatta, Larissa Fernanda Simielli Fonseca, Gabriela Bonfá Frezarim, Natalia Andrea Marín Garzón, Danielly Beraldo Dos Santos Silva, Lucio Flavio Macedo Mota, Marta Serna-García, Sindy Liliana Caivio Nasner, Leonardo Machestropa Arikawa, Patricia Iana Schmidt, Tiago Bresolin, Luis Artur Loyola Chardulo, Jesus Aparecido Ferro, Alexéia Barufatti, Lucia Galvão Albuquerque

{"title":"Candidate genes validation for intramuscular fat content of Nellore Cattle.","authors":"Bruna Maria Salatta, Larissa Fernanda Simielli Fonseca, Gabriela Bonfá Frezarim, Natalia Andrea Marín Garzón, Danielly Beraldo Dos Santos Silva, Lucio Flavio Macedo Mota, Marta Serna-García, Sindy Liliana Caivio Nasner, Leonardo Machestropa Arikawa, Patricia Iana Schmidt, Tiago Bresolin, Luis Artur Loyola Chardulo, Jesus Aparecido Ferro, Alexéia Barufatti, Lucia Galvão Albuquerque","doi":"10.1139/gen-2024-0176","DOIUrl":"https://doi.org/10.1139/gen-2024-0176","url":null,"abstract":"Intramuscular fat is an important factor for the sensory quality and value of meat. However, in tropical breeds such as Nellore, the lower marbling capacity represents a challenge for its positioning in premium markets. Marbling score (MS) and the total lipid (TL) determination methods are complementary methodologies for measuring beef intramuscular fat. Longissimus thoracis samples from the 24 most extreme steers (out of 189 steers) for MS (high = 12 and low = 12) and TL (high = 12 and low = 12) traits were collected to: 1) validate in Nellore cattle differentially expressed genes for MS and TL traits found in the literature in other populations using real-time PCR, and 2) verify if differentially expressed genes were translated into differentially expressed proteins through advanced mass spectrometry (LC-MS/MS). Significant differences in the expression levels of the genes FABP4, DGAT1, DGAT2, BARX2, STAT5A, and SDC were observed in the group with high intramuscular fat content. These genes play important roles in lipid metabolism, adipogenesis and muscle development. Proteins encoded by genes (PRDM1 and COL1A2) regulated by the transcription factor STAT5A were differentially expressed and probably play a key role during intramuscular fat deposition. Our results confirm that the genes FABP4, DGAT1, DGAT2, STAT5A, and BARX2 validated here can potentially be used as biomarkers for intramuscular fat in Nellore cattle.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173104","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

Molecular characterization and chromosomal distribution of Tc1/mariner transposons in Boana species (Anura, Hylidae). Boana物种（无尾目，水螅科）Tc1/mariner转座子的分子特征和染色体分布

IF 2.3 3区生物学

Genome Pub Date : 2025-05-28 DOI: 10.1139/gen-2025-0004

Sebastião Venancio Neto, Matheus Azambuja, Viviane Nascimento, Viviane Nogaroto, Marcelo Ricardo Vicari, Rafael Noleto

{"title":"Molecular characterization and chromosomal distribution of Tc1/mariner transposons in Boana species (Anura, Hylidae).","authors":"Sebastião Venancio Neto, Matheus Azambuja, Viviane Nascimento, Viviane Nogaroto, Marcelo Ricardo Vicari, Rafael Noleto","doi":"10.1139/gen-2025-0004","DOIUrl":"https://doi.org/10.1139/gen-2025-0004","url":null,"abstract":"Transposable elements play an important role in determining the size and structure of eukaryotic genomes. Represented by several families, the Tc1/mariner superfamily is widely distributed in animal and plant genomes, and its structure has been characterized. Boana is a Neotropical genus of treefrogs, and despite the frequent 2n = 24 chromosomes found in its representatives, the karyotypic organization of the species cannot be considered conserved due to the scarcity of studies focusing on chromosomal mapping of repetitive DNA sequences. Here, Tc1/mariner elements were isolated and mapped on the chromosomes of three Boana species, followed by structural and phylogenetic analysis. The physical mapping revealed dispersed signals in euchromatin with small accumulations in some heterochromatic regions. All Tc1/mariner transposons isolated in this study presented high sequence integrity, suggesting that these elements had a recent invasion phase and are active in the host genomes of these frog species. Boana albopuntata and B. faber presented a DD36E signature, while B. prasina showed a new DD37E signature with a similar organizational structure and a close relationship with the known DD36E/Incomer family. These findings improve our understanding of the diversity of Tc1/mariner transposons and their role in the evolution of the hylid frog genome and karyotype.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144173186","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