Genome最新文献 - Book学术

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

Single-cross prediction with imputed multi-omic data: A case study in rapeseed. 基于多组数据的单杂交预测：以油菜为例。

IF 2.3 3区生物学

Genome Pub Date : 2025-05-05 DOI: 10.1139/gen-2025-0010

Sven Ernst Weber, Lennard Roscher-Ehrig, Silvia Zanini, Gözde Yildiz, Amine Abbadi, T Kox, Agnieszka Golicz, Rod J Snowdon

{"title":"Single-cross prediction with imputed multi-omic data: A case study in rapeseed.","authors":"Sven Ernst Weber, Lennard Roscher-Ehrig, Silvia Zanini, Gözde Yildiz, Amine Abbadi, T Kox, Agnieszka Golicz, Rod J Snowdon","doi":"10.1139/gen-2025-0010","DOIUrl":"https://doi.org/10.1139/gen-2025-0010","url":null,"abstract":"Advancements in sequencing technologies enabled the assembly and characterization of plant genomes with high resolution. In breeding programs, this data is combined with phenotypic information in genomic prediction to select genotypes based on their genetic profiles. Although SNP arrays are commonly used for genotyping, they capture only a fraction of the genomewide diversity. To address this, one approach involves genotyping the entire population with arrays, sequence a subset using whole-genome sequencing (WGS) or assessing gene expression profiles, followed by imputing the data across the entire population. This study evaluates the effect of imputed WGS markers (SNPs and structural variants) and expression data on genomic prediction in a rapeseed hybrid breeding population. A combination of SNP arrays, WGS, and RNA sequencing was employed, followed by imputation of marker and expression data. Genomic prediction was utilized to estimate general and specific combining ability effects in untested hybrids. However, while adding imputed whole-genome and expression data increased marker density and linkage disequilibrium, it didn´t enhance prediction accuracy compared to SNP array data. This is attributed to redundancy in relationship, imputation errors, or environmental influences on gene expressions. This suggests that SNP arrays continue to be reliable for genomic prediction in rapeseed hybrid breeding.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009011","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

Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium, and Novosphingobium collected from freshwater sources. 从淡水来源收集的三个假定的烃类降解属Limnohabitans， aquabobacterium和Novosphingobium的全基因组分析。

IF 2.3 3区生物学

Genome Pub Date : 2025-05-02 DOI: 10.1139/gen-2023-0099

Gurpreet Kharey, Vince Palace, Lyle Whyte, Charles Greer

{"title":"Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium, and Novosphingobium collected from freshwater sources.","authors":"Gurpreet Kharey, Vince Palace, Lyle Whyte, Charles Greer","doi":"10.1139/gen-2023-0099","DOIUrl":"https://doi.org/10.1139/gen-2023-0099","url":null,"abstract":"A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of 3 environmentally relevant genera, Limnohabitans, Aquabacterium, and Novosphingobium. These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans, 10 Aquabacterium, and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016944","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