Genome最新文献 - Book学术

Towards a more pluralistic approach to evaluating the farm-level impacts of New Breeding Technologies in sub-Saharan Africa. 在撒哈拉以南非洲采用更多元化的方法来评估新育种技术对农场的影响。

IF 1.7 3区生物学

Genome Pub Date : 2025-09-18 DOI: 10.1139/gen-2025-0023

Matthew A Schnurr, Helena Shilomboleni, Alanna Taylor, Brian Dowd-Uribe

引用次数: 0

In silico analysis of secreted proteins via Sec- and Tat-pathways of Clavibacter spp. unravels functional diversity related to plant host range. 通过对锁骨杆菌（Clavibacter）的Sec-和tat -通路分泌蛋白的计算机分析，揭示了与植物寄主范围相关的功能多样性。

IF 1.7 3区生物学

Genome Pub Date : 2025-09-16 DOI: 10.1139/gen-2025-0037

Victor Adrian Hernandez-Aranda, Ramon Jarquin-Galvez, Gisela Aguilar-Benitez, Delia Xochil Vega-Manriquez, Moisés Roberto Vallejo-Pérez, Martin Escoto-Rodriguez, Robert Winkler, Jose-Pablo Lara-Avila

{"title":"In silico analysis of secreted proteins via Sec- and Tat-pathways of Clavibacter spp. unravels functional diversity related to plant host range.","authors":"Victor Adrian Hernandez-Aranda, Ramon Jarquin-Galvez, Gisela Aguilar-Benitez, Delia Xochil Vega-Manriquez, Moisés Roberto Vallejo-Pérez, Martin Escoto-Rodriguez, Robert Winkler, Jose-Pablo Lara-Avila","doi":"10.1139/gen-2025-0037","DOIUrl":"https://doi.org/10.1139/gen-2025-0037","url":null,"abstract":"Clavibacter genus comprises phytopathogenic and non-phytopathogenic species in a range of plant hosts. We applied structural and functional approaches for comparative genomics to unveil the adaptation of Clavibacter to plant hosts. The structural approach consisted of phylogeny and whole-genome alignment. The phylogeny suggested that C. tessallarius, C. zhangzhiyongii, C. capcisi, C. phaseoli depicted the more divergent species. Notably, C. nebraskensis, C. insidiosus, C. sepedonicus, Clavibacter sp. A6099, C. californiensis, and C. michiganensis formed a recent monophyletic clade. A synteny degree and genome rearrangements were noted. The functional approach based on prediction-annotation of secreted proteins via Sec and Tat pathways, and the prediction of metabolite biosynthetic potential. Regarding to Sec- and Tat-secreted proteins, we focused on carbohydrate-active enzymes (CAZymes) and expansins. The repertoire of secreted CAZymes exhibited variation related to taxonomy of Clavibacter. The predicted expansins harbored domain variability, related to horizontal gene transfer. A heterogeneous distribution-conservation of biosynthetic genetic clusters (BGCs) regarding Clavibacter phylogeny was observed. Our results suggested that farm practices of plant hosts likely influence the evolutive history of Clavibacter spp. Furthermore, Sec-, Tat-mediated secreted proteins and metabolite diversity may underpin plant-Clavibacter interactions. Biological knowledge drives sustainable strategies aimed to control plant diseases caused by Clavibacter spp.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075156","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

Strains of Apis mellifera ligustica honey bees artificially bred for apicultural traits are not consistently differentiated by mitochondrial DNA genome markers. 利用线粒体DNA基因组标记对人工培育的蜜蜂品系进行分化的结果并不一致。

IF 1.7 3区生物学

Genome Pub Date : 2025-08-08 DOI: 10.1139/gen-2025-0033

Steven M Carr

{"title":"Strains of Apis mellifera ligustica honey bees artificially bred for apicultural traits are not consistently differentiated by mitochondrial DNA genome markers.","authors":"Steven M Carr","doi":"10.1139/gen-2025-0033","DOIUrl":"https://doi.org/10.1139/gen-2025-0033","url":null,"abstract":"Strains of the Italian honey bee Apis mellifera ligustica Spinola, 1806 are selectively bred for desirable apiculture traits. Ma et al. (2022) examined SNP differences in mtDNA genomes between a strain bred for enhanced royal jelly production (RJB) with an unselected strain (ITB). Kim et al. (2019) compared SNP and intergenic repeats differences between a Varroa mite resistant strain bred for high-hygienic behavior (HHB) with an unselected low-hygienic strain (LHB). Phylogenetic comparison of 23 complete A. m. ligustica mtDNA sequences, including the two HHB and LHB strains and 15 RJB and ITB haplotypes and those of other subspecies (Carr 2023), shows significant clade structure for SNP differences and amino acid substitutions, however this structure is not diagnostic of the strains under selection. Numbers of repeats show little or no phylogenetic signal: similarities are symplesiomorphic and differences convergent. Differences between the HHB and LHB strains arise from coincidental fixation of alternative SNPs in different clades. Lineages within the RJB and ITB strains are not reciprocally monophyletic, and are often identical or near identical to those in the other strain or to other variant strains. Evaluation of the diagnostic and (or) adaptive significance of mtDNA markers requires broad knowledge of within-subspecies polymorphism.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803962","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