Genome最新文献

{"title":"A quick guide to the calcium-dependent protein kinase family in <i>Brassica napus</i>.","authors":"Virginia Natali Miguel, Jacqueline Monaghan","doi":"10.1139/gen-2024-0053","DOIUrl":"10.1139/gen-2024-0053","url":null,"abstract":"<p><p><i>Brassica napus</i>, commonly known as rapeseed or canola, is an economically valuable oilseed crop grown throughout Canada that currently faces several challenges due to industrial farming practices as well as a changing climate. Calcium-dependent protein kinases (CDPKs) are key regulators of stress signaling in multiple plant species. CDPKs sense changes in cellular calcium levels via a calmodulin-like domain and are able to respond to these changes via their protein kinase domain. In this mini-review, we provide a quick guide to BnaCDPKs. We present an updated phylogeny of the BnaCDPK family in relation to CDPKs from <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i> and we provide a standardized nomenclature for the large BnaCDPK family that contains many co-orthologs. We analyze expression patterns of <i>BnaCDPKs</i> across tissue types and in response to abiotic and biotic stresses, and we summarize known functions of BnaCDPKs. We hope this guide is useful to anyone interested in exploring the prospect of harnessing the potential of <i>BnaCDPKs</i> in the generation of elite cultivars of <i>B. napus</i>.</p>","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":"142580807","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}

{"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":"<p><p>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 <i>Cannabis</i> 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.</p>","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}

{"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":"<p><p>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.</p>","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}

{"title":"Chromosomal and molecular perspectives on <i>Potamotrygon motoro</i> (Müller & Henle, 1841) from central Amazon.","authors":"Alex M V Ferreira, Patrik F Viana, Leandro Marajó, Eliana Feldberg","doi":"10.1139/gen-2024-0153","DOIUrl":"10.1139/gen-2024-0153","url":null,"abstract":"<p><p>Cytogenetic studies on <i>Potamotrygon motoro</i> (Müller & Henle, 1841) are limited to classical cytogenetic techniques, but they do reveal great karyotypic variation. The main differences are related to the karyotypic formula and the absence/presence of sex chromosome systems. Thus, this study aimed to expand knowledge of the karyotypic composition of <i>Potamotrygon motoro</i> from different locations of the Central Amazon using Fluorescence in situ Hybridization to investigate the distribution of ribosomal DNAs (rDNA) and microsatellites sequences (SSRs). In addition, we used the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) to perform neighbor-joining analysis to investigate the relationships among the individuals sampled. In our study, <i>Potamotrygon motoro</i> presented 2n = 66 chromosomes, with 18m + 12sm + 10st + 26a and heterochromatic blocks on centromeric region of all chromosomes. The 18S rDNA is present in three chromosomal pairs and 5S rDNA is located in the pair 16, which is a feature shared among freshwater stingray species. Regarding the mapping of SSRs, dinucleotide sequences showed a greater number of sites, usually on terminal regions of chromosomal pairs, with an accumulation throughout the long arms of the pair 17. Our molecular analyses did not reveal differences between the sequences used. In general, the karyotypic differences previously reported for <i>Potamotrygon motoro</i> indicate the presence of different cytotypes within the species.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"68 ","pages":"1-9"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499364","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}

{"title":"<i>In silico</i> analysis of secreted proteins via Sec- and Tat-pathways of <i>Clavibacter</i> spp. unravels functional diversity related to plant host range.","authors":"Víctor Adrián Hernández-Aranda, Ramón Jarquin-Gálvez, Gisela Aguilar-Benítez, Delia Xochil Vega-Manríquez, Moisés Roberto Vallejo-Pérez, Martín Escoto-Rodríguez, Robert Winkler, Jose Pablo Lara-Avila","doi":"10.1139/gen-2025-0037","DOIUrl":"10.1139/gen-2025-0037","url":null,"abstract":"<p><p><i>Clavibacter</i> genus comprises phytopathogenic and nonphytopathogenic species in a range of plant hosts. We applied structural and functional approaches for comparative genomics to unveil the adaptation of <i>Clavibacter</i> to plant hosts. The structural approach consisted of phylogeny and whole-genome alignment. The phylogeny suggested that <i>Clavibacter tessallarius, Clavibacter zhangzhiyongii, Clavibacter capcisi, Clavibacter phaseoli</i> depicted the more divergent species. Notably, <i>Clavibacter nebraskensis, Clavibacter insidiosus, Clavibacter sepedonicus, Clavibacter</i> sp. A6099, <i>Clavibacter californiensis</i>, and <i>Clavibacter michiganensis</i> 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 <i>Clavibacter</i>. The predicted expansins harbored domain variability, related to horizontal gene transfer. A heterogeneous distribution-conservation of biosynthetic gene clusters (BGCs) regarding <i>Clavibacter</i> phylogeny was observed. Our results suggested that farm practices of plant hosts likely influence the evolutive history of <i>Clavibacter</i> spp. Furthermore, Sec-, Tat-mediated secreted proteins and metabolite diversity may underpin plant-<i>Clavibacter</i> interactions. Biological knowledge drives sustainable strategies aimed to control plant diseases caused by <i>Clavibacter</i> spp.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","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}

{"title":"A second gene for resistance to four pathotypes of <i>Plasmodiophora brassicae</i> identified in the <i>Brassica napus</i> cultivar 'Mendel'.","authors":"Mizanur Rahaman, Stephen E Strelkov, Hao Hu, Fuyou Fu, Fengqun Yu","doi":"10.1139/gen-2025-0017","DOIUrl":"10.1139/gen-2025-0017","url":null,"abstract":"<p><p>Clubroot, caused by the obligate parasite <i>Plasmodiophora brassicae</i>, 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 <i>P. brassicae</i> 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 <i>r</i> ≥ 0.82. In the DH population, 2642 high-quality Single nucleotide polymorphisms were detected by employing the <i>Brassica napus</i> 'ZS11' reference genome. A single quantitative trait locus, <i>Rcr3</i>^Mendel, 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 nucleotide-binding site-leucine-rich repeat (TNL) gene, <i>BnaA08T0102200ZS</i>. This region is homologous to the 13 415 472-15 791 728 bp region of chromosome A08 in <i>Brassica rapa</i> ECD 04, the donor of clubroot resistance in 'Mendel'. Two TNL genes, <i>BraA08g039211E</i> and <i>BraA08g039212E</i>, were identified in the ECD 04 genome. Kompetitive allele-specific PCR analysis identified eight markers that co-segregated with <i>Rcr3</i>^Mendel. Resistance to pathotype 3H was also found to co-segregate with resistance to pathotypes 5C, 3D, and 8J.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","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}

{"title":"Diversity of <i>tet</i>(L)-bearing plasmids found in Eastern Canadian <i>Staphylococcus hyicus</i> isolates from swine.","authors":"Cynthia Gagné-Thivierge, Marie-Lou Gauthier, Martine Denicourt, Marie-Ève Lambert, Antony T Vincent, Steve J Charette","doi":"10.1139/gen-2025-0007","DOIUrl":"10.1139/gen-2025-0007","url":null,"abstract":"<p><p><i>Staphylococcus hyicus</i> is the etiological agent of exudative epidermitis (EE) in suckling and weaned piglets, which is an endemic disease of concern for animal health and welfare on swine farms. <i>Staphylococcus hyicus</i> is not widely studied, and there is no recent scientific literature on Canadian strains. In a preliminary study, we presented an Eastern Canadian <i>S. hyicus</i> strain isolated from an EE case and bearing a plasmidic <i>tet</i>(L) gene conferring resistance to tetracyclines, one of the most commonly used antibiotics in Canadian swine farms. The current study characterized the <i>tet</i>(L)-bearing plasmids present in <i>S. hyicus</i> isolates from pigs in Eastern Canadian to better understand the potential vectors for this gene dissemination. Eleven <i>S. hyicus</i> isolates harboring <i>tet</i>(L) as the only tetracycline resistance gene were sequenced using Oxford Nanopore Technology and analyzed. Eight different <i>tet</i>(L)-bearing plasmids were identified that share similarities with <i>Staphylococcus aureus</i> sequences available in the National Center for Biotechnology Information. Only one of the plasmids was present in more than one isolate and two isolates carried <i>tet</i>(L) on their chromosome. This suggests a high diversity of <i>tet</i>(L)-bearing plasmids in <i>S. hyicus</i> and the possible need to analyze swine farm samples over time to understand the dynamics of <i>tet</i>(L) in <i>S. hyicus</i>.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-7"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006046","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}

{"title":"Genome assembly, analysis, and mining of <i>Kocuria flava</i> NIO_001: a thiopeptide antibiotic synthesizing bacterium isolated from marine sponge.","authors":"Kartik Juyal, Heena Devkar, Aabha Deshpande, Narsinh L Thakur","doi":"10.1139/gen-2024-0162","DOIUrl":"10.1139/gen-2024-0162","url":null,"abstract":"<p><p>Genome mining has been a key strategy for finding biosynthetic gene clusters (BGCs) coding for secondary metabolites in the recent past. Actinomycetia is among the important bacterial classes found in marine habitats, renowned for producing high-value secondary metabolites. <i>Kocuria</i> is one such gram-positive bacteria that has been reported to produce the potent antibacterial molecule kocurin/PM181104. The objective of this study was to confirm the production of kocurin/PM181104 followed by sequencing, assembly, and mining of the genome of <i>Kocuria flava</i> NIO_001. AntiSMASH analysis predicted the BGCs involved in the production of kocurin along with eight promising secondary metabolite-producing BGCs including non-alpha poly-amino acids like e-polylysin (NAPAA), ribosomally synthesized and post-translationally modified peptide like (RiPP-like), non-ribosomal peptide synthetase like (NRPS-like), NRPS-independent IucA/IucC-like siderophores (NI-siderophore), type III polyketide synthase (T3PKS), ε-Poly-l-lysine (NAPAA), terpene, and betalactone. Kyoto Encyclopedia for Genes and Genomes pathway analysis showed the presence of biosynthetic pathways involved in terpenoid backbone synthesis and the presence of certain hemolysin-like proteins. The present investigation is highly valuable for designing experiments to overproduce this potent antibiotic molecule by using a reverse engineering approach.</p>","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":"143624311","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}

{"title":"Transcriptome analysis of <i>Brassica napus</i> near-isogenic lines carrying clubroot resistance from turnip (<i>Brassica rapa</i> var. <i>rapifera</i>).","authors":"Kawalpreet Kaur, Urmila Basu, Nat N V Kav, Habibur Rahman","doi":"10.1139/gen-2024-0182","DOIUrl":"10.1139/gen-2024-0182","url":null,"abstract":"<p><p>Understanding the intricate molecular interplay between Brassica hosts and the pathogen <i>Plasmodiophora brassicae</i>, 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) and clubroot-resistant (CR) NILs of <i>Brassica napus</i>, carrying the clubroot resistance of turnip (<i>Brassica rapa</i> var. <i>rapifera</i>), 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. Notably, we identified defense-related genes associated with jasmonic acid signaling (<i>JAZ2</i>), calcium signaling (<i>CNGC</i>s, <i>GLR</i>s), receptor kinases (<i>WAK</i>s), and glucosinolate biosynthesis (<i>APK</i>; <i>GST</i>s, also involved in ROS homeostasis) that may play pivotal roles in resistance. One of the important novel findings was the association of the <i>JAZ2</i> gene with clubroot resistance in <i>B. napus</i>. This study also highlighted the upregulation of NLRs (RNLs and TNLs) and ERF transcription factors, offering new insights into the molecular mechanisms of clubroot resistance in <i>B. napus</i>. Additionally, we observed the upregulation of pathogenesis-related proteins (PR-3 and PR-4) and WRKY transcription factors (<i>WRKY62, WRKY70</i>), suggesting a coordinated response involving multiple layers of immunity. Based on our results, we propose a comprehensive model delineating the molecular events potentially contributing to clubroot resistance in <i>B. napus</i> 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.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":1.7,"publicationDate":"2025-01-01","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}

{"title":"Single-cross prediction with imputed multiomic data: a case study in rapeseed.","authors":"S E Weber, L Roscher-Ehrig, S Zanini, G Yildiz, A Abbadi, T Kox, A A Golicz, R J Snowdon","doi":"10.1139/gen-2025-0010","DOIUrl":"10.1139/gen-2025-0010","url":null,"abstract":"<p><p>Advancements in sequencing technologies enabled the assembly and characterization of plant genomes with high resolution. In breeding programs, these data are combined with phenotypic information in genomic prediction to select genotypes based on their genetic profiles. Although single nucleotide polymorphism (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 did not 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.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-17"},"PeriodicalIF":2.3,"publicationDate":"2025-01-01","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}