Genome最新文献

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, 2642 high-quality Single nucleotide polymorphisms were detected by employing the Brassica napus 'ZS11' reference genome. A single quantitative trait locus, Rcr3^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, BnaA08T0102200ZS. This region is homologous to the 13 415 472-15 791 728 bp region of chromosome A08 in Brassica 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 Rcr3^Mendel. Resistance to pathotype 3H was also found to co-segregate with resistance to pathotypes 5C, 3D, and 8J.

Staphylococcus hyicus 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. Staphylococcus hyicus is not widely studied, and there is no recent scientific literature on Canadian strains. In a preliminary study, we presented an Eastern Canadian S. hyicus strain isolated from an EE case and bearing a plasmidic tet(L) gene conferring resistance to tetracyclines, one of the most commonly used antibiotics in Canadian swine farms. The current study characterized the tet(L)-bearing plasmids present in S. hyicus isolates from pigs in Eastern Canadian to better understand the potential vectors for this gene dissemination. Eleven S. hyicus isolates harboring tet(L) as the only tetracycline resistance gene were sequenced using Oxford Nanopore Technology and analyzed. Eight different tet(L)-bearing plasmids were identified that share similarities with Staphylococcus aureus 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 tet(L) on their chromosome. This suggests a high diversity of tet(L)-bearing plasmids in S. hyicus and the possible need to analyze swine farm samples over time to understand the dynamics of tet(L) in S. hyicus.

Clavibacter 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 Clavibacter to plant hosts. The structural approach consisted of phylogeny and whole-genome alignment. The phylogeny suggested that Clavibacter tessallarius, Clavibacter zhangzhiyongii, Clavibacter capcisi, Clavibacter phaseoli depicted the more divergent species. Notably, Clavibacter nebraskensis, Clavibacter insidiosus, Clavibacter sepedonicus, Clavibacter sp. A6099, Clavibacter californiensis, and Clavibacter 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 gene 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.

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. Kocuria 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 Kocuria flava 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.

Urochloa P. Beauv. (formerly classified as Brachiaria (Trin.) Griseb.) is a genus of African perennial grasses that is extensively cultivated in tropical countries for cattle nutrition. Three of the most economically relevant species, Urochloa brizantha, Urochloa decumbens, and Urochloa ruziziensis, form the brizantha agamic complex, which includes allopolyploid series with distinct subgenomes. Investigating the composition and organization of repetitive DNA, a major component of grass genomes, can provide insights into their genomic relationships and evolutionary history. This study aimed to characterize the repetitive DNA landscape of selected Urochloa species belonging to the b rizantha agamic complex; identify and compare major repeat classes across species; and evaluate their potential as cytogenetic markers on mitotic chromosomes using fluorescent in situ hybridization (FISH). Clustering analysis revealed that repetitive DNA constitutes 56%-65% of the genomes, with Ty3/Gypsy retrotransposons, particularly the Athila and Retand lineages, representing the most abundant repeat class. Urochloa decumbens exhibited the highest proportion of Ty3/Gypsy retrotransposons, while U. ruziziensis had the highest satellite DNA content. The chromosomal location of representative satellites (UroSat-1a, UroSat-2a, and UroSat-3) was determined in all three species via FISH. UroSat-1a was detected in all centromeres, while UroSat-2a and UroSat-3 signals varied in number and position. Our findings validate the use of satDNA as cytogenetic markers in the brizantha agamic complex of Urochloa and revealed genomic relationships among different species and ploidy levels.

Circadian rhythms are important cellular pathways first described for their essential role in helping organisms adjust to the 24 h day-night cycle and synchronize physiological and behavioral functions. Most organisms have evolved a circadian central clock to anticipate daily environmental changes in light, temperature, and mate availability. It is now understood that multiple clocks exist in organisms to regulate the functions of specific organs. Epidemiological studies in humans reported that disruption of the circadian rhythms caused by sleep deprivation is linked to the onset of immune-related conditions, suggesting the importance of circadian regulation of immunity. Mechanistic studies to define how circadian clocks and immune responses interact have profound implications for human health. However, elucidating the clocks and their tissue-specific functions has been challenging in mammals. Many studies using simple model organisms such as Drosophila melanogaster have been pioneering in discovering that the clock controls innate immune responses and immune challenges can impact circadian rhythms and/or their outcomes. In this review, we will report genetic studies using the humble fruit fly that identified the existence of reciprocal interactions between the circadian pathway and innate immune signaling, contributing to elucidate mechanisms in the growing field of chrono-immunology.

Crematogaster Lund, 1831 is a speciose ant genus globally distributed and easily recognizable. Although biogeographical theories explain some variation among Neotropical Crematogaster, several taxonomical issues remain unresolved. While cytogenetic approaches can help to delimit species, cytogenetic data are only available for 18 taxa. In this study, classical and molecular cytogenetic analyses were performed on five Crematogaster species from the Brazilian Amazon to identify species-specific patterns. Two different cytotypes, both with 2n = 22 chromosomes were observed in Crematogaster erecta Mayr, 1866, suggesting the presence of cryptic species, although with different karyotypic formulas. Crematogaster aff. erecta had 2n = 28, while Crematogaster limata Smith, 1858, Crematogaster tenuicula Forel, 1904, and Crematogaster sp. had 2n = 38. The telomeric motif (TTAGG) _n was found in all five species, and the (TCAGG) _n motif was detected in the telomeres of C. limata. This peculiar motif was also detected in the centromeric regions of C. erecta cytotype I. The microsatellite (GA) _n was dispersed in the chromosomes of all species studied, which also had a single intrachromosomal rDNA site. The cytogenetic results revealed notable interspecific and intraspecific variation, which suggests different chromosomal rearrangements involved in the origin of these variations, also highlighting the taxonomic value of cytogenetic data on Crematogaster.

Chromosomal rearrangements (CRs) can play an important role in evolutionary diversification by preserving linkage among favourable alleles through reduced recombination and/or by reducing hybrid fitness due to genomic incompatibilities. Our goal was to determine to what extent CRs contribute to known patterns of genetic variation in Arctic charr (Salvelinus alpinus). To address this goal, we compared genetic linkage maps to identify whole arm CRs and smaller scale structural variants (SVs) such as translocations/transpositions and inversions found in groups of populations that reflect the temporal sequence of geographic isolation events. If CRs contribute to genetic differentiation, we expected that CRs would be specific to glacial lineages, geographic clusters of populations within lineages, and sympatric morphs. We detected fusions and fissions of whole chromosome arms and SV involving translocations/transpositions of the sex-determining gene (sdY) and inversions. Several CRs were shared across populations from the Arctic and Atlantic glacial lineages, Canadian and Icelandic populations within the Atlantic lineage, between two Icelandic populations and sympatric morphs within Icelandic populations, suggesting that their origin predates geographic isolation in glacial refugia. Other CRs were specific to single populations, which suggests a more recent origin of these variants in refugia, during post-glacial recolonization and/or in contemporary populations. Thus, CRs contribute relatively little to known patterns of genetic differentiation at different geographic scales but represent a pool of standing genetic variation for evolution.

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.

Quaternary climate oscillations significantly influenced the configuration of the Brazilian Atlantic Forest. In this study, mitochondrial DNA analysis of Enoploctenus cyclothorax (Bertkau, 1880) was conducted to investigate potential cryptic diversity within populations across the state of Paraná, Brazil. Two divergent genetic lineages were identified based on genetic distances, haplotype network, and phylogenetic inference. A phylogeographical break separates the lineages into two geographic regions; one lineage is found exclusively in the eastern region and the other is found mainly in the northern and western regions of the state. The coalescence tree estimates the divergence time between 1.8 million years and 500 000 years ago, period marked by glaciation, suggesting historical forest fragmentation as a potential isolating mechanism. These findings support the hypothesis of independently evolving units within E. cyclothorax, possibly representing cryptic species, though broader sampling and integrative approaches are necessary for taxonomic validation.