Genome最新文献

Farlowella is the second most species-rich genus within Loricariinae; however, cytogenetic data for its species remain scarce. In this study, we employed conventional and molecular cytogenetic procedures on Farlowella oxyrryncha, a species widely distributed across the Amazon and Orinoco River basins. Karyotypic analysis revealed a conserved diploid number (2n=58), with 12m+22sm+18st+6a, in addition to notable structural variation compared to other species of the genus. The pattern of constitutive heterochromatin (CH) facilitated the characterization of chromosome pairs. Furthermore, a conspicuous sex-linked heteromorphism was detected in chromosome pair 27, suggesting the presence of an XY sex chromosome system. Fluorescence in situ hybridization (FISH) identified single site of 18S and 5S ribosomal DNA, with 18S colocalizing with U2 small nuclear DNA, simple sequence repeats and CH. Interstitial telomeric sequences (ITS) were found in five pairs, with dimorphic ITS patterns in pair 27, suggesting its role as a proto-sexual pair. The colocalization of repetitive sequences in pair 27 suggests that repetitive DNA plays a key role in the early differentiation of sex chromosomes. These findings indicate that F. oxyrryncha is a structurally dynamic lineage and provide new insights into karyotype evolution and sex chromosome differentiation in Loricariidae.

Platycodon grandiflorus (Jacq.) A. DC., a herbaceous plant belonging to the Campanulaceae family, is recognized for its substantial medicinal properties, attributed to its rich composition of bioactive compounds, including polysaccharides, saponins, and flavonoids. The polysaccharide components have been shown to exhibit significant anti-obesity effects. However, there is a notable lack of research on the biosynthesis of polysaccharides in P. grandiflorus. This study aimed to identify and functionally validate key enzymes involved in the polysaccharide biosynthetic pathway of P. grandiflorus. Based on transcriptomic data, the researchers identified four genes associated with the polysaccharide biosynthetic pathway in P. grandiflorus, specifically including one phosphomannose isomerase gene (PgPMI), one phosphoglucose isomerase gene (PgGPI1), and two phosphomannose mutase genes (PgPMM1 and PgPMM2). The enzymatic activity of genes was verified in Escherichia coli, demonstrating that the recombinant PgPMI protein catalyzes the interconversion of mannose-6-phosphate and fructose-6-phosphate. Additionally, the recombinant PgPMM1 and PgPMM2 proteins were shown to catalyze the interconversion of mannose-1-phosphate and mannose-6-phosphate, while the recombinant PgGPI1 protein is capable of catalyzing the conversion of glucose-6-phosphate to fructose-6-phosphate. This study enhances knowledge of the polysaccharide biosynthetic pathway and underpins subsequent molecular research on polysaccharide metabolism and related physiology.

The E genome of Thinopyrum elongatum is an important alien genetic resource for the breeding of Triticum aestivum. The purpose of this study was to develop chromosome-specific oligonucleotide probes for Th. elongatum. Based on the Th. elongatum reference genome, 1,522,611 tandem repeats were identified using bioinformatics methods. By further merging tandem repeats using bedtools in sliding windows of 10 kb, we obtained 15,500 high-copy sequences with a copy number exceeding 100. We identified 1,609 unique high-copy tandem repeats of Th. elongatum as candidate sequences by comparing them with the wheat reference genome. Based on their chromosome specificity and distribution sites, 19 Th. elongatum oligonucleotide probes were developed and applied to material identification. The results showed that the Oligo-7ES-2 probe produced a clear and stable in situ hybridization signal on the chromosome of the CS-7E addition line material, located on the long arm of 7E chromosome. The Oligo-7ES-2 probe developed in this study can help the traditional E genome GISH probe for mapping chromosomes or chromosome fragments of 7E and 7EL derived lines of wheat and Th. elongatum. This lays a foundation for the efficient identification of exogenous chromosomes of Th. elongatum in wheat genetic improvement.

Soil salinization is an escalating threat to global food security under climate change, necessitating innovative strategies to enhance crop resilience. Native microbial inoculants, sourced from salinity-adapted soils, offer a potential avenue for sustainable agricultural adaptation. Here, we evaluated the effects of saline prairie-derived, AMF-enriched microbial inoculants on the growth of barley (Hordeum vulgare) cultivars under a salinity gradient. Greenhouse trials demonstrated that salinity was the dominant constraint on biomass production, but inoculant identity and genotype significantly influenced plant performance and microbial assembly. Inoculant effects on shoot biomass were heterogeneous, with neutral or negative outcomes predominating under saline conditions. Amplicon sequencing of bacterial, fungal, oomycete, and arbuscular mycorrhizal (AMF) communities revealed that salinity strongly restructured microbial diversity and composition, reducing bacterial and fungal evenness. Genotype and inoculant identity shaped fungal communities, while oomycete responses depended on specific plant-microbe pairings. Model selection confirmed that shoot biomass was primarily explained by salinity, with additional contributions from barley genotype, inoculant identity, and fungal evenness. These results demonstrate that microbial community restructuring under salinity stress outweighs direct benefits of native microbial inoculation, and emphasize that successful microbial interventions in salt-affected soils must account for genotype-specific compatibility and stress-driven community dynamics, rather than assuming universal benefits.

A pair of primers that can bind at multiple loci across the genome and randomly amplify multiple copies increases the analytical sensitivity of the currently used diagnostic assays. We developed a novel genome mining algorithm to identify short identical repeat sequences (IRSs) dispersed across the genome. The genome mining algorithm for IRS identification can be accessed from the GitHub portal (https://github.com/BPaul-bioinfoLAB/IRS-Finder). Using this algorithm, we have identified the IRS from five pathogens, namely, gammaherpesvirus, vaccinia virus, Mycobacterium tuberculosis, Plasmodium falciparum, and Phytophthora palmivora. In-silico PCR revealed that these IRSs can amplify multiple nonhomologous regions of variable amplicon sizes via three priming combinations. We further performed a polymerase chain reaction assay with an IRS pair identified from M. tuberculosis. Interestingly, the PCR with single IRS amplified multiple non-homologous copies and even more variable sized copies in pair. These results indicate that the IRS-based diagnostic assays can detect pathogens in case of low-concentration DNA during disease progression. The genome mining algorithm can be used as a translation technology platform for developing highly sensitive varieties of PCR, microarray, loop-mediated isothermal amplification, fluorescence in-situ hybridization based diagnostic assays.

Wheat defenses against Pyrenophora tritici-repentis (Ptr), the cause of tan spot disease, are complex and require further characterization. We previously identified two wheat genotypes, Robigus (resistant) and Hereward (susceptible), and characterized their differentially expressed genes (DEGs) and accumulated metabolites (DAMs) following challenge with Ptr. In this study we uncover coordinated shifts in gene expression and metabolism triggered by Ptr. The DEGs and DAMs from each genotype were integrated using regularized canonical correlation analysis, yielding scale-free networks with 69 745 edges in Robigus and 760 433 in Hereward. In Robigus, hub genes were upregulated at 48 and 96 h post-inoculation and included hst2 (encoding hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2), located within a QTL for Ptr resistance (QTs.fcu-5D locus), a receptor-like kinase, and a late embryogenesis abundant protein (which play roles in cell wall organization). Pathway enrichment showed significant involvement of catalytic activity, chitinase activity, and cell wall metabolic processes. In contrast, Hereward hub genes were mostly downregulated, except for a hexosyltransferase, with enriched pathways related to energy metabolism, such as ATP binding and phosphorylation. These results suggest that cell wall modifications and chitinase activity are part of an effective defense response against Ptr, whereas costly energetic processes may contribute to tan spot susceptibility.

During evolution, organisms evolve mainly through natural and artificial selection, leaving distinctive signatures on genomic coordinates. Such genomic regions offer valuable insights into the molecular mechanisms that influence quantitative traits. India harbours a diverse buffalo population with Murrah breed exhibiting exceptional milk production and quality, notably a high fat and solids-not-fat content. Therefore, the present investigation focused on exploring selection signatures within the genome of the Murrah buffalo through whole-genome resequencing. A total of 17 472 799 SNPs were identified, which were further utilized for identification of selection signatures using site frequency spectrum-based Tajima's D and Nucleotide Diversity; and linkage disequilibrium-based iHS approaches. A total of 248 regions under selection overlapped with 64 QTLs across various traits (milk, production, reproduction, meat and carcass, health, and exterior) on chromosomes 5, 9, and 17. A majority of the identified QTLs (39) were associated with milk-related traits, with 27 QTLs specifically linked to milk fat content. Notably, genes such as ARHGAP26, ADGRL3, and SUCLG2 mapped within the QTLs under selection are implicated in milk traits, while XPR1 is associated with growth. Hub genes included RPL23A, ADGRL3 (milk); AP3B1, TXN2 (reproduction); CDK6, IGF2R (body confirmation), and HSPA9 (heat tolerance). This study lays the groundwork for targeted breeding efforts aimed at enhancing milk production in buffalo.

Relationships between individuals play an important role in their behaviour and health, ranging from interactions between individuals to symbioses with microorganisms. Defining bee health may benefit from examining these relationships at different levels of biological organization, suggesting that bee genetics could be influencing microbial communities or that the social microbiome may be a unique way of characterizing pollinator health. Here, we review research in bee behaviour and microbiomes to examine different perspectives influencing health and how factors such as an individual's physiology, genetics, behaviour, social role, and environment can interact with its microbiota. As the role of the microbiome is explored across wild bee species and sociality, examining these factors together rather than in isolation provides a more comprehensive understanding of microbial communities and their impact on their bee hosts. Considering increasing environmental threats to bees, holistic perspectives can inform conservation efforts and actionable methods to support pollinators in altered environments.

Plant biotechnology has revolutionized modern agriculture by enabling precise and efficient crop improvement strategies. This review explores the evolution of selective breeding, mutation breeding, and precision breeding, highlighting their applications in Canada's agricultural sector. Conventional selective breeding has been instrumental in developing high-yielding and disease-resistant cultivars, while mutation breeding, through physical and chemical mutagenesis, has introduced valuable genetic diversity. The advent of transgenic breeding allowed for the direct insertion of foreign genes, leading to the development of crops with herbicide tolerance, pest resistance, and improved nutritional content. However, concerns over regulatory restrictions and public acceptance have driven the rapid adoption of genome editing tools, which enable precise modifications without introducing foreign DNA. Canada has played a key role in applying these biotechnological innovations, successfully developing genetically modified canola, CRISPR-edited wheat, stress-resistant soybean, and barley and oat cultivars improved for stress resistance and yield. While each breeding approach presents distinct advantages and limitations, integrating conventional and molecular techniques is essential for maximizing genetic potential, ensuring agriculture, and effectively food security challenges.