Genome最新文献

Understanding the intricate molecular interplay between Brassica hosts and the pathogen Plasmodiophora brassicae, 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 Brassica napus, carrying the clubroot resistance of turnip (Brassica rapa var. rapifera), 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 (JAZ2), calcium signaling (CNGCs, GLRs), receptor kinases (WAKs), and glucosinolate biosynthesis (APK; GSTs, also involved in ROS homeostasis) that may play pivotal roles in resistance. One of the important novel findings was the association of the JAZ2 gene with clubroot resistance in B. napus. 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 B. napus. Additionally, we observed the upregulation of pathogenesis-related proteins (PR-3 and PR-4) and WRKY transcription factors (WRKY62, WRKY70), 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 B. napus 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.

Polyamine oxidases (PAOs) are enzymes associated with polyamine catabolism and play important roles in growth and development and stress tolerance of plants. In the present study, genome-wide discovery and analysis of the PAO family in sorghum was done utilizing model PAO of Arabidopsis. Six PAO genes were found using publicly available genomic data. Sorghum has the PAO gene representatives distributed throughout four chromosomes (chr1, chr3, chr6, and chr7), and most members have eight to nine exons. The molecular weights of PAO proteins range from 53 to 63 kDa. PAO proteins have a theoretical PI between 5.2 and 8.1. The identification and characterization of PAO gene members in sorghum lay the foundation for further experimental studies elucidating their roles in growth, development, and stress responses, ultimately contributing to our understanding of plant biology, with significant implications for plant breeding by providing valuable insights into potential targets for enhancing stress tolerance and improving crop performance.

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 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.

The second iteration of the international conference "Pathway to Increase Standards and Competency of eDNA Surveys" was held at the University of Guelph, Guelph, Ontario, Canada from 18 June to 20 June 2023. During this environmental DNA (eDNA) conference, 60 oral and 25 poster presentations from academia, government, industry, NGOs, and Indigenous partners discussed the latest developments in eDNA research, explored strategies to inform public policy, and presented future directions in the field. The conference also included three panel discussions focused on prominent themes in the eDNA space, and five workshops dedicated to practical eDNA tools and methods. Recordings of presentations at the conference have been made available on YouTube. Here we summarize the major themes covered during the conference, provide our concluding remarks, and share the conference abstracts.

Cenchrus L. is an important genus within the family Poaceae, comprising species of agronomic importance, such as Cenchrus purpureus and Cenchrus americanus. Cenchrus americanus is a diploid species (2n = 2x = 14, AA genome), while C. purpureus is an allotetraploid (2n = 4x = 28, A'A'BB genome). The A' subgenome is proposed to be homeologous to and possibly derived from the A subgenome, while the origin of the B subgenome remains undefined. Despite their distinct subgenomic compositions, both species exhibit a high level of genome homology. This study aimed to characterize and compare the repetitive genome fraction of C. purpureus and C. americanus using genome skimming and a graph-based clustering approach, as well as in situ hybridization. The repetitive genome fraction of C. purpureus and C. americanus corresponds to 52.23% and 76.82%, respectively. The most abundant repetitive elements in both species are the LTR retrotransposons. Satellite DNA sequences correspond to 2.55% and 4.17% of the species' genome, respectively. Four new satellite sequences were identified as A, A', and B subgenome-specific sequences, along with new centromeric variants. The ancestral relationship and the polyploidization-diploidization cycles played a fundamental role in the composition of their repetitive fraction.

The Physalaemus cuvieri-Physalaemus ephippifer species complex is a Neotropical frog group that encompasses seven well-supported major clades. Although very similar morphologically, the five lineages previously karyotyped show notorious cytogenetic signatures. There is also evidence of ancient secondary contact between P. ephippifer, which has heteromorphic sex chromosomes, and the lineage known as L1B, which lacks sex chromosome heteromorphism. Here, to aid comparative analysis within this complex, we mapped the U2 small nuclear RNA (snRNA) gene using fluorescent in situ hybridization (FISH). All samples presented a U2 snRNA gene cluster terminally in the short arm of chromosome 6. Additional small FISH signals were also revealed, particularly in one lineage with previously noted polymorphism of nucleolar organizer regions. Moreover, one additional site contributed for the analysis of sex chromosomes, since the Z chromosome of P. ephippifer harbors a small FISH signal, which is absent in the W chromosome. In lineage L1B, chromosome 9-which is homologous to the sex chromosomes of P. ephippifer-is polymorphic for a small FISH signal, as did the Z chromosome in the group derived from the contact between these lineages. Finally, nucleotide sequence analysis revealed some truncated gene sequences, suggesting the presence of pseudogenes of the U2 snRNA gene in these frogs.

Regulations within the crop agriculture industry exist to ensure that products undergoing risk assessment prior to commercialization are safe for the environment and human consumption. Since 1995, these regulations have provided safe crops and foods for Canadians to consume, as no commercialized innovative product has caused any post-commercialization health or environmental problems. However, Canada suffers from a gap in its innovation pipeline in that far more investments go into the innovation pipeline than products come out. Canada is a global top ten nation in terms of innovation investments yet drops over ten positions when it comes to outputs. Additionally, Canada is one of the lowest ranked on the G30 list of countries in terms of regulatory burden on the economy. This article describes updates to the regulatory framework for plant biotechnology, highlighting recent changes regarding regulation of gene editing technologies and how these changes respond to previously identified innovation barriers.

Soybean seeds are rich in oil and protein; however, the seed composition is influenced by genotype and environment. For years, it has been observed that soybeans grown in western Canada have lower seed protein concentration (by ∼1%-5% total seed weight) than those grown in eastern Canada. In this study, soybean seeds harvested from five varieties were grown in four different locations in Canada (east and west growing regions) and analyzed using RNA-sequencing. Using gene ontology and biological pathway mapping, we identified a difference in cysteine and methionine metabolism between soybeans grown in eastern and western Canada that may attribute to the difference in seed protein concentration. Further, we identified differential gene expression within the oil biosynthesis pathway, specifically upregulation of lipoxygenases in western-grown soybeans, which may also influence seed composition and/or membrane fluidity. The information gained in this study is useful for marker assisted selection in soybean breeding programs across Canada and globally.

In mammals and Drosophila melanogaster, Asp/ASPM proteins contribute to cell proliferation and spindle formation. Recent evidence also suggests interphase roles for Asp/ASPM proteins, but little is known about the regulation allowing distinct roles in different cell cycle phases. In this review, we consider a cross-species comparison of Asp/ASPM protein sequences in light of cyclin-CDK literature, and suggest Asp/ASPM proteins to be prime candidates for cyclin-CDK regulation. Conserved regulatory features include an N-terminal proline directed serine/threonine (S/T-P) "supershift" phosphorylation domain common to proteins with bistable interphase and mitotic roles, as well as putative cyclin-binding sites positioned to allow multisite phosphorylation by cyclin-CDK complexes. Human, mouse, and Drosophila Asp/ASPM protein structural predictions show that multisite phosphorylation of the N-term supershift domain could alter the availability of CH-domains and HEAT-motifs, which can contribute to microtubule binding and protein aggregation likely required for spindle formation. Structural predictions of the smallest reported microcephaly patient truncation also emphasize the importance of the arrangement of these motifs. We position this in silico analysis within recent literature to build new hypotheses for Asp/ASPM regulation in interphase and mitosis, as well as de-regulation in microcephaly and cancer. We also highlight the utility of comparing structural/functional differences between human ASPM and Drosophila Asp to gain further insight.

The analysis of 51 sheep genomes led to the identification of 3624 high-confidence Solitary Long Terminal Repeats (Solo-LTRs), remnants of Long Terminal Repeat retrotransposons (LTR-RTns). These elements, comprising 3308 absence-type and 316 presence-type sites, are integrated into functional regions of the genome, where they can influence gene structures and regulation. Approximately 4.39% of protein-coding genes and 0.54% of long noncoding RNA genes contain sequences derived from these Solo-LTRs. Analysis across 12 diverse sheep breeds revealed that 83.63% of the tested Solo-LTR sites were polymorphic, demonstrating substantial genetic diversity and highlighting their utility as genetic markers. Furthermore, these elements were linked to key genes governing economically important traits such as growth, immunity, and milk production. Notable genes identified include PAG3, ANXA5, KCNJ6, MX2, and XKR4. The findings confirm that Solo-LTRs are major contributors to genomic diversity and breed-specific adaptation in sheep, providing essential insights for future genetic research and breeding programs.