Genome最新文献

Aegilops speltoides (2n = 2x = 14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of Aegilops from the Sitopsis section and wheat and found that Ae. speltoides is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from Ae. speltoides more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and Ae. speltoides and develop Ae. speltoides chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low-coverage sequence data were analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in Ae. speltoides and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. Ae. speltoides had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting Ae. speltoides chromatin in the wheat background using fluorescent in situ hybridization.

The Green Revolution's objective of increasing yields precipitated an approach to impact evaluation that relied predominantly on econometric analyses to measure yield differences and how those differences impact farmer incomes. This paper explores the legacies of this assessment scholarship for New Breeding Technologies (NBTs) in sub-Saharan Africa. It examines three pervasive assumptions underpinning econometric-informed evaluative approaches: farmer homogeneity, profit maximization, and scale neutrality. The paper concludes by introducing Farming Systems Research as a complement to existing econometric approaches, which can serve to create more robust and accurate assessments of the potential farm-level benefits and challenges of NBTs in sub-Saharan Africa.

The sea cucumber Parastichopus tremulus is an important holothuroid species inhabiting the eastern North Atlantic Ocean benthic zone at depths from about 20 to 3000 m. Geographical distribution is from the Barents Sea in the north to the Canary Islands in the south. Along with the increasing commercial interest of new sea cucumber species, research into sea cucumber biology has also advanced. Recently, the genomes of tropical sea cucumber species have become available. However, genomes of cold-water sea cucumbers are still lacking. To fill this knowledge gap, both the mitochondrial genome and the nuclear genome of P. tremulus have been sequenced and assembled. Mitochondrial genome size and gene-organization closely matched what has been found for other holothuroids of the Stichopodidae family. The total nuclear genome assembly length was found to be 775 Mb at 24× coverage and achieved a final BUSCO completeness score of 87.2%.

The worldwide salinization of freshwater ecosystems poses a major threat to the biodiversity, functioning and services that these essential ecosystems provide. We are far from fully understanding the ecological and evolutionary consequences of salinization for freshwater organisms. Here we review current research on the genomic responses to salinity in freshwater zooplankton. Surveying transcriptomic studies, we identify many key ion transport genes critical for osmoregulation of ions in multiple zooplankton species in response to salinity stress. Laboratory investigations of natural zooplankton populations inhabiting gradients of salinity often reveal additional candidate genes that are not identified in gene expression experiments (e.g., trehalose). We suggest that future studies should focus on genomic approaches to explore the molecular mechanisms of adaptation to freshwater salinization in zooplanktons, and to predict the eco-evolutionary consequences of freshwater salinization.

Luteinizing hormone-releasing hormone A3 (LHRH-A3), a reproductive hormone analog, is widely used to stimulate ovulation in female rabbits. However, the long-term impact of sustained LHRH-A3 administration on the reproductive system, particularly ovarian health, remains unclear. In this study, we compared apoptosis levels in ovaries and molecular regulation between LHRH-A3-treated (A3 group) and untreated female rabbits (N group) after their 5th litter. Western blotting showed a significantly lower Bcl-2/Bax ratio in the A3 group compared with the N group (P < 0.01), indicating higher ovarian apoptosis. Ovarian tissues from four rabbits per group were divided into the A3 group and the N group, and RNA-seq technology was then utilized to conduct transcriptome analysis on these two groups. This analysis revealed 220 differentially expressed genes (DEGs), including BMP6, BMP15, CYP1A1, and other reproductive-related genes. KEGG analysis of these DEGs showed their involvement in processes such as the cell cycle, PI3K-Akt signaling pathway, and ovarian steroidogenesis. Subsequently, we selected the key gene Matrix metallopeptidase 7 (MMP7) for functional analysis using CCK8 and Annexin V-FITC/PI techniques. MMP7 was found to promote the proliferation of granulosa cells (GCs) and inhibit apoptosis (P < 0.01). In conclusion, LHRH-A3 treatment can modulate ovarian molecular regulation, with the key gene MMP7 involved in the proliferation and apoptosis of GCs.

Successful resistance to disease-causing pathogens is underpinned by properly regulated immune signalling and defence responses in plants. The plant immune system is controlled at multiple levels of gene and protein regulation-from chromatin-associated epigenetic processes to protein post-translational modifications. Optimal fine-tuning of plant immune signalling and responses is important to prevent plant disease development, which is being exacerbated by a globally changing climate. In this review, we focus on how changing climatic factors mechanistically intercept plant immunity at different levels of regulation (chromatin, transcriptional, post-transcriptional, translational, and post-translational). We specifically highlight recent studies that have provided molecular insights into critically important climate-sensitive nodes and mechanisms of the plant immune system. We then propose several potential future directions to build climate-resilient plant disease resistance using cutting-edge biotechnology. Overall, this conceptual understanding and promising biotechnological advances provide a foundational platform towards novel approaches to engineer plant immune resilience.

This review explores the challenges and potential solutions in plant micropropagation and biotechnology. While these techniques have proven successful for many species, certain plants or tissues are recalcitrant and do not respond as desired, limiting the application of these technologies due to unattainable or minimal in vitro regeneration rates. Indeed, traditional in vitro culture techniques may fail to induce organogenesis or somatic embryogenesis in some plants, leading to classification as in vitro recalcitrance. This paper focuses on recalcitrance to somatic embryogenesis due to its promise for regenerating juvenile propagules and applications in biotechnology. Specifically, this paper will focus on epigenetic factors that regulate recalcitrance as understanding them may help overcome these barriers. Transformation recalcitrance is also addressed, with strategies proposed to improve transformation frequency. The paper concludes with a review of CRISPR-mediated genome editing's potential in modifying somatic embryogenesis-related epigenetic status and strategies for addressing transformation recalcitrance.

Crop breeding, which relies on the presence and/or generation of alterations in DNA, has been essential to the development of agricultural production. Such breeding endeavours are carried out using a wide range of methods, which have diversified immensely over the years as our understanding of genetics has grown. While this expansion in our breeding "toolbox" has provided vast improvements in the specificity, pace and effectiveness of crop trait enhancement, apprehension surrounding the use of biotechnological breeding platforms in particular led countries to develop costly and lengthy regulatory processes for plants deemed to be "genetically modified" as a means of managing safety concerns and assuaging public unease. In this article, we discuss crop regulatory policies in Canada and beyond, in the context of transgenic crops, as well as those developed using newer biotechnological breeding platforms such as gene editing. We also examine the benefits of biotechnologically bred crops, and consider the broader socio-economic, ethical, and environmental impacts of overly restrictive regulatory frameworks, which could very feasibly limit the prospect of food security in the future.

Anthrax, caused by the bacterial pathogen Bacillus anthracis, is a lethal disease affecting both livestock and humans. This study focused on the comparative whole-genome analysis of two Indian virulent Bacillus anthracis strains recovered from anthrax cases in cattle (NIVEDIAX3) and sheep (NIVEDIAX61), and their comparison with available genomes (n = 55) in the NCBI database. Phylogenetic analysis based on average nucleotide identity clustered the 57 strains into 3 groups, with both NIVEDIAX strains grouped under Cluster II, alongside the Ames Ancestor strain. Multilocus sequence typing (MLST) assigned the strains to Bacillus cereus sequence type ST1, Bacillus anthracis core genome MLST ST284, and Bacillus anthracis plasmid ST12 based on typing scheme. A total of 5217 orthologous clusters and 468 single-copy gene clusters shared between the NIVEDIAX strains and the Ames Ancestor strain were identified. Canonical single nucleotide polymorphism (canSNP) analysis classified both strains as A.Br.003 (A.Br.Aust94 sub-lineage). Further, analysis of the 57 Bacillus anthracis genomes revealed that A.Br.003 was the most prevalent canSNP among animal isolates. In India, multiple Bacillus anthracis sub-lineages have been reported. In conclusion, the circulation of diverse Bacillus anthracis sub-lineages in livestock across Southern and Eastern states of India, was noted.