Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Whole genome sequencing (WGS) plays an important role in the advanced characterization of pathogen transmission and is widely used in studies of major bacterial and viral diseases. Although protozoan parasites cause serious diseases in humans and animals, WGS data on them are relatively scarce due to the large genomes and lack of cultivation techniques for some. In this review, we have illustrated bioinformatic analyses of WGS data and their applications in studies of the genomic epidemiology of apicomplexan parasites. WGS has been used in outbreak detection and investigation, studies of pathogen transmission and evolution, and drug resistance surveillance and tracking. However, comparative analysis of parasite WGS data is still in its infancy, and available WGS data are mainly from a few genera of major public health importance, such as , , and . In addition, the utility of third-generation sequencing technology for complete genome assembly at the chromosome level, studies of the biological significance of structural genomic variation, and molecular surveillance of pathogens has not been fully exploited. These issues require large-scale WGS of various protozoan parasites of public health and veterinary importance using both second- and third-generation sequencing technologies.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12017464 | PMC |
| http://dx.doi.org/10.1155/2024/7679727 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Assessment of genomic prediction capabilities of transcriptome data in a barley multi-parent RIL population.
Theor Appl Genet
September 2025
Institute for Breeding Research on Agricultural Crops, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Sanitz, 18190, Germany.
Low-cost and high-throughput RNA sequencing data for barley RILs achieved GP performance comparable to or better than traditional SNP array datasets when combined with parental whole-genome sequencing SNP data. The field of genomic selection (GS) is advancing rapidly on many fronts including the utilization of multi-omics datasets with the goal of increasing prediction ability and becoming an integral part of an increasing number of breeding programs ensuring future food security. In this study, we used RNA sequencing (RNA-Seq) data to perform genomic prediction (GP) on three related barley RIL populations.
View Article and Find Full Text PDFConstruction of a Core Germplasm and Identification of Candidate SNPs Associated with Growth Performance of Epinephelus tukula by Whole-Genome Resequencing.
Mar Biotechnol (NY)
September 2025
Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya, China.
Epinephelus tukula is an economically important aquaculture animal, and a major parent in grouper crossbreeding. To better preserve and exploit E. tukula germplasm resources, a core collection (containing 34 individuals derived from 10 genetic groups) was first constructed based on phenotypic growth traits and whole-genome resequencing (WGS) data.
View Article and Find Full Text PDFGenomic analysis of transmission within an urban region.
Microb Genom
September 2025
Regional Innovative Public Health Laboratory, Rush University Medical Center, Chicago, IL 60612, USA.
emerged in Chicago, IL, USA, in 2016 and has since become endemic. We used whole-genome sequencing (WGS) of 494 isolates, epidemiologic metadata and patient transfer data to describe the transmission of among Chicago healthcare facilities between 2016 and 2021. In total, 99% of isolates formed a single clade IV phylogenetic lineage, suggesting a single introduction.
View Article and Find Full Text PDFAugmenting cost-effectiveness in clinical diagnosis using extended whole-exome sequencing: SNVs, SVs, and beyond.
J Hum Genet
September 2025
Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
In standard short-read whole-exome sequencing (WES), capture probes are typically designed to target the protein-coding regions (CDS), and regions outside the exons-except for adjacent intronic sequences-are rarely sequenced. Although the majority of known pathogenic variants reside within the CDS as nonsynonymous variants, some disease-causing variants are located in regions that are difficult to detect by WES alone, such as deep intronic variants and structural variants, often requiring whole-genome sequencing (WGS) for detection. Moreover, WES has limitations in reliably identifying pathogenic variants within mitochondrial DNA or repetitive regions.
View Article and Find Full Text PDFBenchmarking Ploidy Estimation Methods for Bulk and Single-Cell Whole Genome Sequencing.
Adv Sci (Weinh)
September 2025
Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
Maintaining cellular ploidy is critical for normal physiological processes, although gains in ploidy are frequently observed during development, tissue regeneration, and metabolism, and potentially contribute to aneuploidy, thereby promoting tumor evolution. Although numerous computational tools have been developed to estimate cellular ploidy from whole-genome sequencing (WGS) data at bulk or single-cell resolution, to the knowledge, no systematic comparison of their performance has been conducted. Here, a benchmarking study is presented of 11 methods for bulk WGS and 8 methods for single-cell WGS data, utilizing both experimental and simulated datasets derived from diploid cells mixed with aneuploid or polyploid cells.
View Article and Find Full Text PDF