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Eukaryotic genomes harbour sequences derived from non-retroviral RNA viruses, known as endogenous viral elements (EVEs) or non-retroviral integrated RNA virus sequences (NIRVS). These sequences represent a record of past infections and have been implicated in host anti-viral response. We have created a program to identify viral sequences integrated in a host genome. It begins with a specimen BAM file and outputs candidate NIRVS, along with putative host insertion sites and overlapping genomic features of the host genome in XML and visual formats, with minimal intermediary intervention. We ran through this software short-read data derived from the genomes of 222 wild-caught A. aegypti mosquitoes, from a dozen geographical regions, and located putative NIRVS from seven virus families. This program is as accurate as currently available software for NIRVS detection, and represents a significant improvement in adaptability and user-friendliness. Furthermore, the flexibility of this pipeline allows the user to search for sequence integrations across the genome of any organism, as long as a query sequence database and a reference genome is provided. Potential extended applications include identification of integrated transgenic sequences used for research or vector control strategies.
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http://dx.doi.org/10.1111/1755-0998.14026 | DOI Listing |
ACS Synth Biol
December 2024
Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, PR China.
Industrial biotechnology employs cells for producing valuable products and serving as biocatalysts sustainably, addressing resource, energy, and environmental issues. is a preferred host for creating microbial chassis cells and producing industrial enzymes and functional nutritional products. In this study, a dual-module T7 integration expression system in was established.
View Article and Find Full Text PDFBiol Open
December 2024
Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center,Lebanon, NH 03756, USA.
Parasitoid wasps exert strong selective pressure on their hosts, driving the evolution of diverse defense strategies. Drosophila, a widely studied model organism, hosts a wide range of parasites, including parasitoid wasps, and has evolved immune and behavioral mechanisms to mitigate the risk of parasitization. These defenses range from avoidance and evasion to post-infection immune responses, such as melanotic encapsulation.
View Article and Find Full Text PDFVirus Evol
November 2024
Department of Paraclinical Sciences, Norwegian University of Life Sciences, Post box 5003, Ås 1432, Norway.
Over a decade since its discovery, piscine myocarditis virus (PMCV) remains a significant pathogen in Atlantic salmon aquaculture. Despite this significant impact, the genomic landscape, evolutionary dynamics, and virulence factors of PMCV are poorly understood. This study enhances the existing PMCV sequence dataset by adding 34 genome sequences and 202 new ORF3 sequences from clinical cardiomyopathy syndrome (CMS) cases in Norwegian aquaculture.
View Article and Find Full Text PDFStud Mycol
December 2024
Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
species have commonly been reported as important plant pathogenic fungi with wide host ranges and geographic distributions. With the increase in the number of cryptic species being described, a comprehensive global taxonomic revision of the genus is required. The present study includes 399 isolates from 32 countries.
View Article and Find Full Text PDFFront Cell Infect Microbiol
December 2024
Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian, Shandong, China.
The northern snakehead () is a valuable aquaculture species across certain Asian countries, contributing significantly to economic prosperity and dietary needs. However, its productivity faces significant challenges, particularly from diseases such as nocardiosis, caused by . To date, the majority of research efforts have focused on describing the observed phenomena related to infection.
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