GigaByte (Hong Kong, China)最新文献

{"title":"The major and minor <i>Aedes</i> mosquitoes from southern Nigeria exhibit low resistance towards public health insecticides.","authors":"Udoka C Nwangwu, Patience O Ubachukwu, Peter C Okeke, Muhammad M Mukhtar, Chukwuebuka M Nwosu, Ifeoma M Ngwu, Oscar N Nwaogo, Stephen O Anokwu, Linda C Ikechukwu, John E Ogbu, Nneka O Agashi, Chukwuebuka K Ezihe, Festus A Dogunro, Cosmas O Onwude, Emelda I Eloy, Ijeoma U Ikeakor, Emmanuel O Nwosu, Spencer C Nwangwu, Chiamaka U Nwangwu, Joseph U Anumba, Razaki A Osse, Arthur Sovi, Fiacre R Agossa, Chukwuemeka C Asadu, Okechukwu C Chukwuekezie, Sulaiman S Ibrahim","doi":"10.46471/gigabyte.165","DOIUrl":"10.46471/gigabyte.165","url":null,"abstract":"<p><p>Insecticide-based interventions continue to serve as the cornerstone of <i>Aedes</i> mosquito control, the primary vectors of arboviruses. This study assessed the insecticide resistance profiles of four <i>Aedes</i> mosquitoes in three rural areas in southern Nigeria, where arbovirus outbreaks recently occurred. Using WHO tube tests and CDC bottle bioassays, four <i>Aedes</i> species (<i>Aedes aegypti</i>, <i>Ae. albopictus</i>, <i>Ae. simpsoni</i> complex and <i>Ae. luteocephalus</i>) were evaluated for susceptibility to commonly used public health insecticides, including deltamethrin, alphacypermethrin, permethrin, pirimiphos-methyl, chlorfenapyr and clothianidin. Biochemical assays were conducted using <i>Ae. albopictus</i> to establish the role of metabolic resistance mechanism. Amplification and sequencing of fragment of <i>Ae. luteocephalus</i> ITS1 gene molecularly confirmed its species identity. <i>Aedes aegypti</i> exhibited possible resistance to pirimiphos-methyl but remained susceptible to all other insecticides across study sites. <i>Aedes albopictus</i> showed resistance to DDT and possible resistance to pirimiphos-methyl, while remaining susceptible to pyrethroids. <i>Aedes luteocephalus</i> was resistant to pirimiphos-methyl but susceptible to all other insecticides. <i>Aedes simpsoni</i> complex was fully susceptible to all insecticides. Biochemical assays revealed elevated 𝛼-esterase and monooxygenase activities (3.4-fold and 2.54-fold, respectively) in exposed females of <i>Ae. albopictus</i> compared to the unexposed cohort. Overall, the low resistance levels observed underscore the need for sustained insecticide resistance monitoring and management to maintain the effectiveness of insecticide-based vector control strategies in Nigeria.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte165"},"PeriodicalIF":1.2,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12508653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145281901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution of flies of medical importance in Thailand: a dataset.","authors":"Hassan Niyomdecha, Gerard Duvallet, Watthanasak Lertlumnaphakul, Ratchadawan Ngan-Klan, John Aerol Nobleza, Chauwat Charoenwiriyapap, Sylvie Manguin, Theeraphap Chareonviriyaphap","doi":"10.46471/gigabyte.164","DOIUrl":"10.46471/gigabyte.164","url":null,"abstract":"<p><p>Non-mosquito Diptera of medical and veterinary importance, including both biting and non-biting species in the order <i>Diptera</i>, play a significant role in the transmission of disease pathogens, either as mechanical or biological vectors. In this review, a total of 3,492 records across seven families were identified, comprising 2,512 biting flies and 980 non-biting flies. Among the biting flies, the most frequently recorded family was <i>Simuliidae</i>, followed by <i>Calliphoridae</i>, <i>Muscidae</i>, <i>Psychodidae</i>, and <i>Tabanidae</i>. The majority of these records originated from northern Thailand and were previously published in various peer-reviewed journals.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte164"},"PeriodicalIF":1.2,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12441734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145088371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Chromosome-level genome assembly of the common chiton, <i>Liolophura japonica</i> (Lischke, 1873).","authors":"","doi":"10.46471/gigabyte.159","DOIUrl":"10.46471/gigabyte.159","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.46471/gigabyte.123.].</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte159"},"PeriodicalIF":1.2,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12441733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145088365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Triatomines outside the Americas: a comprehensive dataset for the global surveillance of Chagas disease vectors.","authors":"Soledad Ceccarelli, Maria Eugenia Vicente, Qin Liu, Xiao-Nong Zhou, Di Wu, Agustin Balsalobre, Emiliano A Bruno, S Emilia Barboza, Romina Valente, Gerardo A Marti","doi":"10.46471/gigabyte.163","DOIUrl":"10.46471/gigabyte.163","url":null,"abstract":"<p><p>Chagas disease is caused by <i>Trypanosoma cruzi</i>, which is transmitted to mammals, including humans, mainly by insects of the subfamily Triatominae (Hemiptera: Reduviidae). Also known as \"kissing bugs\", the subfamily includes 159 species in 18 genera and five tribes. Although most species are in the Americas, here we present the first compilation of non-American triatomine occurrences. The data (396 records) corresponds to 16 species of the genera <i>Linschosteus</i> and <i>Triatoma</i> from Africa, Asia, and Oceania collected between 1926 and 2022, and include verified records with geographic coordinates, collection dates, and ecological information. The key novelties of our dataset regard (i) temporal and geographical updates of non-American species, (ii) records of <i>T. rubrofasciata</i> hundreds of kilometers inland, and (iii) geographical records of the last two described <i>Triatoma</i> species (<i>T. atrata</i> and <i>T. picta</i>). Our resource supports global surveillance, ecological modeling, and risk assessment by providing evidence of potential vectors for Chagas disease control outside the Americas.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte163"},"PeriodicalIF":1.2,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12407106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Snail intermediate host occurrence recorded by citizen scientists in rural Uganda and the Democratic Republic of the Congo.","authors":"Noelia Valderrama-Bhraunxs, Larissa Bonifacio, Julius Tumusiime, Germain Kapour, Daisy Namirembe, Casim Umba-Tolo, Grace Kagoro-Rugunda, Patrick Mitashi-Mulopo, Joule Mandinga, Liesbet Jacobs, Tine Huyse","doi":"10.46471/gigabyte.162","DOIUrl":"10.46471/gigabyte.162","url":null,"abstract":"<p><p>Snail-borne parasitic diseases, such as schistosomiasis and fascioliasis, pose significant public health and economic challenges worldwide. Schistosomiasis affects over 250 million people globally, with most cases in sub-Saharan Africa, while fascioliasis contributes substantially to livestock morbidity and economic losses. Freshwater snails (<i>Biomphalaria</i>, <i>Bulinus</i>, and <i>Radix</i> spp.) act as intermediate hosts, making their surveillance critical for disease control. Mass drug administration alone is insufficient, as high reinfection rates highlight the need for complementary strategies, including targeted snail control. To address limited malacological capacity and logistical constraints, the ATRAP project trained 50 citizen scientists in Uganda and the Democratic Republic of the Congo to monitor intermediate host snails at the genus level. Between 2020 and 2023, citizens recorded 31,490 snail occurrences. Data quality was ensured through automatic validation and manual verification of submitted snail pictures. This rigorously curated dataset, combining citizen science with expert validation, provides valuable insights for mapping snail distributions, identifying high-risk transmission areas, and developing sustainable, cost-effective snail control strategies.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte162"},"PeriodicalIF":1.2,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12362264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome sequencing and assembly of the house sparrow, <i>Passer domesticus</i>.","authors":"Vikas Kumar, Gopesh Sharma, Sankalp Sharma, Samvrutha Prasad, Shailesh Desai, Toral Vaishnani, Dalia Vishnudasan, Gopinathan Maheswaran, Kaomud Tyagi, Inderjeet Tyagi, Polavarapu B Kavi Kishor, Gyaneshwer Chaubey, Prashanth Suravajhala","doi":"10.46471/gigabyte.161","DOIUrl":"10.46471/gigabyte.161","url":null,"abstract":"<p><p>The common house sparrow, <i>Passer domesticus</i>, is a small bird belonging to the family Passeridae. Here, we provide high-quality whole-genome sequencing data along with its assembly for the house sparrow. The final genome assembly was generated using a workflow that included Shovill, SPAdes, MaSuRCA, and BUSCO. The assembly consists of contigs spanning 268,193 bases and coalescing around a 922 MB sized reference genome. We used rigorous statistical thresholds to check the coverage, as the Passer genome showed considerable similarity to the <i>Gallus gallus</i> (chicken) and <i>Taeniopygia guttata</i> (Zebra finch) genomes, also providing functional annotations. This new annotated genome assembly will be a valuable resource for comparative and population genomic analyses of passerine, avian, and vertebrate evolution.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte161"},"PeriodicalIF":1.2,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12308067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction.","authors":"Wudmir Y Rojas, Zargham Ahmad, Julia Jakiela, Helge Hecht, Jana Klánová, Elliott J Price","doi":"10.46471/gigabyte.160","DOIUrl":"10.46471/gigabyte.160","url":null,"abstract":"<p><p>High-performance computing (HPC) environments are crucial for computational research, including quantum chemistry (QC), but pose challenges for non-expert users. Researchers with limited computational knowledge struggle to utilise domain-specific software and access mass spectra prediction for <i>in silico</i> annotation. Here, we provide a robust workflow that leverages interoperable file formats for molecular structures to ensure integration across various QC tools. The quantum chemistry package for mass spectral predictions after electron ionization or collision-induced dissociation has been integrated into the Galaxy platform, enabling automated analysis of fragmentation mechanisms. The extended tight binding quantum chemistry package, chosen for its balance between accuracy and computational efficiency, provides molecular geometry optimisation. A Docker image encapsulates the necessary software stack. We demonstrated the workflow for four molecules, highlighting the scalability and efficiency of our solution via runtime performance analysis. This work shows how non-HPC users can make these predictions effortlessly, using advanced computational tools without needing in-depth expertise.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte160"},"PeriodicalIF":0.0,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12257954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144638787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing.","authors":"Kevin Stachelek, Bhavana Bhat, David Cobrinik","doi":"10.46471/gigabyte.158","DOIUrl":"10.46471/gigabyte.158","url":null,"abstract":"<p><p>Chevreul is an open-source R Bioconductor package and interactive R Shiny app for processing and visualising single-cell RNA sequencing (scRNA-seq) data. Chevreul differs from other scRNA-seq analysis packages in its ease of use, capacity to analyze full-length RNA sequencing data for exon coverage and transcript isoform inference, and support for batch correction. Chevreul enables exploratory analyses of scRNA-seq data using Bioconductor SingleCellExperiment objects (or converted Seurat objects), including batch integration, quality control filtering, read count normalization and transformation, dimensionality reduction, clustering at a range of resolutions, and cluster marker gene identification. Processed data can be visualized in the R Shiny app. Gene or transcript expression can be visualized using PCA, tSNE, UMAP, heatmaps, or violin plots; differential expression can be evaluated with several statistical tests. Chevreul also provides accessible tools for isoform-level analyses and alternative splicing detection. Chevreul empowers researchers without programming experience to analyze full-length scRNA-seq data.</p><p><strong>Availability & implementation: </strong>Chevreul is implemented in R, and the R package and integrated Shiny application are freely available at https://github.com/cobriniklab/chevreul with constituent packages hosted on Bioconductor at https://bioconductor.org/packages/chevreulProcess, https://bioconductor.org/packages/chevreulPlot, and https://bioconductor.org/packages/chevreulShiny.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte158"},"PeriodicalIF":1.2,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12320507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144786110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A draft genome assembly for the dart-poison frog <i>Phyllobates terribilis</i>.","authors":"Roberto Márquez, Denis Jacob Machado, Reyhaneh Nouri, Kerry L Gendreau, Daniel Janies, Ralph A Saporito, Marcus R Kronforst, Taran Grant","doi":"10.46471/gigabyte.157","DOIUrl":"10.46471/gigabyte.157","url":null,"abstract":"<p><p>Dendrobatid poison frogs have become well established as model systems in several fields of biology. Nevertheless, the development of molecular and genetic resources for these frogs has been hindered by their large, highly repetitive genomes, which have proven difficult to assemble. Here we present a draft assembly for <i>Phyllobates terribilis</i> (12.6 Gb), generated using a combination of sequencing platforms and bioinformatic approaches. Similar to other poison frog sequencing efforts, we recovered a highly fragmented assembly, likely due to the genome's large size and very high repeat content, which we estimated to be ≍88%. Despite the assembly's low contiguity, we were able to annotate multiple members of three gene sets of interest (voltage-gated sodium channels and <i>Notch</i> and <i>Wnt</i> signaling pathways), demonstrating the usefulness of our assembly to the amphibian research community.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte157"},"PeriodicalIF":1.2,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12208295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosome-level genome assembly of the lemon sole, <i>Microstomus kitt</i> (Pleuronectiformes: Pleuronectidae).","authors":"Marcel Nebenführ, David Prochotta, Maria A Nilsson, Menno J de Jong, Tunca D Yazici, Fabienne Langefeld, Malambo Muloongo, Helena Woköck, Jakob Jilg, Sina C Bender, Marvin M Zangl, Juan-Manuel Ortega Guatame, Kimberley Williams, Moritz Sonnewald, Axel Janke","doi":"10.46471/gigabyte.156","DOIUrl":"10.46471/gigabyte.156","url":null,"abstract":"<p><strong>Background: </strong>The lemon sole (<i>Microstomus kitt</i>) is a culinary fish from the family of righteye flounders (Pleuronectidae), inhabiting sandy, shallow offshore grounds of the North Sea, western Baltic Sea, English Channel, Great Britain and Ireland, Bay of Biscay, and coastal waters of Norway.</p><p><strong>Findings: </strong>Here, we present a chromosome-level genome assembly of the lemon sole. We applied PacBio HiFi sequencing on the PacBio Revio system to generate a highly complete and contiguous reference genome.The resulting assembly has a contig N50 of 17.2 Mbp and a scaffold N50 of 27.2 Mbp. The total assembly length is 628 Mbp, comprising 24 chromosome-length scaffolds. The identification of 99.7% complete BUSCO genes indicates a high level of assembly completeness.</p><p><strong>Conclusions: </strong>The chromosome-level genome assembly of the lemon sole provides a high-quality reference genome for future population-level genomic analyses of this commercially valuable, edible fish.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte156"},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}