{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:48:43Z","timestamp":1760147323396,"version":"build-2065373602"},"reference-count":46,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,1,22]],"date-time":"2023-01-22T00:00:00Z","timestamp":1674345600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea (NRF)","doi-asserted-by":"publisher","award":["2021R1C1C2009518"],"award-info":[{"award-number":["2021R1C1C2009518"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Naegleria fowleri is a pathogenic free-living amoeba, commonly found around the world in warm, fresh water and soil. N. fowleri trophozoites can infect humans by entering the brain through the nose and causing usually fatal primary amebic meningoencephalitis (PAM). Trophozoites can encyst to survive under unfavorable conditions such as cold temperature, starvation, and desiccation. Recent technological advances in genomics and bioinformatics have provided unique opportunities for the identification and pre-validation of pathogen-related and environmental resistance through improved understanding of the biology of pathogenic N. fowleri trophozoites and cysts at a molecular level. However, genomic and transcriptomic data on differential expression genes (DEGs) between trophozoites and cysts of N. fowleri are very limited. Here, we report transcriptome Illumina RNA sequencing (RNA-seq) for N. fowleri trophozoites and cysts and de novo transcriptome assembly. RNA-seq libraries were generated from RNA extracted from N. fowleri sampled from cysts, and a reference transcriptome was generated through the assembly of trophozoite data. In the database, the assembly procedure resulted in 42,220 contigs with a mean length of 11,254 nucleotides and a C+G content of 37.21%. RNA sequencing showed that 146 genes in cysts of N. fowleri indicated 2-fold upregulation in comparison with trophozoites of N. fowleri, and 163 genes were downregulated; these genes were found to participate in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The KEGG pathway included metabolic (131 sequences) and genetic information processing (66 sequences), cellular processing (43 sequences), environmental information processing (22 sequences), and organismal system (20 sequences) pathways. On the other hand, an analysis of 11,254 sequences via the Gene Ontology database showed that their annotations contained 1069 biological processes including the cellular process (228 sequences) and metabolic process (214 sequences); 923 cellular components including cells (240 sequences) and cell parts (225 sequences); and 415 molecular functions including catalytic activities (195 sequences) and binding processes (186 sequences). Differential expression levels increased in cysts of N. fowleri compared to trophozoites of N. fowleri, which were mainly categorized as serine\/threonine protease, kinase, and lipid metabolism-related proteins. These results may provide new insights into pathogen-related genes or environment-resistant genes in the pathogenesis of N. fowleri.<\/jats:p>","DOI":"10.3390\/pathogens12020174","type":"journal-article","created":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T02:01:02Z","timestamp":1674439262000},"page":"174","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["De Novo Transcriptome Profiling of Naegleria fowleri Trophozoites and Cysts via RNA Sequencing"],"prefix":"10.3390","volume":"12","author":[{"given":"Hae-Jin","family":"Sohn","sequence":"first","affiliation":[{"name":"Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3365-8007","authenticated-orcid":false,"given":"Jong-Hyun","family":"Kim","sequence":"additional","affiliation":[{"name":"Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9539-3051","authenticated-orcid":false,"given":"Kyongmin","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3254-4064","authenticated-orcid":false,"given":"Sun","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ho-Joon","family":"Shin","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea"},{"name":"Department of Biomedical Science, Graduate School of Ajou University, Suwon 16499, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/S0140-6736(72)91763-1","article-title":"Primary amoebic meningoencephalitis","volume":"2","author":"Anderson","year":"1972","journal-title":"Lancet"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/0035-9203(72)90147-2","article-title":"Primary amoebic meningo-encephalitis. 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