{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T23:32:32Z","timestamp":1769556752557,"version":"3.49.0"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T00:00:00Z","timestamp":1766534400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T00:00:00Z","timestamp":1769472000000},"content-version":"vor","delay-in-days":34,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100005412","name":"Shahid Chamran University of Ahvaz","doi-asserted-by":"publisher","award":["SCU.SB1403.47678"],"award-info":[{"award-number":["SCU.SB1403.47678"]}],"id":[{"id":"10.13039\/501100005412","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005412","name":"Shahid Chamran University of Ahvaz","doi-asserted-by":"publisher","award":["SCU.SB1403.47678"],"award-info":[{"award-number":["SCU.SB1403.47678"]}],"id":[{"id":"10.13039\/501100005412","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-025-33632-0","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T14:03:54Z","timestamp":1766585034000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["ToxIR: an accurate RNA-seq pipeline for high-precision toxin transcriptome profiling, validated in odontobuthus doriae venom glands"],"prefix":"10.1038","volume":"16","author":[{"given":"Mehran","family":"Ebadi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maryam Naderi","family":"Soorki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,12,24]]},"reference":[{"key":"33632_CR1","doi-asserted-by":"publisher","first-page":"1362824","DOI":"10.3389\/fmars.2024.1362824","volume":"11","author":"C Gon\u00e7alves","year":"2024","unstructured":"Gon\u00e7alves, C., Cabral, M., Alves de Matos, I., Grosso, A. P., Costa, P. M. & A. R. & Transcriptome profiling of the posterior salivary glands of the cuttlefish sepia officinalis from the Portuguese West Coast. Front. Mar. Sci. 11, 1362824 (2024).","journal-title":"Front. Mar. Sci."},{"key":"33632_CR2","doi-asserted-by":"publisher","first-page":"106978","DOI":"10.1016\/j.phrs.2023.106978","volume":"197","author":"Z Xia","year":"2023","unstructured":"Xia, Z., He, D., Wu, Y., Kwok, H. F. & Cao, Z. Scorpion venom peptides: Molecular diversity, structural characteristics, and therapeutic use from channelopathies to viral infections and cancers. Pharmacol. Res. 197, 106978 (2023).","journal-title":"Pharmacol. Res."},{"key":"33632_CR3","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/j.toxicon.2014.11.233","volume":"93","author":"E Ortiz","year":"2015","unstructured":"Ortiz, E., Gurrola, G. B., Schwartz, E. F. & Possani, L. D. Scorpion venom components as potential candidates for drug development. Toxicon 93, 125\u2013135 (2015).","journal-title":"Toxicon"},{"key":"33632_CR4","doi-asserted-by":"crossref","unstructured":"King, G. Venoms To Drugs: Venom as a Source for the Development of Human Therapeutics (Royal Society of Chemistry, 2015).","DOI":"10.1039\/9781849737876"},{"key":"33632_CR5","first-page":"209","volume":"9","author":"VL Petricevich","year":"2013","unstructured":"Petricevich, V. L., Navarro, L. B. & Possani, L. D. Therapeutic use of Scorpion venom. Mol. Asp Inflamm. 9, 209\u2013231 (2013).","journal-title":"Mol. Asp Inflamm."},{"key":"33632_CR6","first-page":"433","volume":"11","author":"R Dehghani","year":"2017","unstructured":"Dehghani, R. & Kassiri, H. Geographical distribution of Scorpion odontobuthus doriae in Isfahan Province, central Iran. J. Arthropod-Borne Dis. 11, 433 (2017).","journal-title":"J. Arthropod-Borne Dis."},{"key":"33632_CR7","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1146\/annurev-animal-021419-083626","volume":"8","author":"CM Modahl","year":"2020","unstructured":"Modahl, C. M., Brahma, R. K., Koh, C. Y., Shioi, N. & Kini, R. M. Omics technologies for profiling toxin diversity and evolution in snake venom: Impacts on the discovery of therapeutic and diagnostic agents. Annu. Rev. Anim. Biosci. 8, 91\u2013116 (2020).","journal-title":"Annu. Rev. Anim. Biosci."},{"key":"33632_CR8","doi-asserted-by":"publisher","first-page":"458","DOI":"10.3390\/toxins16110458","volume":"16","author":"H Roman-Ramos","year":"2024","unstructured":"Roman-Ramos, H. & Ho, P. L. Current technologies in snake venom analysis and applications. Toxins 16, 458 (2024).","journal-title":"Toxins"},{"key":"33632_CR9","doi-asserted-by":"publisher","first-page":"292","DOI":"10.3390\/toxins10070292","volume":"10","author":"BM Von Reumont","year":"2018","unstructured":"Von Reumont, B. M. Studying smaller and neglected organisms in modern evolutionary venomics implementing RNASeq (transcriptomics)\u2014a critical guide. Toxins 10, 292 (2018).","journal-title":"Toxins"},{"key":"33632_CR10","doi-asserted-by":"crossref","unstructured":"von Reumont, B. M. et al. Modern venomics\u2014Current insights, novel methods, and future perspectives in biological and applied animal venom research. GigaScience 11, giac048 (2022).","DOI":"10.1093\/gigascience\/giac048"},{"key":"33632_CR11","unstructured":"Andrews, S. & FastQC A Quality Control Tool for High Throughput Sequence Data. (https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/. Accessed 4 May 2023)."},{"key":"33632_CR12","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"33632_CR13","doi-asserted-by":"crossref","unstructured":"Bushmanova, E., Antipov, D., Lapidus, A. & Prjibelski, A. D. rnaSPAdes: A de novo transcriptome assembler and its application to RNA-Seq data. GigaScience 8, giz100 (2019).","DOI":"10.1093\/gigascience\/giz100"},{"key":"33632_CR14","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","volume":"38","author":"M Manni","year":"2021","unstructured":"Manni, M., Berkeley, M. R., Seppey, M., Sim\u00e3o, F. A. & Zdobnov, E. M. BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647\u20134654 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"33632_CR15","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with bowtie 2. Nat. Methods. 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"33632_CR16","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29, 1072\u20131075 (2013).","journal-title":"Bioinformatics"},{"key":"33632_CR17","doi-asserted-by":"publisher","first-page":"3019","DOI":"10.1093\/bioinformatics\/btab090","volume":"37","author":"U Singh","year":"2021","unstructured":"Singh, U. & Wurtele, E. S. Orfipy: A fast and flexible tool for extracting ORFs. Bioinformatics 37, 3019\u20133020 (2021).","journal-title":"Bioinformatics"},{"key":"33632_CR18","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150\u20133152 (2012).","journal-title":"Bioinformatics"},{"key":"33632_CR19","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","volume":"53","author":"UniProt","year":"2025","unstructured":"UniProt. The universal protein knowledgebase in 2025. Nucleic Acids Res. 53, D609\u2013D617 (2025).","journal-title":"Nucleic Acids Res."},{"key":"33632_CR20","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403\u2013410 (1990).","journal-title":"J. Mol. Biol."},{"key":"33632_CR21","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1038\/s41587-021-01156-3","volume":"40","author":"F Teufel","year":"2022","unstructured":"Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein Language models. Nat. Biotechnol. 40, 1023\u20131025 (2022).","journal-title":"Nat. Biotechnol."},{"key":"33632_CR22","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","volume":"305","author":"A Krogh","year":"2001","unstructured":"Krogh, A., Larsson, B., Von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567\u2013580 (2001).","journal-title":"J. Mol. Biol."},{"key":"33632_CR23","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","volume":"7","author":"SR Eddy","year":"2011","unstructured":"Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).","journal-title":"PLoS Comput. Biol."},{"key":"33632_CR24","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJ Cock","year":"2009","unstructured":"Cock, P. J. et al. Biopython: Freely available python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422 (2009).","journal-title":"Bioinformatics"},{"key":"33632_CR25","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","volume":"30","author":"P Jones","year":"2014","unstructured":"Jones, P. et al. InterProScan 5: Genome-scale protein function classification. Bioinformatics 30, 1236\u20131240 (2014).","journal-title":"Bioinformatics"},{"key":"33632_CR26","doi-asserted-by":"publisher","first-page":"D344","DOI":"10.1093\/nar\/gkaa977","volume":"49","author":"M Blum","year":"2021","unstructured":"Blum, M. et al. The interpro protein families and domains database: 20 years on. Nucleic Acids Res. 49, D344\u2013D354 (2021).","journal-title":"Nucleic Acids Res."},{"key":"33632_CR27","doi-asserted-by":"publisher","first-page":"bbae094","DOI":"10.1093\/bib\/bbae094","volume":"25","author":"A Ringeval","year":"2024","unstructured":"Ringeval, A. et al. DeTox: A pipeline for the detection of toxins in venomous organisms. Brief. Bioinform. 25, bbae094 (2024).","journal-title":"Brief. Bioinform."},{"key":"33632_CR28","doi-asserted-by":"publisher","first-page":"bbab095","DOI":"10.1093\/bib\/bbab095","volume":"22","author":"PG Nachtigall","year":"2021","unstructured":"Nachtigall, P. G. et al. ToxCodAn: A new toxin annotator and guide to venom gland transcriptomics. Brief. Bioinform. 22, bbab095 (2021).","journal-title":"Brief. Bioinform."},{"key":"33632_CR29","doi-asserted-by":"publisher","first-page":"262","DOI":"10.3390\/toxins17060262","volume":"17","author":"J Esp\u00edn-Angulo","year":"2025","unstructured":"Esp\u00edn-Angulo, J. & Vela, D. Computational modeling of Low-Abundance proteins in venom gland transcriptomes: Bothrops Asper and Bothrops Jararaca. Toxins 17, 262 (2025).","journal-title":"Toxins"},{"key":"33632_CR30","doi-asserted-by":"publisher","first-page":"182","DOI":"10.3390\/toxins16040182","volume":"16","author":"MR Popoff","year":"2024","unstructured":"Popoff, M. R. Overview of bacterial protein toxins from pathogenic bacteria: Mode of action and insights into evolution. Toxins 16, 182 (2024).","journal-title":"Toxins"},{"key":"33632_CR31","doi-asserted-by":"crossref","unstructured":"Jenner, R. A., Casewell, N. R. & Undheim, E. A. What is animal venom? Rethinking a manipulative weapon. Trends Ecol. Evol. (2025).","DOI":"10.1016\/j.tree.2025.05.009"},{"key":"33632_CR32","doi-asserted-by":"publisher","first-page":"490","DOI":"10.3390\/toxins13070490","volume":"13","author":"S Nonin-Lecomte","year":"2021","unstructured":"Nonin-Lecomte, S., Fermon, L. & Felden, B. Pinel-Marie, M.-L. Bacterial type I toxins: Folding and membrane interactions. Toxins 13, 490 (2021).","journal-title":"Toxins"},{"key":"33632_CR33","doi-asserted-by":"publisher","first-page":"e5361","DOI":"10.7717\/peerj.5361","volume":"6","author":"J Macrander","year":"2018","unstructured":"Macrander, J., Panda, J., Janies, D., Daly, M. & Reitzel, A. M. Venomix: A simple bioinformatic pipeline for identifying and characterizing toxin gene candidates from transcriptomic data. PeerJ 6, e5361 (2018).","journal-title":"PeerJ"},{"key":"33632_CR34","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.jmb.2006.03.017","volume":"359","author":"S Cheek","year":"2006","unstructured":"Cheek, S., Krishna, S. S. & Grishin, N. V. Structural classification of small, disulfide-rich protein domains. J. Mol. Biol. 359, 215\u2013237 (2006).","journal-title":"J. Mol. Biol."},{"key":"33632_CR35","doi-asserted-by":"publisher","first-page":"e28387","DOI":"10.4161\/trla.28387","volume":"2","author":"K Asano","year":"2014","unstructured":"Asano, K. Why is start codon selection so precise in eukaryotes? Translation 2, e28387 (2014).","journal-title":"Translation"},{"key":"33632_CR36","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1186\/1471-2164-8-222","volume":"8","author":"T Joshi","year":"2007","unstructured":"Joshi, T. & Xu, D. Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genom. 8, 222 (2007).","journal-title":"BMC Genom."},{"issue":"1","key":"33632_CR37","doi-asserted-by":"publisher","first-page":"8304","DOI":"10.1038\/s41598-019-44499-3","volume":"9","author":"P Hsieh","year":"2019","unstructured":"Hsieh, P., Oyang, Y. & Chen, C. Effect of de Novo transcriptome assembly on transcript quantification. Sci. Rep. 9 (1), 8304 (2019).","journal-title":"Sci. Rep."},{"key":"33632_CR38","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1186\/s12864-015-1828-2","volume":"16","author":"CH Tan","year":"2015","unstructured":"Tan, C. H., Tan, K. Y., Fung, S. Y. & Tan, N. H. Venom-gland transcriptome and venom proteome of the Malaysian King Cobra (Ophiophagus hannah). BMC Genom. 16, 687 (2015).","journal-title":"BMC Genom."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-33632-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-33632-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-33632-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T10:16:27Z","timestamp":1769508987000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-025-33632-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,24]]},"references-count":38,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["33632"],"URL":"https:\/\/doi.org\/10.1038\/s41598-025-33632-0","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,24]]},"assertion":[{"value":"24 October 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 December 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This study involved only\n                      Odontobuthus doriae\n                      scorpions and did not require institutional ethical approval for human participation. All procedures for scorpion collection, electroshock milking, and tissue preservation were conducted in accordance with the World Health Organization (WHO) guidelines for the ethical handling of animals and were supervised by Shahid Chamran University of Ahvaz, Iran. The source data were generated under the ethical approval code\n                      IRAJUMS.REC.1396.916\n                      .","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"3529"}}