{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T16:54:00Z","timestamp":1784307240359,"version":"3.55.0"},"reference-count":68,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T00:00:00Z","timestamp":1751500800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Australian Research Council","award":["LP180101334"],"award-info":[{"award-number":["LP180101334"]}]},{"name":"Australian Research Council","award":["LP180101085"],"award-info":[{"award-number":["LP180101085"]}]},{"name":"Australian Research Council","award":["LP190101209"],"award-info":[{"award-number":["LP190101209"]}]},{"name":"Australian Research Council","award":["LP220200614"],"award-info":[{"award-number":["LP220200614"]}]},{"name":"Oz Omics Pty Ltd.","award":["LP180101334"],"award-info":[{"award-number":["LP180101334"]}]},{"name":"Oz Omics Pty Ltd.","award":["LP180101085"],"award-info":[{"award-number":["LP180101085"]}]},{"name":"Oz Omics Pty Ltd.","award":["LP190101209"],"award-info":[{"award-number":["LP190101209"]}]},{"name":"Oz Omics Pty Ltd.","award":["LP220200614"],"award-info":[{"award-number":["LP220200614"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Sparganosis is a neglected food- and water-borne zoonotic disease caused by members of the tapeworm genus Spirometra. More than 1600 human cases have been reported in the literature, primarily in Korea and China; however, the clinical significance of sparganosis is likely underestimated. The control of this disease is challenging in endemic regions because of the complexity of its lifecycle and the involvement of many animal host species, and treatment of clinical disease in humans and animals with selected drugs (e.g., mebendazole and\/or praziquantel), even at elevated doses, is often ineffective, such that novel interventions are needed. It is anticipated that the use of molecular technologies should allow the identification of new intervention targets in crucial biological processes and\/or pathways of Spirometra spp. While some draft genomes of Spirometra have been produced, their assemblies are incomplete. Here, we employed an advanced DNA sequencing\u2013informatic approach to assemble and annotate the first high-quality genome of an isolate of Spirometra from Australia, with chromosome-level contiguity and a curated gene set. This improved genome provides a useful resource to support fundamental and applied molecular investigations of Spirometra species and should assist in the design of new tools for the intervention against sparganosis of companion animals (including dogs and cats) and humans.<\/jats:p>","DOI":"10.3390\/ijms26136417","type":"journal-article","created":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T08:22:07Z","timestamp":1751530927000},"page":"6417","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Chromosome-Contiguous Reference Genome for Spirometra to Underpin Future Discovery Research"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8756-229X","authenticated-orcid":false,"given":"Neil D.","family":"Young","sequence":"first","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6025-194X","authenticated-orcid":false,"given":"Richard","family":"Malik","sequence":"additional","affiliation":[{"name":"Centre for Veterinary Education, The University of Sydney, Sydney, NSW 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexa","family":"Brown","sequence":"additional","affiliation":[{"name":"WAVES Veterinary Hospital, 1\/640 Beeliar Drive, Success, Perth, WA 6164, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1359-8913","authenticated-orcid":false,"given":"Tao","family":"Wang","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8218-7048","authenticated-orcid":false,"given":"Amanda","family":"Ash","sequence":"additional","affiliation":[{"name":"School of Medical and Molecular Forensic Sciences, Murdoch University, Perth, WA 6150, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9957-4674","authenticated-orcid":false,"given":"Pasi K.","family":"Korhonen","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4423-1690","authenticated-orcid":false,"given":"Robin B.","family":"Gasser","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1016\/S1473-3099(15)00133-4","article-title":"Human sparganosis, a neglected food-borne zoonosis","volume":"15","author":"Liu","year":"2015","journal-title":"Lancet Infect. Dis."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"102036","DOI":"10.1016\/j.parint.2019.102036","article-title":"Human proliferative sparganosis update","volume":"75","author":"Kikuchi","year":"2020","journal-title":"Parasitol. Int."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e228396","DOI":"10.1136\/bcr-2018-228396","article-title":"Sparganosis: An under-recognised zoonosis in Australia?","volume":"12","author":"Tran","year":"2019","journal-title":"BMJ Case Rep."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e273","DOI":"10.3346\/jkms.2018.33.e273","article-title":"Human sparganosis in Korea","volume":"33","author":"Kim","year":"2018","journal-title":"J. Korean Med. Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Xiao, L., Ryan, U., and Feng, F. (2015). Diphyllobothrium, Diplogonoporus and Spirometra. Biology of Foodborne Parasites, CRC Press.","DOI":"10.1201\/b18317"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/cid\/ciaa1036","article-title":"Sparganosis (Spirometra) in Europe in the molecular era","volume":"72","author":"Kuchta","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bennett, H.M., Mok, H.P., Gkrania-Klotsas, E., Tsai, I.J., Stanley, E.J., Antoun, N.M., Coghlan, A., Harsha, B., Traini, A., and Ribeiro, D.M. (2014). The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion. Genome Biol., 15.","DOI":"10.1186\/s13059-014-0510-3"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Kikuchi, T., Dayi, M., Hunt, V.L., Ishiwata, K., Toyoda, A., Kounosu, A., Sun, S., Maeda, Y., Kondo, Y., and de Noya, B.A. (2021). Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation. Commun. Biol., 4.","DOI":"10.1038\/s42003-021-02160-8"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.biotechadv.2016.03.001","article-title":"Making sense of genomes of parasitic worms: Tackling bioinformatic challenges","volume":"34","author":"Korhonen","year":"2016","journal-title":"Biotechnol. Adv."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1016\/j.ijpara.2021.10.003","article-title":"Advances in the treatment, diagnosis, control and scientific understanding of taeniid cestode parasite infections over the past 50 years","volume":"51","author":"Lightowlers","year":"2021","journal-title":"Int. J. Parasitol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1007\/s00436-021-07346-x","article-title":"Cestodes in the genomic era","volume":"121","author":"Kamenetzky","year":"2022","journal-title":"Parasitol. Res."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Oey, H., Zakrzewski, M., Gravermann, K., Young, N.D., Korhonen, P.K., Gobert, G.N., Hasan, S., Martine, D.M., You, H., and Lavin, M. (2019). Whole-genome sequence of the bovine blood fluke Schistosoma bovis reveals evidence for introgressive hybridization with S. haematobium. PLoS Pathog., 15.","DOI":"10.1371\/journal.ppat.1007513"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13071-019-3492-x","article-title":"Long-read sequencing reveals a 4.4 kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1","volume":"12","author":"Kinkar","year":"2019","journal-title":"Parasites Vectors"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"giz108","DOI":"10.1093\/gigascience\/giz108","article-title":"High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing","volume":"8","author":"Stroehlein","year":"2019","journal-title":"GigaScience"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Kinkar, L., Young, N.D., Sohn, W.-M., Stroehlein, A.J., Korhonen, P.K., and Gasser, R.B. (2020). First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. PLoS Negl. Trop. Dis., 14.","DOI":"10.1371\/journal.pntd.0008552"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1016\/j.ygeno.2021.03.001","article-title":"High-quality reference genome for Clonorchis sinensis","volume":"113","author":"Young","year":"2021","journal-title":"Genomics"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Stroehlein, A.J., Korhonen, P.K., Lee, V.V., Ralph, S.A., Mentink-Kane, M., You, H., McManus, D.P., Tchuem Tchuent\u00e9, L.-A., Stothard, J.R., and Kaur, P. (2022). Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation. PLoS Pathog., 18.","DOI":"10.1371\/journal.ppat.1010288"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","article-title":"A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping","volume":"159","author":"Rao","year":"2014","journal-title":"Cell"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Amarasinghe, S.L., Su, S., Dong, X., Zappia, L., Ritchie, M.E., and Gouil, Q. (2020). Opportunities and challenges in long-read sequencing data analysis. Genome Biol., 21.","DOI":"10.1186\/s13059-020-1935-5"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1007\/978-1-0716-2561-3_23","article-title":"Sequencing and assembly of polyploid genomes","volume":"2545","author":"Wang","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_21","unstructured":"Bowman, D.D. (2020). Georgis\u2019 Parasitology for Veterinarians, Elsevier. [11th ed.]."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1006\/mcpr.2001.0406","article-title":"Single-strand conformation polymorphism-based analysis reveals genetic variation within Spirometra erinacei (Cestoda: Pseudophyllidea) from Australia","volume":"16","author":"Zhu","year":"2002","journal-title":"Mol. Cell. Probes"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.parint.2016.12.011","article-title":"Establishment of the complete life cycle of Spirometra (Cestoda: Diphyllobothriidae) in the laboratory using a newly isolated triploid clone","volume":"66","author":"Okino","year":"2017","journal-title":"Parasitol. Int."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"S123","DOI":"10.1017\/S0031182000086017","article-title":"Excretory-secretory products of helminth parasites: Effects on host immune responses","volume":"96","author":"Lightowlers","year":"1988","journal-title":"Parasitology"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.molbiopara.2014.03.007","article-title":"Secretory products of helminth parasites as immunomodulators","volume":"195","author":"Harnett","year":"2014","journal-title":"Mol. Biochem. Parasitol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.pt.2022.06.002","article-title":"Improving helminth genome resources in the post-genomic era","volume":"38","author":"Doyle","year":"2022","journal-title":"Trends Parasitol."},{"key":"ref_27","first-page":"237","article-title":"Global genetic diversity of Spirometra tapeworms","volume":"37","author":"Hong","year":"2020","journal-title":"Trop. Biomed."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Liu, W., Gong, T., Chen, S., Liu, Q., Zhou, H., He, J., Wu, Y., Li, F., and Liu, Y. (2022). Epidemiology, diagnosis, and prevention of sparganosis in Asia. Animals, 12.","DOI":"10.3390\/ani12121578"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1093\/jhered\/esl036","article-title":"A genomic perspective on the shortcomings of mitochondrial DNA for \u201cbarcoding\u201d identification","volume":"97","author":"Rubinoff","year":"2006","journal-title":"J. Hered."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-61779-591-6_1","article-title":"DNA barcodes: Methods and protocols","volume":"858","author":"Kress","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s41592-018-0014-2","article-title":"Comprehensive comparative analysis of 5\u2032-end RNA-sequencing methods","volume":"15","author":"Adiconis","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper","volume":"34","author":"Forslund","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3","DOI":"10.2307\/3278670","article-title":"The biology of Spirometra","volume":"60","author":"Mueller","year":"1974","journal-title":"J. Parasitol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"728","DOI":"10.2307\/3278751","article-title":"Sparganum growth factor in New World Spirometra spp. J","volume":"60","author":"Mueller","year":"1974","journal-title":"Parasitol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1017\/S0031182009991727","article-title":"Echinococcus multilocularis as an experimental model in stem cell research and molecular host-parasite interaction","volume":"137","author":"Brehm","year":"2010","journal-title":"Parasitology"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/j.ijpara.2009.10.012","article-title":"RNA interference in a cestode reveals specific silencing of selected highly expressed gene transcripts","volume":"40","author":"Pierson","year":"2010","journal-title":"Int. J. Parasitol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.ijpara.2013.03.004","article-title":"RNA-mediated gene suppression and in vitro culture in Hymenolepis microstoma","volume":"43","author":"Cunningham","year":"2013","journal-title":"Int. J. Parasitol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e41463","DOI":"10.7554\/eLife.41463","article-title":"Programmed knockout mutation of liver fluke granulin attenuates virulence of infection-induced hepatobiliary morbidity","volume":"8","author":"Arunsan","year":"2019","journal-title":"eLife"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e21205","DOI":"10.1096\/fj.202001745RR","article-title":"CRISPR\/Cas9-mediated genome editing of Schistosoma mansoni acetylcholinesterase","volume":"35","author":"You","year":"2021","journal-title":"FASEB J."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e22615","DOI":"10.1096\/fj.202200600RR","article-title":"CRISPR\/Cas9-mediated gene knockout of Sj16 in Schistosoma japonicum eggs upregulates the host-to-egg immune response","volume":"36","author":"Zhang","year":"2022","journal-title":"FASEB J."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Campos, T.L., Korhonen, P.K., Hofmann, A., Gasser, R.B., and Young, N.D. (2022). Machine learning for the prediction and prioritisation of essential genes in eukaryotes\u2014Challenges and prospects. Biotechnol. Adv., 54.","DOI":"10.1016\/j.biotechadv.2021.107822"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Hong, D., Xie, H., Wan, H., An, N., Xu, C., and Zhang, J. (2018). Efficacy comparison between long-term high-dose praziquantel and surgical therapy for cerebral sparganosis: A multicenter retrospective cohort study. PLoS Negl. Trop. Dis., 12.","DOI":"10.1371\/journal.pntd.0006918"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ pre-processor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes","volume":"11","author":"Jaron","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1093\/bioinformatics\/btx304","article-title":"KMC 3: Counting and manipulating k-mer statistics","volume":"33","author":"Kokot","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Zhou, C., McCarthy, S.A., and Durbin, R. (2023). YaHS: Yet another Hi-C scaffolding tool. Bioinformatics, 39.","DOI":"10.1093\/bioinformatics\/btac808"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Waterhouse","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"Flynn","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Tarailo-Graovac, M., and Chen, N. (2009). Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinform., 4.","DOI":"10.1002\/0471250953.bi0410s25"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s13742-015-0089-y","article-title":"Rcorrector: Efficient and accurate error correction for Illumina RNA-seq reads","volume":"4","author":"Song","year":"2015","journal-title":"GigaScience"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Nachtigall, P.G., Kashiwabara, A.Y., and Durham, A.M. (2021). CodAn: Predictive models for precise identification of coding regions in eukaryotic transcripts. Brief. Bioinform., 22.","DOI":"10.1093\/bib\/bbaa045"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1038\/s41467-020-15171-6","article-title":"Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals down-regulation of retained introns","volume":"11","author":"Tang","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1093\/bioinformatics\/17.9.847","article-title":"InterProScan\u2014An integration platform for the signature-recognition methods in InterPro","volume":"17","author":"Zdobnov","year":"2001","journal-title":"Bioinformatics"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/s41587-021-01156-3","article-title":"SignalP 6.0 predicts all five types of signal peptides using protein language models","volume":"40","author":"Teufel","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Edgar, R.C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinform., 5.","DOI":"10.1186\/1471-2105-5-113"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1093\/molbev\/msz189","article-title":"ModelTest-NG: A new and scalable tool for the selection of DNA and protein evolutionary models","volume":"37","author":"Darriba","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst. Biol."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Yu, G. (2020). Using ggtree to visualize data on tree-like structures. Curr. Protoc. Bioinform., 69.","DOI":"10.1002\/cpbi.96"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.ijpara.2018.12.003","article-title":"Somatic proteome of Haemonchus contortus","volume":"49","author":"Wang","year":"2019","journal-title":"Int. J. Parasitol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"103375","DOI":"10.1016\/j.jprot.2019.05.003","article-title":"High throughput LC-MS\/MS-based proteomic analysis of excretory-secretory products from short-term in vitro culture of Haemonchus contortus","volume":"204","author":"Wang","year":"2019","journal-title":"J. Proteomics"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics","volume":"11","author":"Tyanova","year":"2016","journal-title":"Nat. Protoc."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/13\/6417\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:03:56Z","timestamp":1760033036000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/13\/6417"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,3]]},"references-count":68,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["ijms26136417"],"URL":"https:\/\/doi.org\/10.3390\/ijms26136417","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,3]]}}}