{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,30]],"date-time":"2025-03-30T08:10:23Z","timestamp":1743322223458,"version":"3.40.3"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T00:00:00Z","timestamp":1742947200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T00:00:00Z","timestamp":1742947200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Data"],"DOI":"10.1038\/s41597-025-04837-9","type":"journal-article","created":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T16:33:56Z","timestamp":1743006836000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Chromosome-level genome assembly of an endoparasitoid Cotesia ruficrus"],"prefix":"10.1038","volume":"12","author":[{"given":"Xianxin","family":"Zhao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanyuan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0203-0663","authenticated-orcid":false,"given":"Xinhai","family":"Ye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Fang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4937-8867","authenticated-orcid":false,"given":"Gongyin","family":"Ye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,3,26]]},"reference":[{"key":"4837_CR1","unstructured":"Zhang, Z. Q. A study on biological and ecological characteristics of Apanteles ruficrus Haliday. Nat. Enemies Insects 84\u201389 (1986)."},{"key":"4837_CR2","doi-asserted-by":"publisher","first-page":"197","DOI":"10.2307\/2403618","volume":"25","author":"MG Hill","year":"1988","unstructured":"Hill, M. G. Analysis of the biological control of Mythimna separata (Lepidoptera: Noctuidae) by Apanteles ruficrus (Braconidae: Hymenoptera) in New Zealand. J. Appl. Ecol. 25, 197 (1988).","journal-title":"J. Appl. Ecol."},{"key":"4837_CR3","doi-asserted-by":"publisher","first-page":"1055","DOI":"10.1093\/ee\/12.4.1055","volume":"12","author":"GS McCutcheon","year":"1983","unstructured":"McCutcheon, G. S., Salley, W. Z. & Turnipseed, S. G. Biology of Apanteles ruficrus, an imported parasitoid of Pseudoplusia includens, Trichoplusia ni, and Spodoptera frugiperda (Lepidoptera: Noctuidae). Environ. Entomol. 12, 1055\u20131058 (1983).","journal-title":"Environ. Entomol."},{"key":"4837_CR4","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1093\/jee\/tov405","volume":"109","author":"Y Chen","year":"2016","unstructured":"Chen, Y. et al. Cotesia ruficrus (Hymenoptera: Braconidae) parasitizing Cnaphalocrocis medinalis (Lepidoptera: Pyralidae): Developmental interactions and food utilization efficiency of hosts. J. Econ. Entomol. 109, 588\u2013593 (2016).","journal-title":"J. Econ. Entomol."},{"key":"4837_CR5","doi-asserted-by":"publisher","first-page":"193","DOI":"10.18311\/jbc\/2019\/24118","volume":"33","author":"A Gupta","year":"2019","unstructured":"Gupta, A. et al. Cotesia ruficrus (Haliday, 1834) (Hymenoptera: Braconidae) emerging as a common natural parasitoid of Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) in Indian maize fields. J. Biol. Control 33, 193\u2013196 (2019).","journal-title":"J. Biol. Control"},{"key":"4837_CR6","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1080\/00288233.1986.10426984","volume":"29","author":"MG Hill","year":"1986","unstructured":"Hill, M. G. Effects of Cotesia ruficrus (Braconidae: Hymenoptera) parasitism and rearing density on Mythimna separata (Noctuidae: Lepidoptera) food consumption, and implications for biological control. New Zealand J. Agric. Res. 29, 281\u2013287 (1986).","journal-title":"New Zealand J. Agric. Res."},{"key":"4837_CR7","unstructured":"Yu, D. S., van Achterberg, C. & Horstmann, K. Taxapad 2016 \u2013 World Ichneumonoidea 2011. Taxonomy, Biology, Morphology and Distribution. https:\/\/www.bioinfo.org.uk\/html\/b162939.htm (2016)."},{"key":"4837_CR8","doi-asserted-by":"publisher","first-page":"e0165632","DOI":"10.1371\/journal.pone.0165632","volume":"11","author":"G Goergen","year":"2016","unstructured":"Goergen, G., Kumar, P. L., Sankung, S. B., Togola, A. & Tam\u00f2, M. First report of outbreaks of the fall armyworm Spodoptera frugiperda (J E Smith) (Lepidoptera, Noctuidae), a new alien invasive pest in west and central Africa. PLOS ONE 11, e0165632 (2016).","journal-title":"PLOS ONE"},{"key":"4837_CR9","doi-asserted-by":"publisher","first-page":"45","DOI":"10.4001\/003.026.0045","volume":"26","author":"A Jacobs","year":"2018","unstructured":"Jacobs, A., Vuuren, Avan & Rong, I. H. Characterisation of the fall armyworm (Spodoptera frugiperda J.E. Smith) (Lepidoptera: Noctuidae) from South Africa. Afr. Entomol. 26, 45\u201349 (2018).","journal-title":"Afr. Entomol."},{"key":"4837_CR10","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1016\/S2095-3119(19)62839-X","volume":"20","author":"X Sun","year":"2021","unstructured":"Sun, X. et al. Case study on the first immigration of fall armyworm, Spodoptera frugiperda invading into China. J. Integr. Agric. 20, 664\u2013672 (2021).","journal-title":"J. Integr. Agric."},{"key":"4837_CR11","doi-asserted-by":"publisher","first-page":"286","DOI":"10.4001\/003.026.0286","volume":"26","author":"DG Montezano","year":"2018","unstructured":"Montezano, D. G. et al. Host plants of Spodoptera frugiperda (Lepidoptera: Noctuidae) in the Americas. Afr. Entomol. 26, 286\u2013300 (2018).","journal-title":"Afr. Entomol."},{"key":"4837_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1461-9563.2011.00550.x","volume":"14","author":"GM Gurr","year":"2012","unstructured":"Gurr, G. M. et al. Parasitoids of the rice leaffolder Cnaphalocrocis medinalis and prospects for enhancing biological control with nectar plants. Agric. For. Entomol. 14, 1\u201312 (2012).","journal-title":"Agric. For. Entomol."},{"key":"4837_CR13","doi-asserted-by":"publisher","first-page":"107027","DOI":"10.1016\/j.cropro.2024.107027","volume":"188","author":"X Li","year":"2025","unstructured":"Li, X., An, J.-L., Wang, W.-J., Liu, T.-X. & Zhang, S.-Z. Influence of four noctuid pests on preference and offspring fitness of Cotesia ruficrus. Crop Prot. 188, 107027 (2025).","journal-title":"Crop Prot."},{"key":"4837_CR14","first-page":"343","volume":"4","author":"SS Patil","year":"2022","unstructured":"Patil, S. S., Kamble, C. & Sathe, T. V. Biocontrol potential of Cotesia ruficrus Hal. (Hymenoptera: Braconidae) against different Lepidopterous pests. Biolife 4, 343\u2013346 (2022).","journal-title":"Biolife"},{"key":"4837_CR15","doi-asserted-by":"publisher","first-page":"286","DOI":"10.3157\/021.127.0301","volume":"127","author":"S Pal","year":"2017","unstructured":"Pal, S. & Gupta, A. Severe outbreak of rice green semilooper, Naranga aenescens (Moore) (Lepidoptera: Noctuidae) along with its parasitoid complex in Sub-Himalayan West Bengal, India. Entomol. News 127, 286\u2013291 (2017).","journal-title":"Entomol. News"},{"key":"4837_CR16","first-page":"131","volume":"28","author":"C Watanabe","year":"1966","unstructured":"Watanabe, C. Notes on braconid parasites of Naranga aenescens Moore occurring in Japan (Hymenoptera, Braconidae). Insecta matsumurana 28, 131\u2013132 (1966).","journal-title":"Insecta matsumurana"},{"key":"4837_CR17","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1007\/s10526-014-9628-1","volume":"60","author":"P Zhu","year":"2015","unstructured":"Zhu, P. et al. Selective enhancement of parasitoids of rice Lepidoptera pests by sesame (Sesamum indicum) flowers. BioControl 60, 157\u2013167 (2015).","journal-title":"BioControl"},{"key":"4837_CR18","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.biocontrol.2013.06.011","volume":"67","author":"Y-G Lou","year":"2013","unstructured":"Lou, Y.-G., Zhang, G.-R., Zhang, W.-Q., Hu, Y. & Zhang, J. Biological control of rice insect pests in China. Biol. Control 67, 8\u201320 (2013).","journal-title":"Biol. Control"},{"key":"4837_CR19","doi-asserted-by":"publisher","first-page":"133491","DOI":"10.1016\/j.ijbiomac.2024.133491","volume":"274","author":"W-W Wang","year":"2024","unstructured":"Wang, W.-W., Han, K.-R., Jing, X.-F., Liu, T.-X. & Zhang, S.-Z. Odorant-binding protein CrufOBP1 in Cotesia ruficrus females plays a pivotal role in the detection of Spodoptera frugiperda larvae. Int. J. Biol. Macromol. 274, 133491 (2024).","journal-title":"Int. J. Biol. Macromol."},{"key":"4837_CR20","doi-asserted-by":"publisher","first-page":"920","DOI":"10.3390\/insects14120920","volume":"14","author":"K-R Han","year":"2023","unstructured":"Han, K.-R. et al. Characterization of CrufCSP1 and its potential involvement in host location by Cotesia ruficrus (Hymenoptera: Braconidae), an indigenous parasitoid of Spodoptera frugiperda (Lepidoptera: Noctuidae) in China. Insects 14, 920 (2023).","journal-title":"Insects"},{"key":"4837_CR21","doi-asserted-by":"publisher","first-page":"570","DOI":"10.3390\/insects15080570","volume":"15","author":"X Li","year":"2024","unstructured":"Li, X. et al. Effect of Cotesia ruficrus parasitization on diversity and community composition of intestinal bacteria in Spodoptera frugiperda. Insects 15, 570 (2024).","journal-title":"Insects"},{"key":"4837_CR22","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1101\/gr.278232.123","volume":"34","author":"W Yu","year":"2024","unstructured":"Yu, W. et al. Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes. Genome Res. 34, 326\u2013340 (2024).","journal-title":"Genome Res."},{"key":"4837_CR23","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","volume":"18","author":"H Cheng","year":"2021","unstructured":"Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170\u2013175 (2021).","journal-title":"Nat. Methods"},{"key":"4837_CR24","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1111\/1755-0998.13312","volume":"21","author":"A Whibley","year":"2021","unstructured":"Whibley, A., Kelley, J. L. & Narum, S. R. The changing face of genome assemblies: Guidance on achieving high-quality reference genomes. Mol. Ecol. Resour. 21, 641\u2013652 (2021).","journal-title":"Mol. Ecol. Resour."},{"key":"4837_CR25","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/s42003-020-01623-8","volume":"4","author":"J Gauthier","year":"2021","unstructured":"Gauthier, J. et al. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun. Biol. 4, 104 (2021).","journal-title":"Commun. Biol."},{"key":"4837_CR26","doi-asserted-by":"publisher","DOI":"10.1186\/s12915-022-01313-3","volume":"20","author":"X Ye","year":"2022","unstructured":"Ye, X. et al. Genome of the parasitoid wasp Cotesia chilonis sheds light on amino acid resource exploitation. BMC Biol. 20, 118 (2022).","journal-title":"BMC Biol."},{"key":"4837_CR27","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1016\/j.pt.2024.08.003","volume":"40","author":"X Ye","year":"2024","unstructured":"Ye, X., Yang, Y., Zhao, X., Fang, Q. & Ye, G. The state of parasitoid wasp genomics. Trends Parasitol. 40, 914\u2013929 (2024).","journal-title":"Trends Parasitol."},{"key":"4837_CR28","doi-asserted-by":"publisher","first-page":"101298","DOI":"10.1016\/j.cois.2024.101298","volume":"68","author":"X Ye","year":"2024","unstructured":"Ye, X., Yang, Y., Fang, Q. & Ye, G. Genomics of insect natural enemies in agroecosystems. Curr. Opin. Insect. Sci. 68, 101298 (2024).","journal-title":"Curr. Opin. Insect. Sci."},{"year":"2025","key":"4837_CR29","unstructured":"Cruf_RNA4OGS_AM, Genome Sequence Archive, https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264894 (2025)."},{"year":"2025","key":"4837_CR30","unstructured":"Cruf_RNA4OGS_AF, Genome Sequence Archive, https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264895 (2025)."},{"key":"4837_CR31","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"year":"2025","key":"4837_CR32","unstructured":"Cruf_PacBioreads, Genome Sequence Archive, https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264892 (2025)."},{"year":"2025","key":"4837_CR33","unstructured":"Cruf_HiCreads, Genome Sequence Archive, https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264893 (2025)."},{"key":"4837_CR34","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"4837_CR35","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14998-3","volume":"11","author":"TR Ranallo-Benavidez","year":"2020","unstructured":"Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 11, 1432 (2020).","journal-title":"Nat. Commun."},{"key":"4837_CR36","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-024-03252-4","volume":"25","author":"J Hu","year":"2024","unstructured":"Hu, J. et al. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biol. 25, 107 (2024).","journal-title":"Genome Biol."},{"key":"4837_CR37","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/1471-2105-13-238","volume":"13","author":"MJ Chaisson","year":"2012","unstructured":"Chaisson, M. J. & Tesler, G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinform. 13, 238 (2012).","journal-title":"BMC Bioinform."},{"key":"4837_CR38","doi-asserted-by":"publisher","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","volume":"36","author":"J Hu","year":"2020","unstructured":"Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: A fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36, 2253\u20132255 (2020).","journal-title":"Bioinformatics"},{"key":"4837_CR39","unstructured":"Zhao, X. Cruf_HiCgenome. Genome Warehouse. https:\/\/ngdc.cncb.ac.cn\/gwh\/Assembly\/91414\/show (2024)."},{"key":"4837_CR40","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.107","volume":"2","author":"S Chen","year":"2023","unstructured":"Chen, S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. Imeta 2, e107 (2023).","journal-title":"Imeta"},{"key":"4837_CR41","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":"4837_CR42","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand, N. C. et al. Juicer Provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95\u201398 (2016).","journal-title":"Cell Syst."},{"key":"4837_CR43","doi-asserted-by":"publisher","first-page":"5936","DOI":"10.3390\/molecules27185936","volume":"27","author":"Y Zhang","year":"2022","unstructured":"Zhang, Y., Xiong, Y. & Xiao, Y. 3dDNA: A computational method of building DNA 3D Structures. Molecules 27, 5936 (2022).","journal-title":"Molecules"},{"key":"4837_CR44","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/j.cels.2018.01.001","volume":"6","author":"JT Robinson","year":"2018","unstructured":"Robinson, J. T. et al. Juicebox.js Provides a cloud-based visualization system for Hi-C Data. Cell Syst. 6, 256\u2013258.e1 (2018).","journal-title":"Cell Syst."},{"key":"4837_CR45","doi-asserted-by":"publisher","first-page":"5793","DOI":"10.1128\/JVI.76.11.5793-5796.2002","volume":"76","author":"E Belle","year":"2002","unstructured":"Belle, E. et al. Visualization of polydnavirus sequences in a parasitoid wasp chromosome. J. Virol. 76, 5793\u20135796 (2002).","journal-title":"J. Virol."},{"key":"4837_CR46","doi-asserted-by":"crossref","unstructured":"Gokhman, V. E. Karyotypes of Parasitic Hymenoptera. (Springer, Dordrecht, 2009).","DOI":"10.1007\/978-1-4020-9807-9"},{"key":"4837_CR47","first-page":"4.10.1","volume":"Chapter 4","author":"M Tarailo-Graovac","year":"2009","unstructured":"Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics Chapter 4, 4.10.1\u20134.10.14 (2009).","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"4837_CR48","doi-asserted-by":"publisher","first-page":"9451","DOI":"10.1073\/pnas.1921046117","volume":"117","author":"JM Flynn","year":"2020","unstructured":"Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. USA. 117, 9451\u20139457 (2020).","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"4837_CR49","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1101\/gr.88502","volume":"12","author":"Z Bao","year":"2002","unstructured":"Bao, Z. & Eddy, S. R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269\u20131276 (2002).","journal-title":"Genome Res."},{"issue":"Suppl 1","key":"4837_CR50","doi-asserted-by":"publisher","first-page":"i351","DOI":"10.1093\/bioinformatics\/bti1018","volume":"21","author":"AL Price","year":"2005","unstructured":"Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21(Suppl 1), i351\u2013358 (2005).","journal-title":"Bioinformatics"},{"key":"4837_CR51","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho, C. et al. BLAST+: Architecture and applications. BMC Bioinform. 10, 421 (2009).","journal-title":"BMC Bioinform."},{"key":"4837_CR52","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1146\/annurev.genet.40.110405.090448","volume":"41","author":"C Feschotte","year":"2007","unstructured":"Feschotte, C. & Pritham, E. J. DNA transposons and the evolution of eukaryotic genomes. Annu. Rev. Genet. 41, 331\u201368 (2007).","journal-title":"Annu. Rev. Genet."},{"key":"4837_CR53","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907\u2013915 (2019).","journal-title":"Nat. Biotechnol."},{"key":"4837_CR54","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","volume":"33","author":"M Pertea","year":"2015","unstructured":"Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290\u2013295 (2015).","journal-title":"Nat. Biotechnol."},{"key":"4837_CR55","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/978-1-4939-9173-0_5","volume":"1962","author":"KJ Hoff","year":"2019","unstructured":"Hoff, K. J., Lomsadze, A., Borodovsky, M. & Stanke, M. Whole-genome annotation with BRAKER. Methods Mol. Biol. 1962, 65\u201395 (2019).","journal-title":"Methods Mol. Biol."},{"key":"4837_CR56","doi-asserted-by":"publisher","unstructured":"Gabriel, L. et al. BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA. bioRxiv 2023.06.10.544449, https:\/\/doi.org\/10.1101\/2023.06.10.544449 (2024).","DOI":"10.1101\/2023.06.10.544449"},{"key":"4837_CR57","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad014","volume":"39","author":"H Li","year":"2023","unstructured":"Li, H. Protein-to-genome alignment with miniprot. Bioinformatics 39, btad014 (2023).","journal-title":"Bioinformatics"},{"key":"4837_CR58","doi-asserted-by":"publisher","first-page":"D445","DOI":"10.1093\/nar\/gkac998","volume":"51","author":"D Kuznetsov","year":"2023","unstructured":"Kuznetsov, D. et al. OrthoDB v11: Annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res. 51, D445\u2013D451 (2023).","journal-title":"Nucleic Acids Res."},{"key":"4837_CR59","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-1-r7","volume":"9","author":"BJ Haas","year":"2008","unstructured":"Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).","journal-title":"Genome Biol."},{"key":"4837_CR60","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.27853896.v1","author":"X Zhao","year":"2025","unstructured":"Zhao, X. Genome assembly and annotation of Cotesia ruficrus. figshare. Dataset. https:\/\/doi.org\/10.6084\/m9.figshare.27853896.v1 (2025)."},{"key":"4837_CR61","doi-asserted-by":"publisher","first-page":"W84","DOI":"10.1093\/nar\/gky350","volume":"46","author":"P T\u00f6r\u00f6nen","year":"2018","unstructured":"T\u00f6r\u00f6nen, P., Medlar, A. & Holm, L. PANNZER2: A rapid functional annotation web server. Nucleic Acids Res. 46, W84\u2013W88 (2018).","journal-title":"Nucleic Acids Res."},{"key":"4837_CR62","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","volume":"38","author":"CP Cantalapiedra","year":"2021","unstructured":"Cantalapiedra, C. P., Hern\u00e1ndez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic Scale. Mol. Biol. Evol. 38, 5825\u20135829 (2021).","journal-title":"Mol. Biol. Evol."},{"key":"4837_CR63","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1016\/j.gpb.2021.08.001","volume":"19","author":"T Chen","year":"2021","unstructured":"Chen, T. et al. The genome sequence archive family: toward explosive data growth and diverse data types. Genom. Proteom. Bioinf. 19, 578\u2013583 (2021).","journal-title":"Genom. Proteom. Bioinf."},{"key":"4837_CR64","doi-asserted-by":"publisher","first-page":"D18","DOI":"10.1093\/nar\/gkad1078","volume":"52","author":"CNCB-NGDC Members and Partners","year":"2024","unstructured":"CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Res. 52, D18\u2013D32 (2024).","journal-title":"Nucleic Acids Res."},{"key":"4837_CR65","unstructured":"National Genomics Data Center (NGDC) Genome Sequence Archive https:\/\/ngdc.cncb.ac.cn\/gsa\/browse\/CRA020489 (2024)."},{"year":"2025","author":"X Zhao","key":"4837_CR66","unstructured":"Zhao, X. Cotesia ruficrus isolate zhejiang, whole genome shotgun sequencing project. GenBank. https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/JBLUSQ000000000.1 (2025)."},{"key":"4837_CR67","doi-asserted-by":"publisher","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","volume":"32","author":"H Li","year":"2016","unstructured":"Li, H. Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103\u20132110 (2016).","journal-title":"Bioinformatics"},{"key":"4837_CR68","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"4837_CR69","doi-asserted-by":"publisher","first-page":"2404","DOI":"10.1093\/bioinformatics\/btac137","volume":"38","author":"Y Jung","year":"2022","unstructured":"Jung, Y. & Han, D. BWA-MEME: BWA-MEM emulated with a machine learning approach. Bioinformatics 38, 2404\u20132413 (2022).","journal-title":"Bioinformatics"},{"key":"4837_CR70","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1007\/978-1-4939-9173-0_14","volume":"1962","author":"M Seppey","year":"2019","unstructured":"Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: Assessing genome assembly and annotation completeness. Methods Mol. Biol. 1962, 227\u2013245 (2019).","journal-title":"Methods Mol. Biol."}],"container-title":["Scientific Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41597-025-04837-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-025-04837-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-025-04837-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,30]],"date-time":"2025-03-30T07:33:45Z","timestamp":1743320025000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41597-025-04837-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,26]]},"references-count":70,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["4837"],"URL":"https:\/\/doi.org\/10.1038\/s41597-025-04837-9","relation":{"references":[{"id-type":"uri","id":"https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264894","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264895","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264892","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/ngdc.cncb.ac.cn\/gsa\/search?searchTerm=CRX1264893","asserted-by":"subject"},{"id-type":"doi","id":"10.6084\/m9.figshare.27853896.v1","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/JBLUSQ000000000.1","asserted-by":"subject"}]},"ISSN":["2052-4463"],"issn-type":[{"type":"electronic","value":"2052-4463"}],"subject":[],"published":{"date-parts":[[2025,3,26]]},"assertion":[{"value":"16 December 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 March 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 March 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"508"}}