*Result*: InsectBase 3.0: a comprehensive multi-omics resource for insects.
Title:
InsectBase 3.0: a comprehensive multi-omics resource for insects.
Authors:
Wang Z; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Chen H; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Jin S; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Li Z; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Mei Y; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China., Xiao Y; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Zhao C; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Zhou T; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Li F; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China., Liu Y; Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province/Agricultural Environment and Resource Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China., He K; State Key Laboratory of Rice Biology and Breeding and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
Source:
Nucleic acids research [Nucleic Acids Res] 2026 Jan 06; Vol. 54 (D1), pp. D1143-D1151.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Imprint Name(s):
Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
Original Publication: London, Information Retrieval ltd.
MeSH Terms:
References:
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Curr Opin Insect Sci. 2022 Apr;50:100860. (PMID: 34864248)
Genomics. 2024 May;116(3):110842. (PMID: 38608738)
Annu Rev Entomol. 2025 Jan;70(1):379-400. (PMID: 39874145)
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14. (PMID: 19274634)
iScience. 2022 Aug 04;25(9):104873. (PMID: 36039293)
Biol Rev Camb Philos Soc. 2025 Apr;100(2):969-995. (PMID: 39592413)
Curr Opin Insect Sci. 2016 Feb;13:61-69. (PMID: 27436554)
Nucleic Acids Res. 2015 Jan;43(Database issue):D714-9. (PMID: 25332403)
Cell Mol Life Sci. 2022 May 30;79(6):325. (PMID: 35644827)
Nat Methods. 2015 Jan;12(1):59-60. (PMID: 25402007)
Int J Mol Sci. 2023 Nov 30;24(23):. (PMID: 38069282)
Bioinformatics. 2023 Oct 3;39(10):. (PMID: 37758247)
Genome Res. 2024 Jun 25;34(5):769-777. (PMID: 38866550)
Nat Genet. 2025 Sep;57(9):2264-2275. (PMID: 40890361)
Genome Biol. 2008 Jan 11;9(1):R7. (PMID: 18190707)
Biomolecules. 2022 Oct 04;12(10):. (PMID: 36291635)
Insect Biochem Mol Biol. 2011 Oct;41(10):747-69. (PMID: 21658450)
Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457. (PMID: 32300014)
Genome Biol. 2025 Aug 18;26(1):251. (PMID: 40826096)
Nucleic Acids Res. 2021 Jul 2;49(W1):W431-W437. (PMID: 33956157)
Int J Biol Sci. 2014 Sep 05;10(9):983-9. (PMID: 25210496)
Cell Mol Life Sci. 2009 Feb;66(4):565-83. (PMID: 18989625)
Mol Ecol Resour. 2025 Oct;25(7):e70006. (PMID: 40583840)
Nucleic Acids Res. 2020 Jan 8;48(D1):D749-D755. (PMID: 31642484)
Bioinformatics. 2018 Nov 1;34(21):3755-3758. (PMID: 29850778)
Exp Cell Res. 2010 Oct 15;316(17):2932-44. (PMID: 20696153)
Nucleic Acids Res. 2019 Jan 8;47(D1):D759-D765. (PMID: 30364959)
Annu Rev Entomol. 2019 Jan 7;64:297-314. (PMID: 30312555)
Cell Rep. 2024 Mar 26;43(3):113889. (PMID: 38416646)
Methods Mol Biol. 2016;1374:23-54. (PMID: 26519399)
Mol Biol Evol. 2025 Apr 1;42(4):. (PMID: 40154540)
Mol Plant. 2023 Apr 3;16(4):647-649. (PMID: 36809879)
Mol Biol Evol. 2021 Dec 9;38(12):5825-5829. (PMID: 34597405)
Bioinformatics. 2023 Jan 1;39(1):. (PMID: 36648328)
Nucleic Acids Res. 2024 Jan 5;52(D1):D1024-D1032. (PMID: 37941143)
Sci Rep. 2023 Sep 7;13(1):14743. (PMID: 37679371)
Nucleic Acids Res. 2022 Jan 7;50(D1):D1040-D1045. (PMID: 34792158)
Nat Biotechnol. 2019 Aug;37(8):907-915. (PMID: 31375807)
Natl Sci Rev. 2024 Aug 01;12(3):nwae221. (PMID: 39949366)
Nat Biotechnol. 2024 Feb;42(2):243-246. (PMID: 37156916)
Biophysics (Nagoya-shi). 2011 Feb 17;7:21-28. (PMID: 27857589)
Curr Protoc. 2023 Mar;3(3):e697. (PMID: 36943033)
Annu Rev Entomol. 2020 Jan 7;65:409-429. (PMID: 31610135)
Genomics Proteomics Bioinformatics. 2025 Jan 15;22(6):. (PMID: 39400548)
Nat Commun. 2024 Jul 2;15(1):5573. (PMID: 38956036)
Annu Rev Entomol. 2009;54:85-104. (PMID: 18817507)
Nat Biotechnol. 2015 Mar;33(3):290-5. (PMID: 25690850)
Nucleic Acids Res. 2022 Jan 7;50(D1):D20-D26. (PMID: 34850941)
Nature. 2024 Jun;630(8016):493-500. (PMID: 38718835)
Nat Commun. 2024 Jul 26;15(1):6303. (PMID: 39060230)
Mol Biol Evol. 2024 Mar 1;41(3):. (PMID: 38401527)
Nat Biotechnol. 2025 Jan;43(1):124-133. (PMID: 38383603)
Mol Biol Evol. 2023 May 2;40(5):. (PMID: 37155936)
Nucleic Acids Res. 2022 Jan 7;50(D1):D102-D105. (PMID: 34751405)
Methods Mol Biol. 2019;1962:227-245. (PMID: 31020564)
Bioinformatics. 2017 Jul 01;33(13):2037-2039. (PMID: 28205675)
Nat Biotechnol. 2021 Nov;39(11):1348-1365. (PMID: 34750572)
Nucleic Acids Res. 2016 Jan 4;44(D1):D801-7. (PMID: 26578584)
Nucleic Acids Res. 2024 Jan 5;52(D1):D18-D32. (PMID: 38018256)
Fly (Austin). 2012 Apr-Jun;6(2):80-92. (PMID: 22728672)
Curr Opin Insect Sci. 2022 Apr;50:100860. (PMID: 34864248)
Genomics. 2024 May;116(3):110842. (PMID: 38608738)
Annu Rev Entomol. 2025 Jan;70(1):379-400. (PMID: 39874145)
Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:4.10.1-4.10.14. (PMID: 19274634)
iScience. 2022 Aug 04;25(9):104873. (PMID: 36039293)
Biol Rev Camb Philos Soc. 2025 Apr;100(2):969-995. (PMID: 39592413)
Curr Opin Insect Sci. 2016 Feb;13:61-69. (PMID: 27436554)
Nucleic Acids Res. 2015 Jan;43(Database issue):D714-9. (PMID: 25332403)
Cell Mol Life Sci. 2022 May 30;79(6):325. (PMID: 35644827)
Nat Methods. 2015 Jan;12(1):59-60. (PMID: 25402007)
Int J Mol Sci. 2023 Nov 30;24(23):. (PMID: 38069282)
Bioinformatics. 2023 Oct 3;39(10):. (PMID: 37758247)
Genome Res. 2024 Jun 25;34(5):769-777. (PMID: 38866550)
Nat Genet. 2025 Sep;57(9):2264-2275. (PMID: 40890361)
Genome Biol. 2008 Jan 11;9(1):R7. (PMID: 18190707)
Grant Information:
2024CSJZN0900 2024 Yangtze River Delta Science and Technology Innovation Community Joint Research (Basic Research) Project; 2022YFD1401600 National Key Research and Development Program of China; 2021YFD1400100 National Key Research and Development Program of China; 32202366 National Natural Science Foundation of China; LZ23C140002 Natural Science Foundation of Zhejiang Province
Entry Date(s):
Date Created: 20251120 Date Completed: 20260117 Latest Revision: 20260118
Update Code:
20260130
PubMed Central ID:
PMC12807663
DOI:
10.1093/nar/gkaf1248
PMID:
41263103
Database:
MEDLINE
*Further Information*
*Insects represent the most diverse animal group and play essential roles in ecosystems, agriculture, and human health. The rapid accumulation of high-quality genomes and diverse omics datasets provides unprecedented opportunities to advance research in insect biology and evolution, yet also poses challenges in data integration, accessibility, and reuse. To address these demands, we developed InsectBase 3.0 (www.insect-genome.com), an upgraded platform that integrates extensive insect multi-omics data and provides user-friendly tools for furthor analysis. InsectBase 3.0 covers 3020 species across 24 insect orders, including 1651 chromosome-level assemblies and 61 353 curated transcriptomes. In addition, the new version incorporates a large-scale protein structure dataset (474 300 predicted models and 381 experimental entries), genome resequencing and variant resources, curated transposable element libraries, and 3D morphological reconstructions. To organize these heterogeneous resources, InsectBase 3.0 introduces knowledge graphs centered on species and genes, enabling users to navigate cross-dataset relationships more intuitively. In addition, the web framework has been modernized to improve efficiency, interactivity, and visualization. Together, these updates establish InsectBase 3.0 as the most comprehensive open-access insect omics platform to date, providing a valuable resource for evolutionary, functional, and applied research in insects.
(© The Author(s) 2025. Published by Oxford University Press.)*