REFERENCES

The iORbase website citation:

1. iORbase2.0 website. https://iorbase.com/

2. Li, Q., Zhang, Y. F., Zhang, T. M., Wan, J. H., Zhang, Y. D., Yang, H., Huang, Y., Xu, C., Li, G. and Lu, H. M. (2023) iORbase: a database for the prediction of the structures and functions of insect olfactory receptors. Insect Science, doi: 10.1111/1744-7917.13162.

The following references present the previously published iOR annotation results for different insect species (some of the data have been manually checked and supplemented into the iORPDB module):

(2026)

1. Mitchell, R.F., Moran, K.M. & McKenna, D.D. (2026) Early hexapod genomes reveal the deep origin of insect gustatory and odorant receptors. Nat Commun 17, 6881.

2. Gautier, M. et al. (2026) A chromosome-level assembly of the pine processionary moth (Thaumetopoea pityocampa) genome. Journal of Heredity.

(2025)

3. Eldem, V., Çınar, Y.U., Çay, S.B. et al. (2025) De novo genome assembly and annotations of Bombus lapidarius and Bombus niveatus provide insights into the environmental adaptability. Apidologie 56, 10.

4. Persyn, E. et al. (2025) Transcriptomic analyses in thirteen Tephritidae species provide insights into the ecological driving force behind odorant receptor evolution. Molecular Phylogenetics and Evolution 206, 108322.

5. Olvera-Vazquez, S. G. et al. (2025) Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids. Molecular Biology and Evolution 42.

6. Sun, J., Wu, J., Sun, SY. et al. (2025) The expansion and loss of specific olfactory genes in relatives of parasitic lice, the stored-product psocids (Psocodea: Liposcelididae). BMC Genomics 26, 41.

7. Kebaso, F., Diallo, S., Kibet, C. et al. (2025) De novo genome assembly, annotation, and characterization of chemosensory genes in the camel ked (Hippobosca camelina). BMC Genomics 26, 668.

(2024)

8. Li, Y. et al. (2024) Genome-wide investigation of the OR gene family in Helicoverpa armigera and functional analysis of OR48 and OR75 in metamorphosis development. International Journal of Biological Macromolecules 278, 134646.

9. Chen, R., Yan, J., Wickham, J.D. et al. (2024) Genomic identification and evolutionary analysis of chemosensory receptor gene families in two Phthorimaea pest species: insights into chemical ecology and host adaptation. BMC Genomics 25, 493.

10. Biswas, T., Vogel, H., Biedermann, P.H.W. et al. (2024) Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology. BMC Genomics 25, 764.

11. Liu, Y., Zhang, S., Cao, S. et al. (2024) An odorant receptor mediates the avoidance of Plutella xylostella against parasitoid. BMC Biol 22, 61.

12. Ma, W.; Li, Y.; Yang, L.; Yan, S. (2024) Sex Differences in Antennal Transcriptome of Hyphantria cunea and Analysis of Odorant Receptor Expression Profiles. Int. J. Mol. Sci. 25, 9070.

13. Huang, C.; Ou, X.; Wang, Y.; Zhou, Y.; Zhang, G.; Liu, W.; Wan, F.; Jiang, H.; Zhang, Y. (2024) Genome-Wide Identification, Evolution, and Female-Biased Expression Analysis of Odorant Receptors in Tuta absoluta (Lepidoptera: Gelechiidae). Life 14, 872.

(2023)

14. Xu, C., Ji, J., Zhu, X. et al. (2023) Chromosome level genome assembly of oriental armyworm Mythimna separata. Sci Data 10, 597.

15. Yan, B. et al. (2023) Chromosome-Scale Genome Assembly of the Solitary Parasitoid Wasp Microplitis manilae Ashmead, 1904 (Braconidae: Microgastrinae). Genome biology and evolution 15.

16. Wang Q, Dicke M and Haverkamp A (2023) Sympatric Pieris butterfly species exhibit a high conservation of chemoreceptors. Front. Cell. Neurosci. 17:1155405.

(2022)

17. Meslin, C. et al. (2022) Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae. G3 Genes|Genomes|Genetics 12.

(2021)

18. Guo, M. et al. (2021) Odorant Receptors for Detecting Flowering Plant Cues Are Functionally Conserved across Moths and Butterflies. Molecular Biology and Evolution 38, 1413-1427.

(2017)

19. Yang, S., Cao, D., Wang, G. et al. (2017) Identification of Genes Involved in Chemoreception in Plutella xyllostella by Antennal Transcriptome Analysis. Sci Rep 7, 11941.

The following references are resources or toolkits for producing the iORbase data:

(2022)

1. Mei, Y., Jing, D., Tang, S., Chen, X., Chen, H., Duanmu, H., Cong, Y., Chen, M., Ye, X., Zhou, H. et al. (2022) InsectBase 2.0: a comprehensive gene resource for insects. Nucleic Acids Res, 50, D1040-D1045. https://pubchem.ncbi.nlm.nih.gov

2. El-Sayed AM 2022. The Pherobase: Database of Pheromones and Semiochemicals. https://www.pherobase.com

3. Naughton, F.B., Alibay, I., Barnoud, J., Barreto-Ojeda, E., Beckstein, O., Bouysset, C., Cohen, O., Gowers, R.J., MacDermott-Opeskin, H., Matta, M. et al. (2022) MDAnalysis 2.0 and beyond: fast and interoperable, community driven simulation analysis. Biophys. J., 121, 272a-273a.

(2021)

4. Sayers, E.W., Beck, J., Bolton, E.E., Bourexis, D., Brister, J.R., Canese, K., Comeau, D.C., Funk, K., Kim, S., Klimke, W. et al. (2021) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 49, D10-D17.

5. Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B.A., Thiessen, P.A., Yu, B. et al. (2021) PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res, 49, D1388-D1395.

6. Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Zidek, A., Potapenko, A. et al. (2021) Highly accurate protein structure prediction with AlphaFold. Nature, 596, 583-589.

7. Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G.R., Wang, J., Cong, Q., Kinch, L.N., Schaeffer, R.D. et al. (2021) Accurate prediction of protein structures and interactions using a three-track neural network. Science, 373, 871-876.

8. Pereira, J., Simpkin, A.J., Hartmann, M.D., Rigden, D.J., Keegan, R.M. and Lupas, A.N. (2021) High-accuracy protein structure prediction in CASP14. Proteins-Structure Function and Bioinformatics, 89, 1687-1699.

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11. Ruiz-Moreno, A.J., Reyes-Romero, A., Domling, A. and Velasco-Velazquez, M.A. (2021) In Silico Design and Selection of New Tetrahydroisoquinoline-Based CD44 Antagonist Candidates. Molecules, 26.

(2020)

12. Gao, Q., Xiong, Z., Larsen, R.S., Zhou, L., Zhao, J., Ding, G., et al. (2020) High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis. Gigascience, 9.

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(2019)

14. Wallberg, A., Bunikis, I., Pettersson, O.V., Mosbech, M.B., Childers, A.K., Evans, J.D., et al. (2019) A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC Genomics, 20, 275.

(2018)

15. Butterwick, J.A., Del Marmol, J., Kim, K.H., Kahlson, M.A., Rogow, J.A., Walz, T. and Ruta, V. (2018) Cryo-EM structure of the insect olfactory receptor Orco. Nature, 560, 447-452.

16. Fu, Y., Yang, Y., Zhang, H., Farley, G., Wang, J., Quarles, K.A., et al. (2018) The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. Elife, 7.

17. Harrison, M.C., Jongepier, E., Robertson, H.M., Arning, N., Bitard-Feildel, T., Chao, H., et al. (2018) Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology & Evolution, 2, 557–566.

18. McKenzie, S.K. and Kronauer, D.J.C. (2018) The genomic architecture and molecular evolution of ant odorant receptors. Genome Research, 28, 1757–1765.

19. Shields, E.J., Sheng, L., Weiner, A.K., Garcia, B.A. and Bonasio, R. (2018) High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Cell Reports, 23, 3078–3090.

(2017)

20. Karpe, S.D., Dhingra, S., Brockmann, A. and Sowdhamini, R. (2017) Computational genome-wide survey of odorant receptors from two solitary bees Dufourea novaeangliae (Hymenoptera: Halictidae) and Habropoda laboriosa (Hymenoptera: Apidae). Scientific Reports, 7, 10823.

21. Mohanty, S. and Khanna, R. (2017) Genome-wide comparative analysis of four Indian Drosophila species. Molecular Genetics and Genomics, 292, 1197–1208.

22. Pearce, S.L., Clarke, D.F., East, P.D., Elfekih, S., Gordon, K.H.J., Jermiin, L.S., et al. (2017) Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biology, 15, 63.

(2016)

23. Chen, W., Hasegawa, D.K., Kaur, N., Kliot, A., Pinheiro, P.V., Luan, J., et al. (2016) The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. BMC Biology, 14, 110.

24. Sanchez-Flores, A., Peñaloza, F., Carpinteyro-Ponce, J., Nazario-Yepiz, N., Abreu-Goodger, C., Machado, C.A., et al. (2016) Genome evolution in three species of Cactophilic Drosophila. G3 (Bethesda), 6, 3097–3105.

25. Standage, D.S., Berens, A.J., Glastad, K.M., Severin, A.J., Brendel, V.P. and Toth, A.L. (2016) Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect. Molecular Ecology, 25, 1769–1784.

(2015)

26. Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., et al. (2015) Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature Communications, 6, 8212.

27. Park, D., Jung, J.W., Choi, B.S., Jayakodi, M., Lee, J., Lim, J., et al. (2015) Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. BMC Genomics, 16, 1.

28. Patalano, S., Vlasova, A., Wyatt, C., Ewels, P., Camara, F., Ferreira, P.G., et al. (2015) Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Proceedings of the National Academy of Sciences of the United States of America, 112, 13970–13975.

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(2014)

32. Burke, G.R., Walden, K.K., Whitfield, J.B., Robertson, H.M. and Strand, M.R. (2014) Widespread genome reorganization of an obligate virus mutualist. PLoS Genetics, 10, e1004660.

(2013)

33. Xiao, J.H., Yue, Z., Jia, L.Y., Yang, X.H., Niu, L.H., Wang, Z., et al. (2013) Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. Genome Biology, 14, R141.

(2011)

34. Nygaard, S., Zhang, G., Schiøtt, M., Li, C., Wurm, Y., Hu, H., et al. (2011) The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Research, 21, 1339–1348.

35. Smith, C.D., Zimin, A., Holt, C., Abouheif, E., Benton, R., Cash, E., et al. (2011) Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proceedings of the National Academy of Sciences of the United States of America, 108, 5673–5678.

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39. Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V. et al. (2011) Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research, 12, 2825-2830.

(2010)

40. Trott, O. and Olson, A.J. (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem, 31, 455-461.

(2009)

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42. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.

(2008)

43. Richards, S., Gibbs, R.A., Weinstock, G.M., Brown, S.J., Denell, R., Beeman, R.W., et al. (2008) The genome of the model beetle and pest Tribolium castaneum. Nature, 452, 949–955.

44. Haddad, R., Khan, R., Takahashi, Y.K., Mori, K., Harel, D. and Sobel, N. (2008) A metric for odorant comparison. Nat. Meth., 5, 425-429.

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(2007)

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(2004)

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(2003)

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(2001)

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(No year)

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