Research Articles
1. Asma, H.; Tieke, E.; Deem, K. D.; Rahmat, J.; Dong, T.; Huang, X.; Tomoyasu, Y.; Halfon, M. S. (2024). Regulatory genome annotation of 33 insect species. eLife, 13:RP96738.
2. Deem, K. D.; Halfon, M. S.; Tomoyasu, Y. (2024). A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species. Scientific Reports, 14(1):10078.
DOI: 10.1038/s41598-024-60432-9
3. Linz, D. M.; Hara, Y.; Deem, K. D.; Kuraku, S.; Hayashi, S.; Tomoyasu, Y. (2023). Transcriptomic exploration of the coleopteran wings reveals insight into the evolution of novel structures associated with the beetle elytron. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 340(2):197–213.
4. Fernandez-Nicolas, A.; Ventos-Alfonso, A.; Kamsoi, O.; Clark-Hachtel, C.; Tomoyasu, Y.; Belles, X. (2022). Broad complex and wing development in cockroaches. Insect Biochemistry and Molecular Biology, 147:103798.
DOI: 10.1016/j.ibmb.2022.103798
5. Murugesan, S. N.; Connahs, H.; Matsuoka, Y.; Das Gupta, M.; Tiong, G. J. L.; Huq, M.; Gowri, V.; Monroe, S.; Deem, K. D.; Werner, T.; Tomoyasu, Y.; Monteiro, A. (2022). Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings. Proceedings of the National Academy of Sciences of the United States of America, 119:e2108661119.
6. Tomoyasu, Y. (2021). What crustaceans can tell us about the evolution of insect wings and other morphologically novel structures. Current Opinion in Genetics & Development, 69:48–55.
DOI: 10.1016/j.gde.2021.02.008
7. Clark-Hachtel, C. M.; Fernandez-Nicolas, A.; Belles, X.; Tomoyasu, Y. (2021). Tergal and pleural wing-related tissues in the German cockroach and their implication to the evolutionary origin of insect wings. Evolution & Development, 23(5):395–411.
8. Clark-Hachtel, C. M.; Tomoyasu, Y. (2020). Two sets of candidate crustacean wing homologues and their implication to the origin of insect wings. Nature Ecology & Evolution, 4(12):1694–1702.
DOI: 10.1038/s41559-020-1257-8
Featured on the cover and in News & Views.
9. Rathore, S.; Hassert, J.; Clark-Hachtel, C. M.; Stahl, A.; Tomoyasu, Y.; Buschbeck, E. K. (2020). RNA interference in aquatic beetles as a powerful tool for manipulating gene expression at specific developmental time points. Journal of Visualized Experiments, (159):e61477.
10. Tomoyasu, Y.; Halfon, M. S. (2020). How to study enhancers in non-traditional insect models. Journal of Experimental Biology, 223(2):jeb208777.
11. Clark-Hachtel, C. M.; Moe, M. R.; Tomoyasu, Y. (2018). Detailed analysis of the prothoracic tissues transforming into wings in the Cephalothorax mutant of the Tribolium beetle. Arthropod Structure & Development, 47(4):352–361.
DOI: 10.1016/j.asd.2018.06.005
12. Lai, Y.-T.; Deem, K. D.; Borràs-Castells, F.; Sambrani, N.; Rudolf, H.; Suryamohan, K.; El-Sherif, E.; Halfon, M. S.; McKay, D. J.; Tomoyasu, Y. (2018). Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum. Development, 145(7):dev160663.
13. Linz, D. M.; Tomoyasu, Y. (2018). Dual evolutionary origin of insect wings supported by an investigation of the abdominal wing serial homologs in Tribolium. Proceedings of the National Academy of Sciences of the United States of America, 115(4):E658–E667.
14. Tomoyasu, Y.; Ohde, T.; Clark-Hachtel, C. M. (2017). What serial homologs can tell us about the origin of insect wings. F1000Research, 6:268.
DOI: 10.12688/f1000research.10285.1
15. Tomoyasu, Y. (2017). Ultrabithorax and the evolution of insect forewing/hindwing differentiation. Current Opinion in Insect Science, 19:8–15.
DOI: 10.1016/j.cois.2016.10.007
16. Linz, D. M.; Hu, A. W.; Sitvarin, M. I.; Tomoyasu, Y. (2016). Functional value of elytra under various stresses in the red flour beetle, Tribolium castaneum. Scientific Reports, 6:34813.
17. Zattara, E. E.; Busey, H. A.; Linz, D. M.; Tomoyasu, Y.; Moczek, A. P. (2016). Neofunctionalization of embryonic head patterning genes facilitates the positioning of novel traits on the dorsal head of adult beetles. Proceedings of the Royal Society B: Biological Sciences, 283(1834):20160824.
18. Clark-Hachtel, C. M.; Tomoyasu, Y. (2016). Exploring the origin of insect wings from an evo-devo perspective. Current Opinion in Insect Science, 13:77–85.
DOI: 10.1016/j.cois.2015.12.005
19. Ravisankar, P.; Lai, Y.; Sambrani, N.; Tomoyasu, Y. (2016). Comparative developmental analysis of Drosophila and Tribolium reveals conserved and diverged roles of abrupt in insect wing evolution. Developmental Biology, 409(2):518–529.
DOI: 10.1016/j.ydbio.2015.12.006
20. Linz, D. M.; Tomoyasu, Y. (2015). RNAi screening of developmental toolkit genes: A search for novel wing genes in the red flour beetle Tribolium castaneum. Development Genes and Evolution, 225(1):11–22.
DOI: 10.1007/s00427-015-0488-1
21. Linz, D. M.; Clark-Hachtel, C. M.; Borràs-Castells, F.; Tomoyasu, Y. (2014). Larval RNA interference in the red flour beetle, Tribolium castaneum. Journal of Visualized Experiments, (92):e52059.
22. Miyata, K.; Ramaseshadri, P.; Zhang, Y.; Segers, G.; Bolognesi, R.; Tomoyasu, Y. (2014). Establishing an in vivo assay system to identify components involved in environmental RNA interference in the western corn rootworm. PLOS ONE, 9(7):e101661.
DOI: 10.1371/journal.pone.0101661
23. Clark-Hachtel, C. M.; Linz, D. M.; Tomoyasu, Y. (2013). Insights into insect wing origin provided by functional analysis of vestigial in the beetle, Tribolium castaneum. Proceedings of the National Academy of Sciences of the United States of America, 110(42):16951–16956.
24. Miller, S. C.; Miyata, K.; Brown, S. J.; Tomoyasu, Y. (2012). Dissecting systemic RNA interference in the red flour beetle Tribolium castaneum: Parameters affecting the efficiency of RNAi. PLOS ONE, 7(10):e47431.
DOI: 10.1371/journal.pone.0047431
25. Burns, K. A.; Gutzwiller, L. M.; Tomoyasu, Y.; Gebelein, B. (2012). Oenocyte development in the red flour beetle Tribolium castaneum. Development Genes and Evolution, 222(2):77–88.
DOI: 10.1007/s00427-012-0390-z
26. Louse Genome Sequencing Consortium (2010). Genome sequence of the human body louse and its primary endosymbiont provides insights into the permanent parasitic lifestyle. Proceedings of the National Academy of Sciences of the United States of America, 107(27):12168–12173.
27. Arakane, Y.; Dittmer, N. T.; Tomoyasu, Y.; Kramer, K. J.; Muthukrishnan, S.; Beeman, R. W.; Kanost, M. R.(2010). Identification, mRNA expression and functional analysis of several yellow family genes in Tribolium castaneum. Insect Biochemistry and Molecular Biology, 40(3):259–266.
DOI: 10.1016/j.ibmb.2010.01.012
28. Tomoyasu, Y.; Arakane, Y.; Kramer, K. J.; Denell, R. E. (2009). Repeated co-options of exoskeleton formation during wing-to-elytron evolution in beetles. Current Biology, 19(24):2057–2065.
DOI: 10.1016/j.cub.2009.11.014
29. Lommen, S. T. E.; Saenko, S. V.; Tomoyasu, Y.; Brakefield, P. M. (2009). Development of a wingless morph in the ladybird beetle, Adalia bipunctata. Evolution & Development, 11(3):278–289.
DOI: 10.1111/j.1525-142x.2009.00330.x
30. Miller, S. C.; Brown, S. J.; Tomoyasu, Y. (2008). Larval RNAi in Drosophila?. Development Genes and Evolution, 218(9):505–510.
DOI: 10.1007/s00427-008-0238-8
31. Shippy, T. D.; Tomoyasu, Y.; Nie, W.; Brown, S. J.; Denell, R. E. (2008). Do teashirt family genes specify trunk identity? Insights from the single tiptop/teashirt homolog of Tribolium castaneum. Development Genes and Evolution, 218(3–4):141–152.
DOI: 10.1007/s00427-008-0212-5
32. Tribolium Genome Sequencing Consortium (2008). The genome of the model beetle and pest Tribolium castaneum. Nature, 452(7190):949–955.
33. Tomoyasu, Y.; Miller, S. C.; Tomita, S.; Schoppmeier, M.; Grossmann, D.; Bucher, G. (2008). Exploring systemic RNA interference in insects: A genome-wide survey for RNAi genes in Tribolium. Genome Biology, 9(1):R10.
34. Arakane, Y.; Muthukrishnan, S.; Kramer, K. J.; Specht, C. A.; Tomoyasu, Y.; Lorenzen, M. D.; Kanost, M. R.; Beeman, R. W. (2005). The Tribolium chitin synthase genes TcCHS1 and TcCHS2 are specialized for synthesis of epidermal cuticle and midgut peritrophic matrix, respectively. Insect Molecular Biology, 14(5):453–463.
DOI: 10.1111/j.1365-2583.2005.00576.x
35. Tomoyasu, Y.; Wheeler, S. R.; Denell, R. E. (2005). Ultrabithorax is required for membranous wing identity in the beetle Tribolium castaneum. Nature, 433(7026):643–647.
36. Tomoyasu, Y.; Denell, R. E. (2004). Larval RNAi in Tribolium (Coleoptera) for analyzing adult development. Development Genes and Evolution, 214(11):575–578.
DOI: 10.1007/s00427-004-0434-0
37. Tomoyasu, Y.; Ueno, N.; Nakamura, M. (2000). The decapentaplegic morphogen gradient regulates the notal wingless expression through induction of pannier and u-shaped in Drosophila. Mechanisms of Development, 96(1):37–49.
DOI: 10.1016/s0925-4773(00)00374-9
38. Hamada, F.; Murata, Y.; Nishida, A.; Fujita, F.; Tomoyasu, Y.; Nakamura, M.; Toyoshima, K.; Tabata, T.; Ueno, N.; Akiyama, T. (1999). Identification and characterization of E-APC, a novel Drosophila homologue of the tumour suppressor APC. Genes to Cells, 4(8):465–474.
DOI: 10.1046/j.1365-2443.1999.00272.x
39. Adachi-Yamada, T.; Nakamura, M.; Irie, K.; Tomoyasu, Y.; Sano, Y.; Mori, E.; Goto, S.; Ueno, N.; Nishida, Y.; Matsumoto, K. (1999). p38 mitogen-activated protein kinase can be involved in transforming growth factor β superfamily signal transduction in Drosophila wing morphogenesis. Molecular and Cellular Biology, 19(3):2322–2329.
40. Hamada, F.; Tomoyasu, Y.; Takatsu, Y.; Nakamura, M.; Nagai, S.; Suzuki, A.; Fujita, F.; Shibuya, H.; Toyoshima, K.; Ueno, N.; Akiyama, T. (1999). Negative regulation of Wingless signaling by D-axin, a Drosophila homolog of axin. Science, 283(5408):1739–1742.
DOI: 10.1126/science.283.5408.1739
41. Tomoyasu, Y.; Nakamura, M.; Ueno, N. (1998). Role of dpp signalling in prepattern formation of the dorsocentral mechanosensory organ in Drosophila melanogaster. Development, 125(21):4215–4224.
Book Chapters and Other Publications
42. Tomoyasu, Y. (2020). Breaking bad in the rice field by breaking the Hox code. National Science Review, 7(10):1616.
43. McDonald, J. A.; Tomoyasu, Y. (2020). Extracellular matrix: Sculpting new structures. eLife, 9:e57668.
44. Tomoyasu, Y. (2018). Evo–Devo: The double identity of insect wings. Current Biology, 28(2):R75–R77.
DOI: 10.1016/j.cub.2017.12.004
45. Tomoyasu, Y.; Fujiwara, H. (2017). Editorial overview: Development and regulation: The diverse traits that have facilitated the successful radiation of insects. Current Opinion in Insect Science, 19:iv–vi.
DOI: 10.1016/j.cois.2017.04.004
46. Philip, B. N.; Tomoyasu, Y. (2011). Gene knockdown analysis by double-stranded RNA injection. Molecular Methods for Evolutionary Genetics, Methods in Molecular Biology, 772:471–497.
DOI: 10.1007/978-1-61779-228-1_28
47. Shippy, T. D.; Coleman, C. M.; Tomoyasu, Y.; Brown, S. J. (2009). Concurrent in situ hybridization and antibody staining in red flour beetle (Tribolium) embryos. Cold Spring Harbor Protocols, 2009(8):pdb.prot5257.