Reference
Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., . . . Hanski, I. (2014). The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature Communications, 5 , 4737. doi:10.1038/ncomms5737
Altschul, S., Gish, W., Miller, W., Myers, E., & Lipman, D. (1990). Basic local alignment search tool. Journal of molecular biology, 215 (3), 403-410.
Belaghzal, H., Dekker, J., & Gibcus, J. H. (2017). Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods, 123 , 56-65.
Bi, Z., Yang, X., Yu, W., Shu, J., & Zhang, Y. (2014). Diapause-Associated Protein3 Functions as Cu/Zn Superoxide Dismutase in the Chinese Oak Silkworm (Antheraea pernyi ). PLoS ONE, 9 (3). doi:10.1371/journal.pone.0090435
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30 (15), 2114-2120. doi:10.1093/bioinformatics/btu170
Campbell, M. S., Holt, C., Moore, B., & Yandell, M. (2014). Genome Annotation and Curation Using MAKER and MAKER-P. Current Protocols in Bioinformatics, 48 (1), 4.11.11-14.11.39. doi:10.1002/0471250953.bi0411s48
Cantarel, B. L., Korf, I., Robb, S. M., Parra, G., Ross, E., Moore, B., . . . Yandell, M. (2008). MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research, 18 (1), 188-196. doi:10.1101/gr.6743907
Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant , doi.org/10.1016/j.molp.2020.1006.1009. doi:10.1101/289660 %J bioRxiv
Chen, W., Yang, X., Tetreau, G., Song, X., Coutu, C., Hegedus, D., . . . Wang, P. (2019). A high-quality chromosome-level genome assembly of a generalist herbivore, Trichoplusia ni . Molecular Ecology Resources, 19 (2), 485-496. doi:10.1111/1755-0998.12966
Cheng, T., Wu, J., Wu, Y., Chilukuri, R. V., Huang, L., Yamamoto, K., . . . Mita, K. (2017). Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest. Nature Ecology & Evolution, 1 (11), 1747-1756. doi:10.1038/s41559-017-0314-4
Chiba, T., & Kobayashi, M. (1985). Seasonal prevalence of the peach fruit moth, Carposina niponensis Walsingham, in the apple orchards in Iwate Prefecture. Bulletin of the Iwate Horticultural Experiment Station, 6 , 1-14.
Cong, Q., Borek, D., Otwinowski, Z., & Grishin, N. V. (2015). Tiger swallowtail genome reveals mechanisms for speciation and caterpillar chemical defense. Cell Rep, 10 (6), 910-919. doi:10.1016/j.celrep.2015.01.026
Dasmahapatra, K. K., Walters, J. R., Briscoe, A. D., Davey, J. W., Whibley, A., Nadeau, N. J., . . . Consortium, H. G. (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487 (7405), 94-98. doi:10.1038/nature11041
Dudchenko, O., Batra, S. S., Omer, A. D., Nyquist, S. K., Hoeger, M., Durand, N. C., . . . Aiden, A. P. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.Science, 356 (6333), 92-95.
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016). Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems, 3 (1), 95-98. doi:10.1016/j.cels.2016.07.002
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., . . . Smart, A. (2018). The Pfam protein families database in 2019. Nucleic Acids Research, 47 (D1), D427-D432.
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., . . . Finn, R. D. (2019). The Pfam protein families database in 2019. Nucleic Acids Research, 47 (D1), D427-D432. doi:10.1093/nar/gky995
Emms, D. M., & Kelly, S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology, 16 (157), 1-14. doi:10.1186/s13059-015-0721-2
Espinosa-Chaurand, D., Vega-Villasante, F., Carrillo-Farnes, O., & Nolasco-Soria, H. (2017). Effect of circadian rhythm, photoperiod, and molt cycle on digestive enzymatic activity of Macrobrachium tenellum juveniles. Aquaculture, 479 , 225-232. doi:10.1016/j.aquaculture.2017.05.029
Finn, R. D., Clements, J., & Eddy, S. R. (2011). HMMER web server: interactive sequence similarity searching. Nucleic Acids Research, 39 (suppl_2), W29-W37.
He, C., Meng, Q.-K., Yang, X.-B., & Hua, L. (2013). Carbohydrate metabolism and antioxidant defense during diapause development in larvae of oriental fruit moth (Grapholita molesta ) at low temperature.International Journal of Agriculture and Biology, 15 (1), 101-106.
Hu, B., Zhang, S. H., Ren, M. M., Tian, X. R., Wei, Q., Mburu, D. K., & Su, J. Y. (2019). The expression of Spodoptera exigua P450 and UGT genes: tissue specificity and response to insecticides. Insect Science, 26 (2), 199-216. doi:10.1111/1744-7917.12538
Hua, B.-Z., Zeng, X.-H., & Zhang, H. (1998). Diapause ofCarposina sasakii Matsumura ( Lepidoptera Carposinidae) on various host plants. Acta Universitatis Agriculturae Boreali-occidentalis, 26 (5), 25-29.
Hua, L., & Hua, B. Z. (1995). Preliminary study on the host-biotypes of peach fruit borer. Acta Phytophylacica Sinica, 22 (2), 165-170.
Huang, K. X., Wang, Y. Z., Ye, Z. X., Zhang, N. X., & Zhang, L. Y. (1976). Influence of photoperiod and temperature on diapause of the peach fruit moth Carposina sasakii Matsumura. Acta Entomologica Sinica, 19 (2), 149-156.
Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017). Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper.Molecular Biology and Evolution, 34 (8), 2115-2122. doi:10.1093/molbev/msx148 %J Molecular Biology and Evolution
Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernandez-Plaza, A., Forslund, S. K., Cook, H., . . . Bork, P. (2019). eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47 (D1), D309-D314. doi:10.1093/nar/gky1085
Isobe, M., Kai, H., Kurahashi, T., Suwan, S., Pitchayawasin-Thapphasaraphong, S., Franz, T., . . . Nishida, H. (2006). The molecular mechanism of the termination of insect diapause, part 1: A timer protein, TIME-EA4, in the diapause eggs of the silkwormBombyx mori is a metallo-glycoprotein. Chembiochem, 7 (10), 1590-1598. doi:10.1002/cbic.200600138
Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., . . . Hunter, S. (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics, 30 (9), 1236-1240. doi:10.1093/bioinformatics/btu031
Kanost, M. R., Arrese, E. L., Cao, X., Chen, Y. R., Chellapilla, S., Goldsmith, M. R., . . . Blissard, G. W. (2016). Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochemistry and Molecular Biology, 76 , 118-147. doi:10.1016/j.ibmb.2016.07.005
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability.Molecular Biology and Evolution, 30 (4), 772-780. doi:10.1093/molbev/mst010
Kim, D.-S., Lee, J.-H., & Yiem, M.-S. (2000). Spring Emergence Pattern ofCarposina sasakii(Lepidoptera: Carposinidae) in Apple Orchards in Korea and its Forecasting Models Based on Degree-Days.Environmental Entomology, 29 (6), 1188-1198. doi:10.1603/0046-225x-29.6.1188
Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37 (8), 907-915. doi:10.1038/s41587-019-0201-4
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14 (4), R36. doi:10.1186/gb-2013-14-4-r36
Kim, D. S., Lee, J. H., & Yiem, M. S. (2001). Temperature-dependent development of Carposina sasakii (Lepidoptera : Carposinidae) and its stage emergence models. Environmental Entomology, 30 (2), 298-305.
Kim, Y. I., Kim, H. J., Kwon, Y. M., Kang, Y. J., Lee, I. H., Jin, B. R., . . . Seo, S. J. (2010). Modulation of MnSOD protein in response to different experimental stimulation in Hyphantria cunea .