Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology
157 (4), 343-350. doi:10.1016/j.cbpb.2010.08.003
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017). Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation. Genome Research, 27 (5), 722-736. doi:10.1101/gr.215087.116
Korf, I. (2004). Gene finding in novel genomes. BMC Bioinformatics, 5 , 59. doi:10.1186/1471-2105-5-59
Kozak, G. M., Wadsworth, C. B., Kahne, S. C., Bogdanowicz, S. M., Harrison, R. G., Coates, B. S., & Dopman, E. B. (2019). Genomic Basis of Circannual Rhythm in the European Corn Borer Moth. Curr Biol, 29 (20), 3501-3509 e3505. doi:10.1016/j.cub.2019.08.053
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.Molecular Biology and Evolution, 33 (7), 1870-1874. doi:10.1093/molbev/msw054
Kwon, D., Kwon, H., Kim, D., & Yang, C. (2018). Larval species composition and genetic structures of Carposina sasakii, Grapholita dimorpha, and Grapholita molesta from Korea. Bulletin of entomological research, 108 (2), 241-252.
Kwon, D. H., Kim, D. H., Kim, H. H., Lee, S. H., & Yang, C. Y. (2017). Genetic diversity and structure in apple-infesting pests ofCarposina sasakii , Grapholita dimorpha andGrapholita molesta in Korea. Journal of Asia-Pacific Entomology, 20 (1), 13-16. doi:10.1016/j.aspen.2016.11.002
Lagesen, K., Hallin, P., Rodland, E. A., Staerfeldt, H. H., Rognes, T., & Ussery, D. W. (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research, 35 (9), 3100-3108. doi:10.1093/nar/gkm160
Lange, A., Beier, S., Huson, D. H., Parusel, R., Iglauer, F., & Frick, J. S. (2018). Genome Sequence of Galleria mellonella (Greater Wax Moth). Genome Announcement, 6 (2), e01220-01217. doi:10.1128/genomeA.01220-17
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9 (4), 357-359. doi:10.1038/nmeth.1923
Lowe, T. M., & Eddy, S. R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25 (5), 955-964. doi:10.1093/nar/25.5.955
Lu, S., Wang, J., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., . . . Marchler-Bauer, A. (2020). CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Research, 48 (D1), D265-D268. doi:10.1093/nar/gkz991
Lu, S., Yang, J., Dai, X., Xie, F., He, J., Dong, Z., . . . Li, X. (2019). Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor ) based on third-generation DNA sequencing and Hi-C analysis. Gigascience, 8 (11). doi:10.1093/gigascience/giz128
Ma, W., Zhao, X., Yin, C., Jiang, F., Du, X., Chen, T., . . . Lin, Y. (2020). A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis . Molecular Ecology Resources, 20 (1), 268-282. doi:10.1111/1755-0998.13078
Marçais, G., & Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.Bioinformatics (Oxford, England), 27 (6), 764-770. doi:10.1093/bioinformatics/btr011
Mitter, C., Davis, D. R., & Cummings, M. P. (2017). Phylogeny and evolution of Lepidoptera. Annu Rev Entomol, 62 , 265-283. doi:10.1146/annurev-ento-031616-035125
Nishikawa, H., Iijima, T., Kajitani, R., Yamaguchi, J., Ando, T., Suzuki, Y., . . . Fujiwara, H. (2015). A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly.Nature Genetics, 47 (4), 405-409. doi:10.1038/ng.3241
Pearce, S. L., Clarke, D. F., East, P. D., Elfekih, S., Gordon, K. H. J., Jermiin, L. S., . . . Wu, Y. D. (2017). Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpapest species. BMC Biology, 15 (1), 63. doi:10.1186/s12915-017-0402-6
Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T. C., Mendell, J. T., & Salzberg, S. L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33 (3), 290-295. doi:10.1038/nbt.3122
Price, M. N., Dehal, P. S., & Arkin, A. P. (2009). FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution, 26 (7), 1641-1650. doi:10.1093/molbev/msp077
Ragland, G. J., Armbruster, P. A., & Meuti, M. E. (2019). Evolutionary and functional genetics of insect diapause: a call for greater integration. Current Opinion in Insect Science
36 , 74-81. doi:10.1016/j.cois.2019.08.003
Ramzanzadeh, F., Yeganeh, S., JaniKhalili, K., & Babaei, S. S. (2016). Effects of different photoperiods on digestive enzyme activities in rainbow trout (Oncorhynchus mykiss ) alevin and fry.Canadian Journal of Zoology, 94 (6), 435-442. doi:10.1139/cjz-2015-0180
Rane, R. V., Ghodke, A. B., Hoffmann, A. A., Edwards, O. R., Walsh, T. K., & Oakeshott, J. G. (2019). Detoxifying enzyme complements and host use phenotypes in 160 insect species. Current Opinion in Insect Science, 31 , 131-138.
Roach, M. J., Schmidt, S. A., & Borneman, A. R. (2018). Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics, 19 (1), 460. doi:10.1186/s12859-018-2485-7
Sato, N., & Ishitani, M. (1976). Life-cycle of the peach fruit moth,Carposina niponensis Walsingham. Bulletin of the Aomori Field Crops and Horticultural Experiment Station, 1 , 1-16.
Servant, N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C. J., Vert, J. P., . . . Barillot, E. (2015). HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biology, 16 , 259. doi:10.1186/s13059-015-0831-x
Shan, X. J., Xiao, Z. Z., Huang, W., & Dou, S. Z. (2008). Effects of photoperiod on growth, mortality and digestive enzymes in miiuy croaker larvae and juveniles. Aquaculture, 281 (1-4), 70-76. doi:10.1016/j.aquaculture.2008.05.034
Sim, C., & Denlinger, D. L. (2011). Catalase and superoxide dismutase-2 enhance survival and protect ovaries during overwintering diapause in the mosquito Culex pipiens . Journal of Insect Physiology, 57 (5), 628-634. doi:10.1016/j.jinsphys.2011.01.012
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31 (19), 3210-3212. doi:10.1093/bioinformatics/btv351
Song, S. V., Downes, S., Parker, T., Oakeshott, J. G., & Robin, C. (2015). High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep.Heredity (Edinb), 115 (5), 460-470. doi:10.1038/hdy.2015.53
Stanke, M., & Waack, S. (2003). Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics, 19 Suppl 2 , ii215-225. doi:10.1093/bioinformatics/btg1080
Subala, S. P., & Shivakumar, M. S. (2017). Circadian variation affects the biology and digestive profiles of a nocturnal insectSpodoptera litura (Insecta: Lepidoptera). Biological Rhythm Research, 48 (2), 207-226. doi:10.1080/09291016.2016.1251928
Tarailo‐Graovac, M., & Chen, N. (2009). Using RepeatMasker to identify repetitive elements in genomic sequences. Current protocols in bioinformatics, 25 (1), unit 4.10.
Toshima, A., Honma, K., Masaki, S. J. J. J. o. A. E., & Zoology. (1961). Factors Influencing the Seasonal Incidence and Breaking of Diapause in Carposina niponensis WALSHINGHAM. Japanese Journal of Applied Entomology and Zoology, 5 (4), 260-269.
Vizueta, J., Sánchez-Gracia, A., & Rozas, J. (2019). BITACORA: A comprehensive tool for the identification and annotation of gene families in genome assemblies. bioRxiv , 593889. doi:10.1101/593889
Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., & Schatz, M. C. (2017). GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics, 33 (14). doi:10.1093/bioinformatics/btx153
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., . . . Earl, A. M. (2014). Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE, 9 (11), e112963. doi:10.1371/journal.pone.0112963
Wan, F. H., Yin, C. L., Tang, R., Chen, M. H., Wu, Q., Huang, C., . . . Li, F. (2019). A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance. Nature Communications, 10 , doi.org/10.1038/s41467-41019-12175-41469. doi:ARTN 4237
10.1038/s41467-019-12175-9
Wang, J., Yu, Y., Li, L. L., Guo, D., Tao, Y. L., & Chu, D. (2015).Carposina sasakii (Lepidoptera: Carposinidae) in its native range consists of two sympatric cryptic lineages as revealed by mitochondrial COI gene sequences. Journal of Insect Science, 15 (1), 1-6. doi:10.1093/jisesa/iev063
Wang, Y. Z., Li, B. Y., Hoffmann, A. A., Cao, L. J., Gong, Y. J., Song, W., . . . Wei, S. J. (2017). Patterns of genetic variation among geographic and host-plant associated populations of the peach fruit mothCarposina sasakii (Lepidoptera: Carposinidae). BMC Evolutionary Biology, 17 (1), 265. doi:10.1186/s12862-017-1116-7
Xia, Q., Zhou, Z., Lu, C., Cheng, D., Dai, F., Li, B., . . . Biology Analysis, G. (2004). A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science, 306 (5703), 1937-1940. doi:10.1126/science.1102210
Xiang, H., Liu, X., Li, M., Zhu, Y. n., Wang, L., Cui, Y., . . . Zhan, S. (2018). The evolutionary road from wild moth to domestic silkworm.Nature Ecology & Evolution, 2 (8), 1268-1279. doi:10.1038/s41559-018-0593-4
Xiao, H., Ye, X., Xu, H., Mei, Y., Yang, Y., Chen, X., . . . Li, F. (2020). The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion.Molecular Ecology Resources, 20 (4), 1050-1068. doi:10.1111/1755-0998.13182
Xu, Q. G., & Hua, B. Z. (2004). RAPD analysis on the speciation in host races of Carposina sasakii Matsumura (Lepidoptera: Carposinidae).Acta Entomologica Sinica, 47 (3), 379-383.
Yang, P., Tanaka, H., Kuwano, E., & Suzuki, K. (2008). A novel cytochrome P450 gene (CYP4G25) of the silkmoth Antheraea yamamai : Cloning and expression pattern in pharate first instar larvae in relation to diapause. Journal of Insect Physiology, 54 (3), 636-643. doi:10.1016/j.jinsphys.2008.01.001
You, M. S., Yue, Z., He, W. Y., Yang, X. H., Yang, G., Xie, M., . . . Wang, J. (2013). A heterozygous moth genome provides insights into herbivory and detoxification. Nature Genetics, 45 (2), 220-225.
Zhan, S., Merlin, C., Boore, J. L., & Reppert, S. M. (2011). The monarch butterfly genome yields insights into long-distance migration.Cell, 147 (5), 1171-1185. doi:10.1016/j.cell.2011.09.052
Zhang, B., Peng, Y., Zhao, X. J., Hoffmann, A. A., Li, R., & Ma, C. S. (2016). Emergence of the overwintering generation of peach fruit moth (Carposina sasakii ) depends on diapause and spring soil temperatures. Journal of Insect Physiology, 86 , 32-39. doi:10.1016/j.jinsphys.2015.12.007
Zhang, S., Shen, S., Peng, J., Zhou, X., Kong, X., Ren, P., . . . Zhang, Z. (2020). Chromosome-level genome assembly of an important pine defoliator, Dendrolimus punctatus (Lepidoptera; Lasiocampidae).Molecular Ecology Resources, 20 (4), 1023-1037.
Zhao, L., & Shi, L. (2009). Metabolism of hydrogen peroxide in univoltine and polyvoltine strains of silkworm (Bombyx mori ).Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology, 152 (4), 339-345. doi:10.1016/j.cbpb.2008.12.014