References
Bao, Z., & Eddy, S. R. (2002). Automated De Novo Identification of
Repeat Sequence Families in Sequenced Genomes. Genome Research, 12(8),
1269–1276. https://doi.org/10.1101/gr.88502
Bateman, A. (2019). UniProt: A worldwide hub of protein knowledge.
Nucleic Acids Research, 47(D1), D506–D515.https://doi.org/10.1093/nar/gky1049
Bateman, A. (2019). UniProt: a worldwide hub of protein knowledge.
Nucleic Acids Research, 47(D1), D506–D515.https://doi.org/10.1093/nar/gky1049
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA
sequences. Nucleic Acids Research, 27(2), 573–580.https://doi.org/10.1093/nar/27.2.573
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible
trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120.https://doi.org/10.1093/bioinformatics/btu170
Brahma, D., Swargiary, A., & Dutta, K. (2015). A comparative study on
morphology and rearing performance of Samia ricini and Samia canningi
crossbreed with reference to different food plants. Journal of
Entomology and Zoology Studies, 3(5), 12–19.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J.,
Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and
applications. BMC Bioinformatics, 10, 1–9.https://doi.org/10.1186/1471-2105-10-421
Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009).
trimAl: A tool for automated alignment trimming in large-scale
phylogenetic analyses. Bioinformatics, 25(15), 1972–1973.https://doi.org/10.1093/bioinformatics/btp348
Chaitanya, R. K., & Dutta-Gupta, A. (2010). Light chain fibroin and P25
genes of Corcyra cephalonica: Molecular cloning, characterization,
tissue-specific expression, synchronous developmental and
20-hydroxyecdysone regulation during the last instar larval development.
General and Comparative Endocrinology, 167(1), 113–121.https://doi.org/10.1016/j.ygcen.2010.02.007
Challis, R. J., Kumar, S., Dasmahapatra, K. K., Jiggins, C. D., &
Blaxter, M. (2016). Lepbase: The Lepidopteran genome database. BioRxiv,
056994. https://doi.org/10.1101/056994
Chen, Z., Nohata, J., Guo, H., Li, S., Liu, J., Guo, Y., … Mita,
K. (2015). A comprehensive analysis of the chorion locus in silkmoth.
Scientific Reports, 5, 1–11.https://doi.org/10.1038/srep16424
Cheong, W. H., Tan, Y. C., Yap, S. J., & Ng, K. P. (2015). ClicO FS: An
interactive web-based service of Circos. Bioinformatics, 31(22),
3685–3687.https://doi.org/10.1093/bioinformatics/btv433
Chernomor, O., Von Haeseler, A., & Minh, B. Q. (2016). Terrace Aware
Data Structure for Phylogenomic Inference from Supermatrices. Systematic
Biology, 65(6), 997–1008. https://doi.org/10.1093/sysbio/syw037
Chikhi, R., & Medvedev, P. (2014). Informed and automated k-mer size
selection for genome assembly. Bioinformatics, 30(1), 31–37.https://doi.org/10.1093/bioinformatics/btt310
Conesa, A., & Götz, S. (2008). Blast2GO: A comprehensive suite for
functional analysis in plant genomics. International Journal of Plant
Genomics, 2008.https://doi.org/10.1155/2008/619832
Dong, Y., Dai, F., Ren, Y., Liu, H., Chen, L., Yang, P., Liu, Y., Li,
X., Wang, W., & Xiang, H. (2015). Comparative transcriptome analyses on
silk glands of six silkmoths imply the genetic basis of silk structure
and coloration. BMC Genomics, 16(1), 1–14.https://doi.org/10.1186/s12864-015-1420-9
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high
accuracy and high throughput. Nucleic Acid Research, 32(5), 1792–1797.https://doi.org/10.1093/nar/gkh340
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A.,
Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart,
A., Sonnhammer, E. L. L., Hirsh, L., Paladin, L., Piovesan, D., Tosatto,
S. C. E., & Finn, R. D. (2019). The Pfam protein families database in
2019. Nucleic Acids Research, 47(D1), D427–D432.https://doi.org/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(1), 1–14.https://doi.org/10.1186/s13059-015-0721-2
Finn, R. D., Attwood, T. K., Babbitt, P. C., Bateman, A., Bork, P.,
Bridge, A. J., Chang, Hsin Yu
Dosztanyi, Z., El-Gebali, S., Fraser, M., Gough, J., Haft, D., Holliday,
G. L., Huang, H., Huang, X., Letunic, I., Lopez, R., Lu, S.,
Marchler-Bauer, A., Mi, H., Mistry, J., Natale, D. A., Necci, M., Nuka,
G., Orengo, C. A., Park, Y., Pesseat, S., Piovesan, D., Potter, S. C.,
Rawlings, N. D., Redaschi, N., Richardson, L., Rivoire, C.,
Sangrador-Vegas, A., Sigrist, C., Sillitoe, I., Smithers, B., Squizzato,
S., Sutton, G., Thanki, N., Thomas, P. D., Tosatto, Silvio C.E., Wu,
Cathy H., Xenarios, I., Yeh, L. S., Young, S. Y., & Mitchell, A. L.
(2017). InterPro in 2017-beyond protein family and domain annotations.
Nucleic Acids Research, 45(D1), D190–D199.https://doi.org/10.1093/nar/gkw1107
Gu, L., Reilly, P. F., Lewis, J. J., Reed, R. D., Andolfatto, P., &
Walters, J. R. (2019). Dichotomy of Dosage Compensation along the Neo Z
Chromosome of the Monarch Butterfly. Current Biology, 29(23),
4071-4077.e3. https://doi.org/10.1016/j.cub.2019.09.056
Haas, B. J., Salzberg, S. L., Zhu, W., Pertea, M., Allen, J. E., Orvis,
J., White, O., Robin, C. B., Wortman, J. R. (2008). Automated eukaryotic
gene structure annotation using EVidenceModeler and the Program to
Assemble Spliced Alignments. Genome Biology, 9(1), 1–22.https://doi.org/10.1186/gb-2008-9-1-r7
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D.,
Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M., MacManes,
M.D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman,
R., William, T., Dewey, C.N., Henschel, R., LeDuc, R.D., Friedman, N.,
& Regev, A. (2013). De novo transcript sequence reconstruction from
RNA-seq using the Trinity platform for reference generation and
analysis. Nature Protocols, 8, 1494. Retrieved fromhttps://doi.org/10.1038/nprot.2013.084
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L.
S. (2018). UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Molecular biology and evolution. Molecular Biology and Evolution, 35(2),
518–522. https://doi.org/10.5281/zenodo.854445
Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M., & Stanke, M.
(2016). BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with
GeneMark-ET and AUGUSTUS: Table 1. Bioinformatics, 32(5), 767–769.https://doi.org/10.1093/bioinformatics/btv661
Hoff, K. J., Lomsadze, A., Borodovsky, M., & Stanke, M. (2019).
Whole-Genome Annotation with BRAKER (pp. 65–95).https://doi.org/10.1007/978-1-4939-9173-0_5
Inoue, S., Tanaka, K., Arisaka, F., Kimura, S., Ohtomo, K., & Mizuno,
S. (2000). Silk fibroin of Bombyx mori is secreted, assembling a high
molecular mass elementary unit consisting of H-chain, L-chain, and P25,
with a 6:6:1 molar ratio. Journal of Biological Chemistry, 275(51),
40517–40528.https://doi.org/10.1074/jbc.M006897200
Jurka, J., Kapitonov, V. V., Pavlicek, A., Klonowski, P., Kohany, O., &
Walichiewicz, J. (2005). Repbase Update, a database of eukaryotic
repetitive elements. Cytogenetic and Genome Research, 110(1–4),
462–467.https://doi.org/10.1159/000084979
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., &
Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate
phylogenetic estimates. Nature Methods, 14(6), 587–589.
https://doi.org/10.1038/nmeth.4285
Katoh, K., Misawa, K., Kuma, K., & Miyata, T. (2002). MAFFT: a novel
method for rapid multiple sequence alignment based on fast Fourier
transform. Nucleic Acids Research, 30(14), 3059–3066.https://doi.org/10.1093/nar/gkf436
Kikkawa, H. (1941). Mechanism of Pigment Formation in Bombyx and
Drosophila. Genetics, 26(6), 587–607. Retrieved from
http://www.ncbi.nlm.nih.gov/pubmed/17247024
Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: a fast spliced
aligner with low memory requirements. Nature Methods, 12, 357. Retrieved
fromhttps://doi.org/10.1038/nmeth.3317
Kim, S.R., Kwak, W., Kim, H., Caetano-Anolles, K., Kim, K. Y., Kim, S.
B., Choi, K. H., Kim, S. W., Hwang, J. S., Kim, M., Kim, I., Goo, T. W.,
& Park, S. W. (2018). Genome sequence of the Japanese oak silk moth,
Antheraea yamamai: the first draft genome in the family Saturniidae.
GigaScience, 7(1), 1–11.https://doi.org/10.1093/gigascience/gix113
Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R.,
Horsman, D., Jones, S. J., & Marra, M. A. (2009). Circos: An
information aesthetic for comparative genomics. Genome Research, 19(9),
1639–1645.https://doi.org/10.1101/gr.092759.109
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X:
Molecular evolutionary genetics analysis across computing platforms.
Molecular Biology and Evolution, 35(6), 1547–1549.https://doi.org/10.1093/molbev/msy096
Lecanidou, R., Rodakis, G. C., Eickbush, T. H., & Kafatos, F. C.
(1986). Evolution of the silk moth chorion gene superfamily: gene
families CA and CB. Proceedings of the National Academy of Sciences of
the United States of America, 83(17), 6514–6518.https://doi.org/10.1073/pnas.83.17.6514
Lee, J., Kiuchi, T., Kawamoto, M., Shimada, T., & Katsuma, S. (2018).
Accumulation of uric acid in the epidermis forms the white integument of
Samia ricini larvae. PLOS ONE, 13(10), e0205758.https://doi.org/10.1371/journal.pone.0205758
Li, H. (2016). Minimap and miniasm: Fast mapping and de novo assembly
for noisy long sequences. Bioinformatics, 32(14), 2103–2110.https://doi.org/10.1093/bioinformatics/btw152
Lomsadze, A., Burns, P. D., & Borodovsky, M. (2014). Integration of
mapped RNA-Seq reads into automatic training of eukaryotic gene finding
algorithm. Nucleic Acids Research, 42(15), 1–8.https://doi.org/10.1093/nar/gku557
Ma, S., Shi, R., Wang, X., Liu, Y., Chang, J., Gao, J., Lu, W., Zhang,
J., Zhao, P., & Xia, Q. (2014). Genome editing of BmFib-H gene provides
an empty Bombyx mori silk gland for a highly efficient bioreactor.
Scientific Reports, 4, 1–7.https://doi.org/10.1038/srep06867
Marçais, G., & Kingsford, C. (2011). A fast, lock-free approach for
efficient parallel counting of occurrences of k-mers. Bioinformatics,
27(6), 764–770.https://doi.org/10.1093/bioinformatics/btr011
Meng, Y., Katsuma, S., Daimon, T., Banno, Y., Uchino, K., Sezutsu, H.,
Tamura, T., Mita, K., & Shimada, T. (2009). The silkworm mutant lemon
(lemon lethal) is a potential insect model for human sepiapterin
reductase deficiency. Journal of Biological Chemistry, 284(17),
11698–11705.https://doi.org/10.1074/jbc.M900485200
Minh, B. Q., Nguyen, M. A. T., & Von Haeseler, A. (2013). Ultrafast
approximation for phylogenetic bootstrap. Molecular Biology and
Evolution, 30(5), 1188–1195. https://doi.org/10.1093/molbev/mst024
Nguyen, L.T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015).
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating
Maximum-Likelihood Phylogenies. Molecular Biology and Evolution, 32(1),
268–274.https://doi.org/10.1093/molbev/msu300
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. https://doi.org/10.1038/ng.3241
Papantonis, A., Swevers, L., & Iatrou, K. (2015). Chorion Genes: A
Landscape of Their Evolution, Structure, and Regulation. Annual Review
of Entomology, 60(1), 177–194.https://doi.org/10.1146/annurev-ento-010814-020810
Peigler, R. S., & Naumann, S. (2003). A revision of the silkmoth genus
Samia. University of the Incarnate Word.
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, 290.
Retrieved fromhttps://doi.org/10.1038/nbt.3122
Price, A. L., Jones, N. C., & Pevzner, P. A. (2005). De novo
identification of repeat families in large genomes. Bioinformatics
(Oxford, England), 21 Suppl 1(suppl_1), i351-8.https://doi.org/10.1093/bioinformatics/bti1018
Rodakis, G. C., & Kafatos, F. C. (1982). Origin of evolutionary novelty
in proteins: how a high-cysteine chorion protein has evolved.
Proceedings of the National Academy of Sciences of the United States of
America, 79(11), 3551–3555.https://doi.org/10.1073/pnas.79.11.3551
Saitoh, H. (2011). Yamamayuga-ka youtyu no aoirosikisoketugoutanpakusitu
–sinjusanyoutyutaieki to hihusosiki ni okeru Biliverdin
ketugoutanpakusitu no seisitu. Kankyo, (23), 26–34. Retrieved fromhttp://hdl.handle.net/10212/2037
Sezutsu, H., & Yukuhiro, K. (2014). The complete nucleotide sequence of
the eri-silkworm (Samia cynthia ricini) fibroin gene. Journal of Insect
Biotechnology and Sericology, 83(3), 59–70.
Singh, B. K., Kumar, R., Ahmed, S. A., & Pathania, P. C. (2017).
Diversity and their clarification of species Genus Samia (
Lepidoptera : Saturniidae ) in India and their prospects for
utilization ( LEPIDOPTERA : SATURNIIDAE ) IN INDIA AND THEIR PROSPECTS.
Journal of Insect Science, 30(1), 43–52.
Slater, G. S. C., & Birney, E. (2005). Automated generation of
heuristics for biological sequence comparison. BMC Bioinformatics, 6(5),
31.https://doi.org/10.1186/1471-2105-6-31
Stanke, M., Schöffmann, O., Morgenstern, B., & Waack, S. (2006). Gene
prediction in eukaryotes with a generalized hidden Markov model that
uses hints from external sources. BMC Bioinformatics, 7(1), 62.https://doi.org/10.1186/1471-2105-7-62
Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008). Using
native and syntenically mapped cDNA alignments to improve de novo gene
finding. Bioinformatics, 24(5), 637–644.https://doi.org/10.1093/bioinformatics/btn013
Sternburg, J., & Waldbauer, G. (1984). Diapause and Emergence Patterns
in Univoltine and Bivol Tine Populations of Promethea (Lepidoptera:
Saturniidae). The Great Lakes Entomologist, 17(3), 8.
Takasu, Y., Hata, T., Uchino, K., & Zhang, Q. (2010). Identification of
Ser2 proteins as major sericin components in the non-cocoon silk of
Bombyx mori. Insect Biochemistry and Molecular Biology, 40(4), 339–344.https://doi.org/10.1016/j.ibmb.2010.02.010
Tamura, T., & Kubota, T. (1988). A determination of molecular weight of
fibroin polypeptides in the saturnid silkworms, Antheraea yamamai,
Antheraea pernyi and Philosamia cynthia ricini by SDS PAGE. In
International Society for Wild Silkmoths.
Tarailo-Graovac, M., & Chen, N. (2009). Using RepeatMasker to identify
repetitive elements in genomic sequences. Current Protocols in
Bioinformatics, (SUPPL. 25), 1–14.https://doi.org/10.1002/0471250953.bi0410s25
Toyama, K. (1906). Studies on the hybridology of insects. I. On some
silkworm crosses, with special reference to Mendel’s law of heredity.
The Bulletin of the College of Agriculture, Tokyo Imperial University.,
7, 259–393.https://doi.org/10.1192/bjp.111.479.1009-a
Triant, D. A., Cinel, S. D., & Kawahara, A. Y. (2018). Lepidoptera
genomes: current knowledge, gaps and future directions. Current Opinion
in Insect Science, 25, 99–105.https://doi.org/10.1016/j.cois.2017.12.004
Tsubota, T., Yamamoto, K., Mita, K., & Sezutsu, H. (2015). Gene
expression analysis in the larval silk gland of the eri silkworm Samia
ricini. Insect Science, 1–14.https://doi.org/10.1111/1744-7917.12251
Vaser, R., Sovic, I., Nagarajan, N., & Sikic, M. (2016). Fast and
accurate de novo genome assembly from long uncorrected reads. BioRxiv,
068122.https://doi.org/10.1101/068122
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), 2202–2204.https://doi.org/10.1093/bioinformatics/btx153
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A.,
Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., &
Earl, A. M. (2014). Pilon: An integrated tool for comprehensive
microbial variant detection and genome assembly improvement. PLoS ONE,
9(11).https://doi.org/10.1371/journal.pone.0112963
Waterhouse, R. M., Seppey, M., Simao, F. A., Manni, M., Ioannidis, P.,
Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018). BUSCO
applications from quality assessments to gene prediction and
phylogenomics. Molecular Biology and Evolution, 35(3), 543–548.https://doi.org/10.1093/molbev/msx319
Yoshido, A., Yasukochi, Y., & Sahara, K. (2011). Samia cynthia versus
Bombyx mori: Comparative gene mapping between a species with a
low-number karyotype and the model species of Lepidoptera. Insect
Biochemistry and Molecular Biology, 41(6), 370–377.https://doi.org/10.1016/j.ibmb.2011.02.005
Zhang, J., Cong, Q., Rex, E. A., Hallwachs, W., Janzen, D. H., Grishin,
N. V., & Gammon, D. B. (2019). Gypsy moth genome provides insights into
flight capability and virus–host interactions. Proceedings of the
National Academy of Sciences of the United States of America, 116(5),
1669–1678. https://doi.org/10.1073/pnas.1818283116
Zurovec, M., Yonemura, N., Kludkiewicz, B., Sehnal, F., Kodrik, D.,
Vieira, L. C., Kucerova, L., Strnad, H., Konik, P., & Sehadova, H.
(2016). Sericin Composition in the Silk of Antheraea yamamai.
Biomacromolecules, 17(5), 1776–1787.https://doi.org/10.1021/acs.biomac.6b00189