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Data may be preliminary. aeyhaycan(i-) ih-hi FbL n boeaei p5 Ioee l,20) twsbio- was it 2000), al., of et fibroin (Inoue Although (p25) fibrohexamerin protein. and silk (Fib-L) light-chain of (Fib-H), component heavy-chain major namely the is Fibroin 1982). sericin Kafatos, and Fibroin & that to plausible (Rodakis, seemed highly genes winter proteins is protein chorion the chorion it Hc Hc in species, analysis, the because diapause high-cysteine phylogenetic in diapause, survive and absent subfamilies, embryonic search to be three BLAST for embryos the the role to for Among important according eggshells Interestingly, an 2015). of play al., hardness to et increase considered Papantonis is 1986; chorion al, (Hc) et (Lecanidou respectively 63 duplication apparent above-mentioned high the the to of addition ground In the be conversion. can gene which or cluster, duplication specific gene tandem These a through as respectively. rate 1 consist genes, are chromosome protein OG0000131) and on chorion Ortholog (OG0000113 proximity 30 OGs 3C). two and OGs, (Fig. these 33 Of species of 159. 5 were OGs the related tree among non-retrotransposon 205 phylogenetic identified relationships a 2015) and genetic Kelly, 3B, & ricini the Fig. (Emms, explains in OrthoFinder shown orthologs using is copy analysis species single Lepidoptera 5 3,907 almost among of that (OGs) suggesting orthogroups of plot, number the The in observed hardly were rearrangements, regions. links chromosomal specific’ few frequent of extremely despite ancestor However, of or the regions links 2009). entire in no al., happened of et Krzywinski regions fusion, 2015; genomic chromosome al., and et translocation (Cheong 3A) as such among orthologs chromosomes, copy among single of links domains which plot populous circos 2). of The 2 proportion Fig. large in top LTR 000477) the al., the LINE, (IPR that et (SINE, are domain reflect Stanke elements transcriptase may (IPR001584) 2014; Reverse which of domain al., that S3), assembly et shows core genome (Fig. analysis Lomsadze the catalytic 2017) 2019; in Integrase al., genes al., et protein-coding and et (Finn 16,702 Hoff InterProScan predicted 2016; software 1). al., 2008) (Table et al., et Hoff Stanke 2009; 2006; al., et (Camacho BRAKER2 initio Ab sequences. repetitive of expansion independent on in independently SINEs and the the parallel While that 2A). in (Fig. was occurred feature have noteworthy to Another seems sequences branches. repetitive phylogenetic of own expansion their the 2A), (Fig. and in family in family aao,18;Ppnoi,Sees aru 05 oai,&Kfts 92.Bsdo euneho- sequence on Based ( groups & 1982). two Eickbush, Kafatos, into Rodakis, & categorized (Lecanidou, chorion Rodakis, environment be that 2015; the can suggesting Iatrou, to proteins environment, & adaptations chorion the Swevers, reflect mology, Papantonis, from to embryos evolve 1986; 3D). to Kafatos, protect (Fig. clades likely and distinct are eggshell into proteins fell comprise OG0000131 proteins and OG0000113 Chorion from genes chorion because plexippus proteins D. chorion and xuthus P. xylostella, in present .mori B. seicOs ot-i G r eae ortornpsbeeeet Fg ) Thus, 2). 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S. hc hwylo neuetclu hntp,ad‘eo’ad‘lemon and ‘lemon’ and phenotype, colour integument yellow show which .ricini S. n So’idvdasi nfrl omdi vr emn flarval of segment every in formed uniformly is individuals ‘Spot’ and eeoyoi or heterozygotic .ricini S. .ricini S. nIdaaekont pnrdccos iia oor‘Red our to similar cocoons, red spin to known are India in 1 individuals. 9 .c pryeri c. S. (and h eerpror of repertoire gene The . .ricini S. .c pryeri c. S. .c pryeri c. S. .mori B. - .ricini S. n F and chorion .c pryeri c. S. iiednIX Biliverdin , 1 .Atog h epnil genes responsible the Although ). a ohn od ih‘elw of ‘Yellow’ with do to nothing has niiul sge,adtu,this thus, and grey, is individuals ee,and genes, ooyoi,adntchimeric. not and homozygotic, .ricini S. r oiat responsible dominant, are γ sericin id oBiliverdin- to binds .ricini S. a o odistinct so not was .c pryeri c. S. ee,seemed genes, 1 and individ- .c. 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Waack, & B., Morgenstern, O., ¨ offmann, https://doi.org/10.1038/nbt.3122 https://doi.org/10.1073/pnas.79.11.3551 https://doi.org/10.1186/1471-2105-6-31 ) i351-8. 1), 13 https://doi.org/10.1093/bioinformatics/bti1018 https://doi.org/10.1002/0471250953.bi0410s25 https://doi.org/10.1146/annurev-ento- https://doi.org/10.1093/bioinformatics/btn013 http://hdl.handle.net/10212/2037 Posted on Authorea 27 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158802211.15119012 — This a preprint and has not been peer reviewed. Data may be preliminary. al h euto ikg analysis. linkage of result The 2 Table of Features 1 Table results. Figures the for discussed and library J.L. the Table Illumina and prepared prepared S.K. Y.S. T.K., T.N. runs. T.S., sequence manuscript. runs. the the sequence performed the wrote S.S. performed and and and data K.Y. sequencing the RNA sequencing. analyzed genome and for experiments libraries the designed J.L. Contributions DRA009718 and Author DRA009717 numbers accession the under available https://datadryad.org/stash/share/5hfxrylqOiDgzbXoM at available are is study assembly Genome this respectively. (DDBJ), in obtained data NGS Biomacro- Accessibility yamamai. Antheraea Data Strnad, of L., Silk Kucerova, the C., in L. Composition Vieira, Sericin D., (2016). Kodrik, 1776–1787. H. 17(5), F., (2019). Sehadova, molecules, B. Sehnal, & P., D. B., Konik, Gammon, Kludkiewicz, the & H., of https://doi.org/10.1073/pnas.1818283116 N., V., Yonemura, Proceedings 1669–1678. N. 116(5), M., interactions. America, Grishin, Zurovec, virus–host of H., States and Insect United D. capability the of Lepidoptera. 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Walker, C. from profiling Underwood, from genome M., assembly reference-free Fast genome Nattestad, 2202–2204. novo GenomeScope: J., de (2017). F. C. accurate Sedlazeck, M. and Fast W., (2016). G. M. Vurture, Sikic, 068122. & BioRxiv, N., reads. uncorrected gland Nagarajan, silk long I., larval 1–14. the Sovic, Science, in R., analysis Insect Vaser, expression ricini. Gene Samia and (2015). silkworm H. gaps eri Sezutsu, knowledge, & the current K., of genomes: Mita, 99–105. K., Lepidoptera Yamamoto, 25, (2018). T., Science, Y. Tsubota, Insect A. in Kawahara, Opinion 259– & Current 7, D., University., directions. S. Imperial future Tokyo Cinel, Agriculture, A., of D. reference Triant, College special the with of crosses, silkworm Bulletin some The On heredity. 393. I. of insects. law of Mendel’s hybridology the to on Studies (1906). K. Toyama, https://doi.org/10.1192/bjp.111.479.1009-a https://doi.org/10.1093/bioinformatics/btx153 .ricini S. https://doi.org/10.1021/acs.biomac.6b00189 genome. https://doi.org/10.1101/068122 14 https://doi.org/10.1016/j.ibmb.2011.02.005 https://doi.org/10.1111/1744-7917.12251 https://doi.org/10.1371/journal.pone.0112963 https://doi.org/10.1016/j.cois.2017.12.004 https://doi.org/10.1093/molbev/msx319 8esv8rQGyOO056G9X732hKlP8 Posted on Authorea 27 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158802211.15119012 — This a preprint and has not been peer reviewed. Data may be preliminary. h rtsqecn eentsffiin o seby ons1ad2ma h rtadscn sequencing, second and first the mean 2 and 1 via Rounds reads assembly. obtained of for amounts sufficient because not respectively. libraries were same sequencing the data. first re-using the read twice conducted short was illumina sequencing of *Illumina statistics of Summary S1 Table Information Supporting phenotypes. BC (D)’ the cocoon ‘Red in cocoon.’ and markers ‘Red (C),’ PCR-based and ‘Spot of ‘Spot’ ‘Yellow,’ patterns ‘Blue,’ Segregation of mapping Linkage 5. Fig of Cocoon (C) x of larvae 5th-instar (B) of larva Fifth-instar (A) of view Orange–DpCho. Graphical Green–PxuCho; 4. Purple–PxyCho; Fig Blue–SrCho; BmCho; Red– are: colors Branch (PxyCho), proteins chorion of orthologs. tree copy Phylogenetic single (D) 3,907 of alignments on the based indicates species lepidopteran section xylostella five each of in tree Number Phylogenetic (C) species. lepidopteran five in orthogroups. orthogroups of protein number of diagram Venn (B) al. et of chromosomes putative of chromosomes represents ‘Sr ideogram of ricini side Left (A) of presence The 3 Table mut(p )adpooto % )o eeiiesqecsi v eiotrnseis including species, lepidopteran five in between sequences Comparison repetitive 3. of Fig B) (%; proportion the in and ricini sequences A) repeat (bp; of Amount proportion and Amount 2. 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2.1175 A0A194Q5Y9

2.1092 XM_011566431.1

2.1091 A0A194Q567 mori Bombyx XM_011566430.1

H9JJD2 A0A194PST0 XM_011565373.1 XM_011565370.1 A0A194PUT4 XM_011565368.1 XM_011565371.1A0A0K2S2P4

XM_011565377.1 XM_011565384.1 A0A0K2S2Z0

XM_011563823.1 H9J162

XM_011566435.1 A0A0K2S2Q6 H9JJM0

2.1094

A0A194PT66 H9JJL4

C

A0A194PT46 2.1174 A0A194PST5 H9J161

1012 85

A0A194PZB0 2.1142

A0A194PUS5 2.1145

A0A194PZB5 2.1151

A0A194PUS0 2.1149

2.1150

A0A0N1PG09 A0A0K2S351 2.1148

DPOGS206743-PA A0A0K2S2X8 48 77 A0A194PU50 H9JJM1 150

DPOGS206744-PAA0A194PT56 A0A0K2S3R0 A0A0K2S2Y2 93

0mm 10 DPOGS206759-PA DPOGS206755-PA

DPOGS206751-PA

DPOGS212790-PA 2.1122 447 101

2.1140 A0A194PZA5

ai ricini Samia 2.1095

A0A194Q703 XM_011556205.1 2.1127 247

81

2.1119 200

H9JJD1 A0A0K2S2Y9 A0A0K2S3462.1093 A0A0K2S3Q5

42

2.1144 2.1120 O 2.1147 2.1124 G 183

0 2.1161 2.1138

0

8604

2.1163 2.1125 0 0

2.1157 2.1129 1

1

2.1154 2.1131 3 166

O

2.1164 2.1132

Q17215 174

G 2.1172 42

2.1170 A0A0K2S2Z1

0 2.1168 A0A0K2S3P5

0 2.1166 A0A0K2S306

0

2.1152 A0A0K2S3H1

0

2.1158 A0A0K2S2Z4 83 1

2.1116 2.1097 3

2.1106 2.1099 353

1

2.1111 2.1098

2.1113 2.1109 90

2.1104 2.1117

2.1102 2.1114

2.1108 2.1107 49 60

2.1118 2.1112

2.1100 2.1101

302

2.1096 2.1115

A0A0K2S2W5

2.1103 O

A0A0K2S2Y8 2.1105 127 108 G

A0A0K2S2S0 2.1110

0

A0A0K2S2S1 2.1141

0 116

A0A0K2S2T8 2.1143

0 1322

A0A0K2S2R5 2.1146 105 0

A0A0K2S2Q9

2.1173 1

B A0A0K2S3K4

2.1165 1

o A0A0K2S309

2.1167 3 323

m A0A0K2S2S9 2.1169

b A0A0K2S2V5 2.1171

y A0A0K2S2T7 2.1160

BC1 x A0A0K2S2R2 2.1162

m A0A0K2S3J6 2.1159 plexippus Danaus F1

A0A0K2S2U0 2.1153

o A0A0K2S2U6 2.1155 xylostella Plutella r A0A0K2S2Z8 2.1156 106

i

H A0A0K2S2S8 A0A0K2S2Z9

A0A0K2S2T6 A0A0K2S354

c A0A0K2S2U3 A0A0K2S323

A A0A0K2S2Y4 A0A0K2S3G9

c A0A0K2S3I6 A0A0K2S3R4

h A0A0K2S2Z5 A0A0K2S326

o A0A0K2S2W2 A0A0K2S372

r A0A0K2S2V2 A0A0K2S3M6

i A0A0K2S2X5 A0A0K2S333

o A0A0K2S3L8 A0A0K2S321

n A0A0K2S3H2 A0A0K2S314

A0A0K2S2Q7 A0A0K2S2S6

A0A0K2S3N0 A0A0K2S2U8

A0A0K2S301 A0A0K2S2Q3

A0A0K2S300 A0A0K2S2R7

A0A0K2S305 A0A0K2S2V6

A0A0K2S375 A0A0K2S2S2

A0A0K2S303 A0A0K2S2U4

A0A0K2S2P5 A0A0K2S2X0

A0A0K2S2W7 A0A0K2S2V8

A0A0K2S2X1 A0A0K2S2X9

S

A0A0K2S2W1 A0A0K2S2W6

A0A0K2S2V4 A0A0K2S2U9

A0A0K2S3M2 A0A0K2S2P9

A0A0K2S328 A0A0K2S2Q4

A0A0K2S2Y6 A0A0K2S2R0

A0A0K2S338 A0A0K2S2S4 macynthia amia

A0A0K2S2P8 A0A0K2S2R6

A0A0K2S2R4 A0A0K2S3J1

2.1130 A0A0K2S2Y0

2.1126 A0A0K2S2T3

2.1139 A0A0K2S3K9

2.1134 A0A0K2S3L4

2.1133 A0A0K2S2W0

2.1121 A0A0K2S2V1

A0A0K2S2Z6 A0A0K2S2T4

A0A0K2S310 A0A0K2S2T0

A0A0K2S368 A0A0K2S318

A0A0K2S2Y7 A0A0K2S2S5

A0A0K2S2X3 A0A0K2S2Z3

A0A0K2S2Y3 A0A0K2S2U2

A0A0K2S359 A0A0K2S3K0 XM_011561028.1 A0A0K2S2T2

DPOGS206742-PA 2.1135(outgroup)

1.0 pryeri

1

3

1

0

0

0

0 G O

B

o

m

b

y

x

m

o

r

i

H

c

B

c h o r i o n Posted on Authorea 27 Apr 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158802211.15119012 — This a preprint and has not been peer reviewed. Data may be preliminary. of-samia-ricini-a-new-model-species-of-lepidopteran-insect Table3.xlsx file Hosted of-samia-ricini-a-new-model-species-of-lepidopteran-insect Table2.xlsx file Hosted of-samia-ricini-a-new-model-species-of-lepidopteran-insect Table1.xlsx file Hosted vial at available at available at available A Chr13 https://authorea.com/users/315693/articles/446018-the-genome-sequence- https://authorea.com/users/315693/articles/446018-the-genome-sequence- https://authorea.com/users/315693/articles/446018-the-genome-sequence- Chr1 Chr9 Chr5 Chr6 Chr2 Chr10 ChrZ i.5 Fig. 19 Chr7 Chr3 Chr11 Chr8 Chr4 Chr12