Table S1. B. mori genes studied using transposon-based technologies and genome-editing technologies Target genes Type of manipulation Results/Phenotypes BmFtz-F1 Inducible expression using Dmhsp70 promoter Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Inducible transgenic RNAi using Dmhsp70 promoter Binary transgenic RNAi using Gal4/UAS system Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Ubiquitous expression using BmNPV ie1 promoter Ubiquitous expression using BmNPV ie1 promoter Overexpression using Gal4/UAS system Ubiquitous expression using BmActin3 promoter Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Ubiquitous expression using BmNPV ie1 promoter Expression of BmFtz-F1 in transgenic silkworms was induced at different stages of development and in diverse tissues after heat shock. Overexpression of BmCBP in both the midgut and middle silk gland of transgenic silkworms restored the carotenoid-based yellow phenotype in a colorless hemolymph strain. Overexpression of BmKIT3R in the pupa stage of transgenic silkworms resulted in the failure of some pupae to metamorphose into moths. Expression of BmEH in the whole body of transgenic silkworms was significantly repressed after heat shock, and caused the hamperness of pupal–adult eclosion and reduction of egg fertility. Knockdown of ecdysis-triggering hormone gene BmETH with Gal4/UAS RNAi system leads to lethal ecdysis deficiency in transgenic silkworm. Overexpression of Bmnsd-2 in the midgut of transgenic silkworms restored virus susceptibility of silkworm to B. mori densovirus type 2, a parvo-like virus that replicates only in midgut columnar cells. Overexpression of BmBLOS2 in the whole body of transgenic silkworms partially rescued the translucent phenotype observed in distinct oily (od) mutants, which is characterized by translucent larval integument. Overexpression of the wild-type allele of BmCYP15C1 in corpus allatum of transgenic dimolting (mod) mutants rescued precocious metamorphosis of mod larvae. Overexpression of BmaaNAT in the whole body of transgenic silkworms changed the color of first-instar larvae from black to a distinctive light brown color, and lightened adult antenna coloration. Overexpression of Bmebony in the whole body of transgenic silkworms changed the larval body color of older instars, and lightened adult antenna coloration. Expression of female-specific spliced form of Bmdsx (BmdsxF) in the whole body of transgenic males repressed expression of the pheromone-binding protein gene that is preferentially expressed in males. Expression of Bmdsx minigene in the whole body of transgenic silkworms resulted in sex-specific alternative splicing similar with the pattern of endogenous Bmdsx. Overexpression of BmJHE in the whole body of transgenic silkworms induced premature metamorphosis at the third-instar larvae. Expression of BmKMO in the whole body of transgenic silkworms rescued the phenotypic change observed in the white egg 1 (w-1) mutant, which is characterized by white eyes and white eggs. Overexpression of BmCameo2 in the middle silk gland of transgenic silkworms restored the accumulation of lutein in the middle silk gland, and produced yellowish colored cocoons. Overexpression of BmRas1CA in the posterior silk gland of transgenic silkworms increased cell size and protein synthesis in the posterior silk gland, and improved silk yield. Expression of Bmlipase-1 in the whole body of transgenic silkworms enhanced resistance of silkworms to BmNPV. BmCBP BmKIT3R BmEH BmETH Bmnsd-2 BmBLOS2 BmCYP15C1 BmaaNAT Bmebony BmdsxF Bmdsx minigene BmJHE BmKMO BmCameo2 BmRas1CA Bmlipase-1 References 1 [22] [28] [33] [47] [48] [55] [56] [87*] [88*] [88*] [89*] [90*] [91*] [92*] [93*] [94*] [95*] BmSCRB15 BmBLOS2 Overexpression using Gal4/UAS system Ubiquitous and ectopic expression using B. mori ecdysone receptor B1, BmActin3, and Dmhsp70 promoter Ubiquitous expression using BmActin4 promoter Ectopic expression using B. mori vasa-like promoter Ectopic expression using BmfibL promoter Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Overexpression using Gal4/UAS system Ubiquitous expression using BmActin3 promoter Gene knockout using ZFN Bmwh3 Gene knockout using ZFN BmfibH Gene knockout using ZFN BmBLOS2 Gene knockout using TALEN Bmre Gene knockout using TALEN Bm702 Gene knockout using TALEN Bmdsx Gene knockout using TALEN Bmapontic-like Gene knockout using TALEN BmfibH Gene knockout using TALEN BmWnt1 BmdsxM Bmovo-1 BmcecropinB BmAntp BmCYP18A1 BmLet-7 Bmapontic-like Overexpression of BmSCRB15 in the middle silk gland of transgenic silkworms enhanced selective β-carotene uptake by the middle silk gland, and produced yellowish colored cocoons. Expression of BmWnt1 in the larval stage of transgenic silkworms caused ectopic pigmentation in the larval cuticle as observed in normal mutant, multi lunar (L). [96*] Expression of male-specific spliced form of Bmdsx (BmdsxF) in the whole body of transgenic females affected the formation of the chitin plate in females and reduced female copulation. Expression of Bmovo-1 in the gonad of transgenic silkworms increased oviposition number and elevated the trehalose contents of hemolymph and ovaries. Expression of BmcecropinB in the posterior silk gland of transgenic silkworm enhanced the antibacterial properties of cocoons. Overexpression of BmAntp in the fifth-instar larvae of transgenic silkworms induced ectopic expression of ser1 in the posterior silk gland. Overexpression of BmCYP18A1 in the middle silk gland or in all tissues resulted in developmental arrestment of transgenic animals during the final instar larval stage. Overexpression of microRNA BmLet-7 spongeubiquitously decreased expression of BmLet-7, leading to developmental arrestment during the larvalelarval and larvalepupal transition. Expression of Bmapontic-like in the larval stage of transgenic silkworms induced additional melanin pigmentation in the larval epidermis. Knockout of BmBLOS2 resulted in somatic and germ-line phenotypes similar with the od mutant, which is characterized by translucent larval integument. Knockout of Bmwh3 resulted in somatic phenotypes similar with the Bmwh3 mutant, which is characterized by translucent larval skin and white eggs, but failed to obtain germ-line mutants. Knockout of BmfibH resulted in germ-line mutants, in which the posterior silk gland was strongly degraded and negligible amounts of fibroin was detected. Knockout of BmBLOS2 resulted in somatic and germ-line phenotypes similar with the od mutant, which is characterized by translucent larval integument. Knockout of Bmre resulted in somatic and germ-line phenotypes similar with the red egg mutant, which is characterized by an orange egg color. Comicroinjection of TALEN pairs for Bm702 (an endogenous gene which is 8.9 Mb downstream BmBLOS2) and BmBLOS2 induced heritable large chromosomal structure variation. Knockout of female-specific exon of Bmdsx resulted in somatic mutations and female mutants lost fecundity because of lack of egg storage. Knockout of Bmapontic-like caused white patches in the larval epidermis of marking mutants Striped (pS), which is characterized by solid black larval skin except for the posterior margin of each segment. Knockout of BmfibH resulted in germ-line mutants, in which the posterior silk gland was strongly degraded and negligible amounts of fibroin was detected. [98*] 2 [97*] [99*] [100*] [101*] [102*] [103*] [104*] [66] [66] [68] [73-75,77,105*] [75] [77] [84] [104*] [106*] BmBLOS2 Gene knockout using CRISPR/Cas9 BmKu70 Gene knockout using CRISPR/Cas9 BmTh Gene knockout using CRISPR/Cas9 Bmok Gene knockout using CRISPR/Cas9 BmKMO Gene knockout using CRISPR/Cas9 Bmtan Gene knockout using CRISPR/Cas9 Bmre Gene knockout using CRISPR/Cas9 Bmfl Gene knockout using CRISPR/Cas9 Bmyellow-e Gene knockout using CRISPR/Cas9 BmKynu Gene knockout using CRISPR/Cas9 Bmebony Gene knockout using CRISPR/Cas9 Knockout of BmBLOS2 resulted in somatic and germ-line phenotypes similar with the od mutant, which is characterized by translucent larval integument. Knockout of BmKu70 resulted in germ-line mutants with no significant phenotype, in which the frequency of homologous recombination mediated targeted gene knockin could be enhanced. BmTh gene interruption was effectively induced by the CRISPR/Cas9 system in the injected generation (G0). The phenotype of knockout mutants was not mentioned in the reference. Knockout of Bmok resulted in somatic and germ-line phenotypes similar with the ok mutant, which is characterized by a change in the larval cortex from translucent to turbid. BmKMO gene interruption was effectively induced by the CRISPR/Cas9 system in G0 mosaics. The phenotype of knockout mutants was not mentioned in the reference. Bmtan gene interruption was effectively induced by the CRISPR/Cas9 system in G0 mosaics. The phenotype of knockout mutants was not mentioned in the reference. Bmre gene interruption was effectively induced by the CRISPR/Cas9 system in G0 mosaics. The phenotype of knockout mutants was not mentioned in the reference. Bmfl gene interruption was effectively induced by the CRISPR/Cas9 system in in G0 mosaics. The phenotype of knockout mutants was not mentioned in the reference. Bmyellow-e gene interruption was effectively induced by the CRISPR/Cas9 system in G0 mosaics. 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