Computational protocol: Genome Editing of Wnt-1, a Gene Associated with Segmentation, via CRISPR/Cas9 in the Pine Caterpillar Moth, Dendrolimus punctatus

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Protocol publication

[…] To search for the Wnt-1 homolog, nucleotide sequence of BmWnt-1 (NM_001043850.1) was used as a query to BLAST against a D. punctatus transcriptome (HHL, unpublished data). RACE was used to obtain the full length cDNA of DpWnt-1. The predicted open reading frame (ORF) was subjected to motif search, pattern analysis, and phylogenetic analysis. The MEME online server was used for motif analysis, and parameters were as follows: a minimum width was 6; a maximum width was 12; and a maximum number of motif was 8 (http://meme-suite.org/tools/meme). To understand the phylogenetic relationship of DpWnt-1 with homologs from other animals, a neighbor-joining tree was constructed using MEGA5, http://www.mega-software.net/ (Tamura et al., ). The Wnt-1 ORFs included in the analysis are as follows: B. mori (NM_001043850), H. armigera (KJ206240), Amyelois transitella (XM_013345048), P. xylostella (XM_011569928), M. sexta (Z30280), P. xuthus (XM_013325799), Danio rerio (XP_005162280), Fopius arisanus (XM_011300877), Bombus terrestris (XM_003393116), Nasonia vitripennis (XM_001603338), Bactrocera dorsalis (XM_011204079), Drosophila willistoni (XM_002066877), Drosophila melanogaster (NM_078778), Tribolium castaneum (EFA04660), Periplaneta americana (KC311252), Gryllus bimaculatus (BAB19660), Homo sapiens (NP_005421) and Mus musculus (NP_067254). […]

Pipeline specifications

Software tools MEME, MEME Suite, MEGA
Databases Full Length cDNA
Application Phylogenetics
Organisms Dendrolimus punctatus, Dicentrarchus punctatus
Diseases Musculoskeletal Diseases