Table 1.

Unique PgABCA2 transcript variants and cDNA mutations in Cry2Ab-resistant pink bollworm from Arizona.

Varianta	Sourceb	cDNA mutationc	Codond	Exone	Mis-splicingf	Typeg	Effecth
Bt4-R2a	Bt4-R2	c.3556_3588delinsi	1186	20	complete intron 20 retention	fs	stop at 1220
Bt4-R2b	Bt4-R2	c.3556_3589_delinsi	1186	20	alternative 5′ splice site in intron 20	fs	stop at 1275
Bt4-R2c	Bt4-R2	c.3419_3589delinsTAA	1140–1197	20	alternative 5′ splice site in intron 19 and exon 20 skip	InF	In-frame indel
Bt4-R2d	Bt4-R2	c.3419_3590del	1140	20	exon 20 skip	fs	stop at 1147
Bt4-R2e	H-5	c.3556_3734delinsi	1186	20–22	alternative 5′ splice site in intron 20, exon 21 skip, and alternative 3′ splice site in exon 22	fs	stop at 1291
Bt4-R2f	J-3	c.3419_4093del	1140–1364	20–24	exon 20–23 skip and alternative 3′ splice site in exon 24	InF	In-frame indel
Bt4-R2g	H-5	c.3313_3589del	1105	19–20	exon 19–20 skip	fs	stop at 1112
Bt4-R2h	H-1	c.1090_1234del	364	6	exon 6 skip	fs	stop at 373
		c.3313_3589del	1105	19–20	exon 19–20 skip	fs	stop at 1112
Bt4-R2i	G-2	c.1090_1234del	364	6	exon 6 skip	fs	stop at 373
		c.3419_3590del	1140	20	exon 20 skip	fs	stop at 1147

^aTranscript variant names include the strain (Bt4-R2) followed by a lower-case letter designating the specific transcript variant. Only unique transcript variants are shown. Bt4-R2a-d transcript variants are from cloning and Sanger sequencing. Bt4-R2e-i transcript variants are from PacBio® targeted sequencing of r_A1r_A1 backcross survivors from genetic linkage crosses. ^bBt4-R2a-d were identified from a pool of 10 larvae from Bt4-R2; for Bt4-R2e-i, the backcross family name is listed for each of the individual larvae analyzed that had survived exposure to Cry2Ab in the linkage analysis (Supplementary Table S2). ^ccDNA mutation nomenclature is based on the recommendations by the Human Genome Variation Society (http://www.hgvs.org/). ^dCodon number beginning from the initiation codon and indicating disrupted position within the coding sequence. ^eDisrupted exon within the coding sequence. ^fEvent causing mis-spliced transcripts (complete intron retention, alternative 5′- or 3′-splice sites, and/or exon skip). ^gType of mutation (fs, frame shift; InF, In-frame mutation). ^hResult and codon position of mutation in the coding sequence (introduction of premature stop codon or In-frame indel). ⁱActual sequences corresponding to insertions not shown here due to large number of nucleotide bases.