Predatory fireflies and their toxic firefly prey have evolved distinct toxin resistance strategies

. Author manuscript; available in PMC: 2024 Dec 4.

Published in final edited form as: Curr Biol. 2023 Nov 20;33(23):5160–5168.e7. doi: 10.1016/j.cub.2023.10.063

Key Resources Table

REAGENT or RESOURCE	SOURCE	IDENTIFIER

Chemicals, peptides, and recombinant proteins
RNAlater	Invitrogen^™	AM7020
TRIzol	Ambion, Life Technologies	15596018
Phusion High-Fidelity DNA Polymerase	Thermo Fisher Scientific	F530
Taq polymerase	New England Biolabs	M0273
Ouabain octahydrate	Sigma-Aldrich	Cat# O-3125
Nutri-fly Instant media	Flystuff	66-117

Critical commercial assays
TruSeq RNA Library Prep Kit v2	Illumina	RS-122-2001
TruSeq Stranded mRNA	Illumina	20020594
QIAquick PCR Purification Kit	Qiagen	28104
MEGAscript^™ T7 Transcription Kit	Invitrogen^™	AMB13345
Quick-change Lightning site-directed mutagenesis kit	Agilent	210518

Deposited data
RNAseq data for firefly tissues	This study	PRJNA891306, PRJNA922528, PRJNA891248
ATPα1 coding sequences	This study	MT897473.1 to MT897482.1

Experimental models: Organisms/strains
Drosophila melanogaster injection strain	Well Genetics	w1118
Drosophila melanogaster injection strain with germline Cas9 expression	Well Genetics	w1118; attP40{nos-Cas9} / CyO
Drosophila melanogaster w[*];;TM6B, Tb[1] / TM2, y+	Well Genetics	w[*];;TM6B, Tb[1] / TM2, y+
Drosophila melanogaster w[*]; CyO, P{Tub-PBac}/ Sp; +/TM6B	Bloomington Drosophila Stock Center	Bloomington #8285
Drosophila melanogaster w[*]; TM3, Sb[1] Ser[1]/TM6B, Tb[1]	Bloomington Drosophila Stock Center	Bloomington #2537
Drosophila melanogaster y1, w67c23, P{y[+mDint2]=Crey}1b;; D*/TM3, Sb1	Bloomington Drosophila Stock Center	Bloomington #851
Drosophila melanogaster w*;;ry506 Dr1/TM6B, P{w[+mC]=Dfd-EYFP}3, Sb1,Tb1,ca1	Bloomington Drosophila Stock Center	Bloomington #8704
Drosophila melanogaster A119I	This study	A119I
Drosophila melanogaster Y108F-Q111E-A112S-S115L-E117T-A119N-D120N	This study	FESLTNN
Drosophila melanogaster Q111E-A112S-A119I-D120A/TM6,Tb	This study	ESIA/TM6,Tb
Drosophila melanogaster T797I/TM6,EYFP	This study	T797I/TM6,EYFP
Drosophila melanogaster F786Y	This study	F786Y
Drosophila melanogaster I787M	This study	I787M
Drosophila melanogaster founder strain for targeted editing	Taverner et al. ²³	w1118;;ATPαΔ2-6b attP/TM6B,Tb1
Drosophila melanogaster Q111E	This study	Q111E
Drosophila melanogaster A112S	This study	A112S
Drosophila melanogaster A119N	This study	A119N
Drosophila melanogaster Q111E+A112S	This study	ES
Drosophila melanogaster Q111E+A112S+A119N	This study	ESN

Oligonucleotides
Forward PCR primer Photuris versicolor ATPα paralog A	This study	Ptu_ver_AF: CGCTGACTTTGATTCATCCCCAGT
Reverse PCR primer Photuris versicolor ATPα paralog A	This study	Ptu_ver_AR: TTGGCAGTGCGCATCATTCT
Forward PCR primer Photuris versicolor ATPα paralog B	This study	Ptu_ver_BF: TCGGAGTTTGGCCGTACAGA
Reverse PCR primer Photuris versicolor ATPα paralog B	This study	Ptu_ver_BR: TTGGTCAGTGAACGGCAGTG
Forward PCR primer Photuris versicolor ATPα paralog C	This study	Ptu_ver_CF: TCGACTTCAGGATTTGTTGACGG
Reverse PCR primer Photuris versicolor ATPα paralog C	This study	Ptu_ver_CR: TGGCAGTACGCACCATTCAC
Forward PCR primer Photuris versicolor ATPα paralog D	This study	Ptu_ver_DF: CGTTCAGACTCATACCGTGTAGC
Reverse PCR primer Photuris versicolor ATPα paralog D	This study	Ptu_ver_DR: TGAACTCATCCGTAACCATGCAG
CRISPR reagents	This study	See Table S3

Recombinant DNA
TOPO TA-cloning vector	Invitrogen	K457502
Expression vector containing a U6 promoter	Well genetics	pBFv-U6.2
Expression vector for germline Cas9 expression	Well genetics	pBFv-nosP-Cas9
Plasmid donor template for A119I	This study	pUC57-Kan-A119I-pBacDsRed
Plasmid donor template for “ESIA”	This study	pUC57-Kan-Q111E-A112S-A119I-D120A-pBacDsRed
Plasmid donor template for “FESSLTN”	This study	pUC57-Kan-Y108F-Q111E-A112S-S115L-E117T-A119N-D120N-pBacDsRed
Plasmid donor template for T797I	This study	pUC57-Kan-T797I-pBacDsRed
Vector for targeted editing of exons 2-6 of ATPα	Taverner et al. ²³	pGX-attB-ATPαΔ2-6b

Software and algorithms
TQSfastq.py	Howard Hughes Medical Institute	https://github.com/JaneliaSciComp/msg/blob/master/TQSfastq.py
trim_galore		https://github.com/FelixKrueger/TrimGalore
cutadapt	Martin ⁶³	https://cutadapt.readthedocs.io/
Trinity	Haas et al. ⁶⁴	https://github.com/trinityrnaseq/trinityrnaseq/wiki
Picard	Broad Institute	https://broadinstitute.github.io/picard/
Velvet	Zerbino and Birney ⁵³	https://github.com/dzerbino/velvet
Oases	Schulz et al. ⁵⁴	https://github.com/dzerbino/oases
SeaView	Gouy et al. ⁵⁵	https://doua.prabi.fr/software/seaview
Samtools	Li et al ⁵⁸	https://github.com/samtools/samtools
BLAST	NCBI	https://blast.ncbi.nlm.nih.gov/Blast.cgi
MUSCLE	EMBL-EBI	https://www.ebi.ac.uk/Tools/msa/muscle/
Gatk3	Broad Institute	https://gatk.broadinstitute.org/hc/en-us
Geneious prime	Domatics	https://www.geneious.com/
PhyML	ATGC Montpellier	http://www.atgc-montpellier.fr/phyml/
PAML	Yang ⁵⁶	http://abacus.gene.ucl.ac.uk/software/paml.html
gmod_fasta2gff3.pl		(https://github.com/GMOD/Chado/).
htseq-count	Putri et al. ⁶⁵	https://htseq.readthedocs.io/en/master/index.html
Deseq2 R package	Love et al. ⁵⁹	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Minipack.lm R package		https://cran.r-project.org/web/packages/minpack.lm/index.html
Variant calling scripts		https://github.com/YourePrettyGood/PseudoreferencePipeline
bwa mem	Yang ⁵⁷	https://janis.readthedocs.io/en/latest/tools/bioinformatics/bwa/bwamem.html