Insect rearing
The B. dorsalis strain is reared under laboratory condition (27 ± 1°C, 12:12 h light:dark cycle, 70–80% RH). The larva is fed by a maize-based artificial diet containing 150 g of corn flour, 150 g of banana, 0.6 g of sodium benzoate, 30 g of yeast, 30 g of sucrose, 30 g of paper towel, 1.2 mL of hydrochloric acid and 300 mL of water. The adult is manually fed by solid diet (consisting of 50 g yeast hydrolysate and 50 g sucrose) and sterile water in daily.
Recording of female mating frequency at various time intervals throughout the day
To record the mating numbers of mature females (15 days old) at different time of day, 15 mature males and 15 mature females were placed in a 35× 35×35 cm wooden cage. The day was divided into three observation periods (0:00–8:00, 8:00–16:00, 16:00–24:00), and the number of mated females during each period was recorded individually. Five replicate cages were observed for each time period.
Females attracted by sex pheromone at different time periods in a day
The attractiveness of sex pheromones (TMP and TTMP) to mature females was assessed at various time intervals throughout the day. Briefly, 100 ml of TMP and TTMP, diluted in ethanol (TMP: 2 mg/mL, TTMP: 1 mg/mL), were placed in traps made of transparent plastic vials (20 x 6 cm) sealed with a yellow lid featuring small entrances for fly entry. The attraction assay was conducted in a test chamber assembled with a ventilated lid-covered plastic cylinder (120 x 30 cm). The day was divided into three observation periods (0:00–8:00, 8:00–16:00, 16:00–24:00), and the number of females trapped by the sex pheromone during each period was recorded separately. Eight replicates were recorded for each period.
EAG response recording
EAG analysis was conducted to assess the electrogram responses in the antenna of mature females exposed to TMP and TTMP. For EAG preparations, the antenna of a female was excised and positioned between two glass electrodes (with one electrode connected to the antenna tip). The antenna tip was gently trimmed to facilitate electrical contact. Diluted solutions of TMP and/or TTMP in ethanol were utilized as stimulants. Ten microliters of sex pheromone (TMP: 2 mg/mL, TTMP: 1 mg/mL) were applied onto the filter paper, which was then positioned near the air inlet and stimulated five times. The signals from the antennae were analyzed using GC-EAD 2014 software (version 4.6, Syntech).
Transcriptome sequencing and gene identification
To identify the clock and olfactory genes that contribute to female mating preference, the female RNA-seq was done for mature female head at different time periods in a day (0:00, 4:00, 8:00, 12:00, 16:00, 20:00). Five replicate samples were prepared for each period, with five heads dissected for RNA extraction per sample. Subsequently, paired-end RNA-seq libraries were prepared and sequenced on an Illumina HiSeq2000 platform. Briefly, raw reads were generated in FASTQ format and sorted by barcodes for further analysis. Prior to assembly, preprocessing of paired-end raw reads from each cDNA library was conducted to remove adapters, low-quality sequences (Q < 20), and reads contaminated with microbial sequences. Clean reads were then de novo assembled to produce contigs. An index of the reference genome of B. dorsalis was constructed, and paired-end clean reads were mapped to the reference genome using HISAT2 2.4 with parameters including '-rna-strandness RF' and defaults. StringTie software was utilized to calculate normalized gene expression values (FPKM) for evaluating transcript expression abundances. Subsequently, gene differential expression analysis was performed using DESeq2 software. Genes/transcripts with a false discovery rate (FDR) below 0.01 and absolute fold change ≥ 2 were considered DEGs. Principal component analysis (PCA) was conducted using the R package gmodels to elucidate the structure/relationship of the samples. Pathway enrichment analysis was carried out to identify clock genes in circadian rhythm pathway. Expression validation of candidate genes by qRT-PCR
qRT-PCR analysis was used to validate gene expression in antenna and other tissues. Total RNA in the tissues of mature female was extracted using TRIzol reagent. Subsequently, cDNA synthesis was conducted utilizing the One-Step gDNA Removal and cDNA Synthesis SuperMix Kit (TransGen Biotech, Beijing, China). qRT-PCR was then performed using the PerfectStarTM Green qPCR SuperMix Kit (TransGen Biotech, Beijing, China) to assess gene expression levels. Gene-specific primers for the target genes were designed via primer blast on the NCBI website (Table S2). The α-tubulin and actin genes were utilized as reference genes39. PCR procedures were conducted following the manufacturer's instructions.
Phylogenetic sequence analysis
Phylogenetic analysis was conducted using amino acid sequence alignments for Obp sequences identified from insect genomes. Obp amino acid sequence analyses were performed with MEGA11, and maximum likelihood (ML) tree reconstruction was performed using the Poisson model and uniform rates. The ML heuristic search was performed with the nearest neighbor-change method, and the initial tree was selected by applying the neighbor-joining method to a matrix of pairwise distances estimated using the JTT method. The accuracy of the tree was tested with bootstrapping using 100 replicates. The conservation of the Obp proteins was determined using the WebLogo tool (https://weblogo.berkeley.edu/logo.cgi).
RNA interference
Double-stranded RNA (dsRNA) primers, containing the T7 promoter sequence, were designed utilizing the coding sequences (CDSs) of the target genes as templates (Table S2). The MEGAscript RNAi Kit (Thermo Fisher Scientific, United States) was employed for the synthesis and purification of dsRNA following the manufacturer's instructions. The GFP gene (GenBank accession number: AHE38523) served as the RNAi negative control. To induce knockdown effect to the target genes, 0.5 µL dsRNA (1000ng/µL) was injected into the abdomen. The knockdown efficiency of the genes was assessed using qRT-PCR 24h after dsRNA injection. Besides, the survival rate of 30 dsRNA injected females was also recorded.
Mating competition assay
Mating competition assays between females with different treatments were conducted in a wooden cage (35 cm×35 cm×35 cm). Briefly, pronota of females injected with dsRNA of Obp99a (Pbp5) and GFP were colored with different colors. Then 30 females injected dsRNA of Obp99a (Pbp5) and 30 females injected dsRNA of GFP were introduced into the wooden cage, in which 30 mature unmated males were placed. Then the mated female number was recorded during 20:00 to 22:00. Each assay was replicated five times.
For mating ability comparison between female with changed biological clocks and the controls. The same assays were done as the above methods.
Binding ability of Pbp5 to TMP and TTMP
The recombinant Pbp5 protein was primarily obtained through in vitro expression in Escherichia coli Rosetta (DE3) cells, following a previously established protocol40. In brief, PCR primers with restriction sites were designed according to the CDS of Pbp5. Subsequently, PCR products were purified and ligated to the pet-sumo prokaryotic expression vector. The resulting vector was then transformed into Escherichia coli Rosetta (DE3) cells for expression. Positive clones were selected based on kanamycin resistance, and their sequences were confirmed through sequencing to ensure the correct sequence. Verified clones were cultured in LB medium supplemented with kanamycin at 37℃ for 16 hours. Subsequently, 100 ml of bacterial culture was inoculated into LB medium containing 0.1 mM IPTG and incubated at 18℃ for 8 hours. The bacteria were then harvested by centrifugation at 8000 rpm and resuspended in lysis buffer (80 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, 4% glycerol, pH 7.2, 0.5 mM PMSF). Sonication (3 s, five passes) was performed to lyse the bacterial cells. The recombinant proteins present in the supernatant were collected by centrifugation. Subsequently, the proteins were purified by two rounds of anion-exchange chromatography and concentrated using an ultrafiltration cube. The purity of the purified recombinant proteins was confirmed by SDS-PAGE analysis.
The fluorescence binding assay using 1-NPN with Pbp was conducted on a Microplate Reader (ThermoScientific Varioskan LUX), following a method previously described in locust studies41. The excitation wavelength was set at 337 nm, and the emission wavelength was set at 380–520 nm. Pbp (2 µM dissolved in 50 mM Tris-HCl, pH = 7.4) was mixed with 1-NPN (2 µM-16 µM dissolved in chromatographic methanol), and the maximum fluorescence intensity was recorded. The dissociation constant of 1-NPN binding to Pbp was calculated using the one-site specific binding method in GraphPad 8.0 software. Subsequently, dissociation constants for Pbp5 were determined. For competitive binding assays, TMP and TTMP (0, 4, 8, 12, 16 µM dissolved in chromatographic methanol) were used as competitors to bind Pbp in the Pbp/1-NPN complex.
Protein-ligand docking simulation
After homologous protein modeling was conducted using the Swiss-Model software, models with high scores were selected for subsequent model validation. The quality of the Pbp5 model was assessed by Verify-3D, and ERRAT, within the SAVES V7.0 software42. TMP and TTMP models were downloaded from the NCBI website. Protein-ligand docking simulations were performed using Autodock Vina. The binding result with the lowest binding energy was selected, processed using PyMOL, and further analyzed and visualized using ProteinPlus and Protein-Ligand Interaction Profiler.
Data analysis
Statistical analysis methods used in the study were indicated in the figure legends. Differences were considered significant when P < 0.05. All data were analyzed using the GraphPad Prism version 10, GraphPad Software, La Jolla, CA, USA, https://www.graphpad.com/.