GSM3597291: PAP2amp1; Solenopsis invicta; RNA-Seq - SRA

SRX5371517: GSM3597291: PAP2amp1; Solenopsis invicta; RNA-Seq
2 ILLUMINA (Illumina HiSeq 2000) runs: 30.7M spots, 9.3G bases, 4.8Gb downloads

Submitted by: NCBI (GEO)

Study: Worker antennal gene expression in Solenopsis invicta identifies candidate genes for queen discrimination (Nugen_lib_RNA-seq-1)

PRJNA522069 • SRP185783 • All experiments • All runs

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Queen discrimination behavior in the red imported fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. While monogyne workers, all SB/SB, reject all additional queens regardless of genotype. Because the SB and Sb alleles do not recombine, it is difficult to determine which genes within the supergene mediate this differential worker behavior. We hypothesized that the alternate worker genotypes sense queens differently because of different patterns of gene expression in their main sensory organ, the antennae. To identify such differentially expressed genes, we sequenced RNA from four biological replicates of pooled antennae from three groups of workers: monogyne SB/SB, polygyne SB/SB, and polygyne SB/Sb. We identified 81 differentially expressed protein coding genes with 14 encoding potential odor metabolism and perception proteins. We focused on the two differentially expressed odorant perception genes: an odorant binding protein SiOBP12 and an odorant receptor SiOR463. We found that the SiOR463 was lost in the Sb-genome. In contrast, the SiOBP12 has an Sb-specific duplication SiOBP12b', which was expressed in the SB/Sb worker antennae, while both paralogs SiOBP12 and SiOBP12b' were expressed in the body. This result indicates that SiOBP12b' has gained an antennal promoter or enhancer and suggests neofunctionalization, perhaps for queen discrimination behavior. Overall design: Extracted total mRNA of antennae of three worker types: monogyne SB/SB, polygyne SB/SB and polygyne SB/Sb. Four biorelicates were conducted (total 12 samples). RNA samples were amplified using Nugen Ovation v.2 kit and sequenced on the Illumina HiSeq platform with a 150 paired-end protocol. The 12 samples were run on 2 lanes.

Sample: GEO accession GSM3597291 is currently private and is scheduled to be released on Feb 17, 2022.

SAMN10924299 • SRS4361108 • All experiments • All runs

Organism: Solenopsis invicta

Library:

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: We used a droplet of honey to attract workers in the forage area and collected workers of ca. 1.5 cm in length. Workers were decapitated one-by-one on a pre-chilled -20oC metal block sitting on ice. Worker heads were placed individually in 5 ul cold RNAlater ICE (AM7023, ThermoFisher) in a numbered 0.2 ml PCR-tube and temporarily stored in liquid nitrogen. Worker bodies were put in 2 ml tubes containing 50 ul QuickExtract solution (QE09050, Epicenter) and processed for Gp-9 genotyping. The processing of each individual, from sampling to head storage in liquid nitrogen was less than a minute. We sampled 96 individuals/polygyne and 50 individuals/monogyne colony each time. The head samples were stored in a -80oC freezer for subsequent antennae dissection. We sampled polygyne workers until we obtained at least 45 individuals of each genotype. We dissected the antennae of workers of the same genotype on a metal block sitting on ice, under a dissecting microscope (Leica, 20X magnification). We used a clean sheet of Kimwipe tissue to blot away any remaining RNAlater ICE on the samples before placing them into 200 ul cold TRIzol (15596018, Invitrogen). To minimize RNA degradation, we processed at most five heads at once. To minimize cross-sample contamination, we cleaned the metal block and forceps with RNase-Zap after each dissection. Antennae were stored in a -80oC freezer until RNA extraction. We extracted RNA using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch) following a modification of the manufacturer's instructions (Zhang et al. 2013). Frozen antennae in 200 ul Trizol were homogenized using a FastPrep-24 bead homogenizer (MP Biomedicals). Tissue destruction was checked under a microscope. If extra homogenization was required, we re-froze the sample in liquid nitrogen and repeated the homogenization (three times was the maximum needed). After the tissue was completely homogenized, we added an additional 400 ul Trizol into each sample, followed by vortexing for 10 secs and incubation at room temperature for 15 minutes. Samples were then phase separated with 120 ul chloroform. The aqueous phase was kept for RNA purification using the Direct-zol column with on-column DNase I treatment. RNA was eluted once in 25 ul RNase-free water. cDNA was amplified from each RNA samples using the Nugen Ovation V.2 kit (M01206, NuGEN Technologies), following the manufacturer's instructions. follow the manufacturer's instructions of Illumina

Experiment attributes:

GEO Accession: GSM3597291

Links:

NCBI link: NCBI Entrez (gds)

Runs: 2 runs, 30.7M spots, 9.3G bases, 4.8Gb

Run	# of Spots	# of Bases	Size	Published
SRR8570213	15,180,094	4.6G	2.4Gb	2020-04-14
SRR8570214	15,490,567	4.7G	2.4Gb	2020-04-14

ID:: 7262247

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