Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism

Foquet, Bert; Castellanos, Adrian A.; Song, Ho‐Jun

doi:10.1038/s41598-021-91317-w

“…S4: https://doi.org/10.6084/m9.figshare.20174255.v1). The previous studies showed that ebony, Mcm2, and Mcm7 were upregulated in response to crowded condition, and Duox, Mdr49 and Cyp6a14 were downregulated in response to crowded condition (i. e. upregulated in response to isolated condition) [14,33,34]. In this study, CI score of these genes showed high or low values (Figure 1).…”

Section: Gene Set Enrichment Analysissupporting

confidence: 56%

Meta-analysis of transcriptomes in insects showing density-dependent polyphenism

Toga

¹

,

Bono

²

2022

Preprint

5

0

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With increasing public data, a statistical analysis approach called meta-analysis, which combines transcriptome results obtained from multiple studies, has succeeded in providing novel insights into targeted biological processes. Locusts and aphids are representative of insect groups that exhibit density-dependent plasticity. Although the physiological mechanisms underlying density-dependent polyphenism have been identified in aphids and locusts, the underlying molecular mechanisms remain largely unknown. In this study, we performed a meta-analysis of public transcriptomes to gain additional insights into the molecular underpinning of densitydependent plasticity. We collected RNA sequencing data of aphids and locusts from public databases and detected differentially expressed genes (DEGs) between crowded and isolated conditions. Gene set enrichment analysis was performed to reveal the characteristics of the DEGs. DNA replication (GO:0006260), DNA metabolic processes (GO:0006259), and mitotic cell cycle (GO:0000278) were enriched in response to crowded conditions. To date, these processes have scarcely been the focus of research. The importance of the oxidative stress response and neurological system modifications under isolated conditions has been highlighted. These biological processes, clarified by meta-analysis, are thought to play key roles in the regulation of density-dependent plasticity.Simple SummaryPopulation density can be an environmental cue to induce modification of insect morphology, physiology, and behavior. This phenomenon is called density-dependent plasticity. Aphids and locusts exhibit textbook examples of density-dependent plasticity but there is a lack of integrative understanding for insect density-dependent plasticity. To address this problem, we combined public gene expression data obtained from multiple studies and re-analyzed them (this process is called meta-analysis). The present study provides additional insight into the regulatory mechanisms of density-dependent plasticity, demonstrating the effectiveness of metaanalyses of public transcriptomes.

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“…Consequently, 66 pairs of transcriptome data were collected from the public databases ( Table 1 ). Full information about the dataset used in this study is provided in Table S2 [ 10 , 31 , 32 , 33 , 34 , 35 ]. These data comprised transcriptomes from seven insect species, including aphids and locusts.…”

Section: Resultsmentioning

confidence: 99%

“…CI scores were calculated based on the CI ratio table ( Table S4 ). The previous studies showed that ebony , Mcm2 , and Mcm7 were upregulated in response to crowded condition, and Duox , Mdr49 and Cyp6a14 were downregulated in response to crowded condition (i.e., upregulated in response to isolated condition) [ 14 , 33 , 34 ]. In this study, the CI score of these genes showed high or low values ( Figure 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…This means that the expression patterns of these genes were consistent with previous results. Previous transcriptome analyses also showed that GO:0008061 [cuticle binding] and GO:0006979 [oxidative stress] were enriched in crowded and isolated condition, respectively [ 14 , 33 , 34 ]. CI score of genes that was included in these GO terms (GO:0008061; obst-E , GO:0006979; spz , Glaz , srl ) showed high or low values ( Figure 1 ).…”

Section: Resultsmentioning

confidence: 99%

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Meta-Analysis of Transcriptomes in Insects Showing Density-Dependent Polyphenism

Toga

¹

,

Yokoi

²

,

Bono

³

2022

Insects

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With increasing public data, a statistical analysis approach called meta-analysis, which combines transcriptome results obtained from multiple studies, has succeeded in providing novel insights into targeted biological processes. Locusts and aphids are representative of insect groups that exhibit density-dependent plasticity. Although the physiological mechanisms underlying density-dependent polyphenism have been identified in aphids and locusts, the underlying molecular mechanisms remain largely unknown. In this study, we performed a meta-analysis of public transcriptomes to gain additional insights into the molecular underpinning of density-dependent plasticity. We collected RNA sequencing data of aphids and locusts from public databases and detected differentially expressed genes (DEGs) between crowded and isolated conditions. Gene set enrichment analysis was performed to reveal the characteristics of the DEGs. DNA replication (GO:0006260), DNA metabolic processes (GO:0006259), and mitotic cell cycle (GO:0000278) were enriched in response to crowded conditions. To date, these processes have scarcely been the focus of research. The importance of the oxidative stress response and neurological system modifications under isolated conditions has been highlighted. These biological processes, clarified by meta-analysis, are thought to play key roles in the regulation of density-dependent plasticity.

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“…The assembled de novo unigenes were obtained, which were the encoding sequences. The redundancy was filtered using the Cd-hit-EST (Foquet et al, 2021). The Transrate (v1.0.3) was used to map reads to contigs and inspect the alignments (Marx et al, 2021).…”

Section: De Novo Assembly and Annotationmentioning

confidence: 99%

Comparative transcriptomics analyses of chemosensory genes of antenna in male red swamp crayfish Procambarus clarkii

Zhou

¹

,

Mo

²

,

Li

³

et al. 2022

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The red swamp crayfish, Procambarus clarkii, is a globally invasive species and has caused huge damage to aquaculture, biodiversity, and ecology worldwide. Antenna-expressed receptors are important for P. clarkii to detect chemosensory cues for mate attraction. In this study, we tested the behavior of male P. clarkii to the conditioned water from female P. clarkii during the mating and non-mating periods, and performed RNA sequencing to investigate the chemosensory-related genes of the antenna of male P. clarkii. The results of the behavioral assay have shown that for the female-conditioned water, male P. clarkii within the mating period can be significantly attracted, but not during the non-mating period. This suggested that the expressions of chemosensory-related genes in the antenna of male P. clarkii may change significantly with mating seasonal variation. Antenna transcriptomes found that a total of 59,218 unigenes with an average length of 1,056.41 bp, and 4,889 differentially expressed unigenes (DEGs), among which 2,128 were upregulated, while 2,761 were downregulated were obtained. A total of 12 upregulated and nine downregulated DEGs were associated with chemical reception, including four ionotropic receptors (IRs) or ionotropic glutamate receptors (iGluRs), eight G-protein-coupled receptors (GPCRs), five transient receptor potential channels (TRP channels), one sodium–calcium exchanger, one isomerase, and two uncharacterized proteins (chemosensory proteins-like, CSPs). CSPs were preliminarily classified as pheromone receptors in the antenna of male P. clarkii. Furthermore, the calcium transduction-related pathways may play an important role in the sex pheromone reception of the male P. clarkii’s antenna. The results of quantitative real-time reverse transcriptase PCR (RT-qPCR) showed that the trends of expression of eight selected unigenes were consistent with RNA-Seq results. Our results provide more comprehensive data for chemical communication mechanisms after P. clarkii enter the mating period and eventually would develop better control strategies in further.

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Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism

Cited by 20 publications

References 102 publications

Meta-analysis of transcriptomes in insects showing density-dependent polyphenism

Meta-analysis of transcriptomes in insects showing density-dependent polyphenism

Meta-Analysis of Transcriptomes in Insects Showing Density-Dependent Polyphenism

Comparative transcriptomics analyses of chemosensory genes of antenna in male red swamp crayfish Procambarus clarkii

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