De novo comparative transcriptome analysis of a rare cicada, with identification of candidate genes related to adaptation to a novel host plant and drier habitats

Abstract

Background: Although the importance of host plant chemistry in plant-insect interactions is widely recognized, our understanding about the genetic basis underlying the relationship between changes in midgut proteins and adaptation of plant-feeding insects to novel host plants and habitats is very limited. To address this knowledge gap, the transcriptional profiles of midguts among three populations of the cicada Subpsaltria yangi Chen were compared. Among which, the Hancheng (HC) and Fengxiang (FX) populations occurring in the Loess Plateau feed on Ziziphus jujuba Mill. var. spinosa (Bunge) Hu ex H. F. Chow, while the population occurring in a much drier habitat in the Helan (HL) Mountains is locally specialized on a chemically divergent plant, Ephedra lepidosperma C. Y. Cheng.

Results: Based on comparative analysis, 1826 (HL vs HC) differentially expressed genes (DEGs) and 723 DEGs (HL vs FX) were identified between the populations utilizing different host plants, including 20, 36, 2, 5 and 2 genes related to digestion, detoxification, oxidation-reduction, stress response and water-deprivation response, respectively, and 35 genes presumably associated with osmoregulation. However, only 183 DEGs were identified between the HC and FX populations, including two genes related to detoxification, two genes related to stress response, and one gene presumably associated with osmoregulation. These results suggest that the weakest expression differences were between the populations utilizing the same host plant and occurring in the closest habitats, which may help explain the metabolic mechanism of adaptation in S. yangi populations to novel host plants and new niches.

Conclusions: The observed differences in gene expression among S. yangi populations are consistent with the hypothesis that the host plant shift and habitat adaptation in the HL population was facilitated by differential regulation of genes related to digestion, detoxification, oxidation-reduction, stress response, water-deprivation response and osmoregulation. The results may inform future studies on the molecular mechanisms underlying the relationship between changes in midgut proteins and adaptation of herbivorous insects to novel host plants and new niches.

Keywords: Cicadidae; Host adaptation; Host shift; Midgut; Plasticity; RNA-Seq; Transcriptional variation.

Fig. 1

Host plants of Subpsaltria yangi. a A S. yangi feeding on Ziziphus jujuba var. spinosa. b A S. yangi feeding on Ephedra lepidosperma. Both taken by Z. Hou

Fig. 2

Distribution of SSR motifs. The different color bars represent different repeat types (repeat number ranges of SSR motif unit)

Fig. 3

Analysis of DEGs expression among the three populations of S. yangi. a The number of common and unique unigenes express among the three populations. b The number of significantly up- and down-regulated unigenes between two compared populations. FX: the population occurring in Fengxiang; HC: the population occurring in Hancheng; HL: the population occurring in the Helan Mountains

Fig. 4

Heatmap of normalized FPKM of DEGs related to digestion. The Z-score represents the deviation from the mean by standard deviation units. Red color indicates up-regulated expression, whereas green color indicates down-regulated expression. FPKM: fragments per kilobase of transcript per million fragments mapped; FX: the population occurring in Fengxiang; HC: the population occurring in Hancheng; HL: the population occurring in the Helan Mountains

Fig. 5

Heatmap of normalized FPKM of DEGs related to detoxification and oxidation-reduction. The Z-score represents the deviation from the mean by standard deviation units. Red color indicates up-regulated expression, whereas green color indicates down-regulated expression. FPKM: fragments per kilobase of transcript per million fragments mapped; FX: the population occurring in Fengxiang; HC: the population occurring in Hancheng; HL: the population occurring in the Helan Mountains

Fig. 6

Heatmap of normalized FPKM of DEGs related to stress response, water-deprivation response and putative osmoregulation. The Z-score represents the deviation from the mean by standard deviation units. Red color indicates up-regulated expression, whereas green color indicates down-regulated expression. FPKM: fragments per kilobase of transcript per million fragments mapped; FX: the population occurring in Fengxiang; HC: the population occurring in Hancheng; HL: the population occurring in the Helan Mountains

Fig. 7

Gene expression levels of differentially expressed genes through RNA-seq and qRT-PCR analysis. FPKM: fragments per kilobase of transcript per million fragments mapped; FX: the population occurring in Fengxiang; HC: the population occurring in Hancheng; HL: the population occurring in the Helan Mountains