Mori T et al. (2015), Gene expression profiles in Rana pirica tadpole...

XB-ART-50594

BMC Genomics 2015 Apr 02;16:258. doi: 10.1186/s12864-015-1389-4.

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Gene expression profiles in Rana pirica tadpoles following exposure to a predation threat.

Mori T , Yanagisawa Y , Kitani Y , Sugiyama M , Kishida O , Nishimura K .

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BACKGROUND: Rana pirica tadpoles show morphological changes in response to a predation threat: larvae of the dragonfly Aeshna nigroflava induce heightened tail depth, whereas larval salamander Hynobius retardatus induce a bulgy morphology with heightened tail depth. Although both predators induce similar tail morphologies, it is possible that there are functional differences between these tail morphs. RESULTS: Here, we performed a discriminant microarray analysis using Xenopus laevis genome arrays to compare tail tissues of control and predator-exposed tadpoles. We identified 9 genes showing large-scale changes in their expression profile: ELAV-like1, methyltransferase like 7A, dolichyl-phosphate mannosyltransferase, laminin subunit beta-1, gremlin 1, BCL6 corepressor-like 1, and three genes of unknown identity. A further 80 genes showed greater than 5 fold differences in expression after exposure to dragonfly larvae and 81 genes showed altered expression after exposure to larval salamanders. Predation-threat responsive genes were identified by selecting genes that reverted to control levels of expression following removal of the predator. Thirteen genes were induced specifically by dragonfly larvae, nine others were salamander-specific, and sixteen were induced by both. Functional analyses indicated that some of the genes induced by dragonfly larvae caused an increase in laminins necessary for cell adhesion in the extracellular matrix. The higher expression of gremlin 1 and HIF1a genes after exposure to dragonfly larvae indicated an in vivo hypoxic reaction, while down-regulation of syndecan-2 may indicate impairment of angiogenesis. Exposure to larval salamanders caused down-regulation of XCIRP-1, which is known to inhibit expression of adhesion molecules; the tadpoles showed reduced expression of cα(E)-catenin, small muscle protein, dystrophin, and myosin light chain genes. CONCLUSION: The connective tissue of tadpoles exposed to larval salamanders may be looser. The differences in gene expression profiles induced by the two predators suggest that there are functional differences between the altered tail tissues of the two groups of tadpoles.

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Species referenced: Xenopus laevis
Genes referenced: bcl6 cirbp dmd.2 grem1 hif1a

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	Figure 1. Experimental design showing control, continuous exposure treatment to dragonfly larvae or larval salamanders, and removal of the predation threat to allow the tadpoles to recover. These five treatment groups were used to produce the RNAs used in the microarray analysis with the Xenopus genome array. In the group with continuous exposure to predators (Drago or Salam), the tadpoles were under predation threat for the full 8 days. In the groups exposed for a limited period and then allowed to recover (âDrago or âSalam), tadpoles were initially kept with dragonfly larvae or larval salamanders for 4 days to produce the predator-induced phenotype; after 4 days, the predation threat was removed and the tadpoles were allowed to revert to their normal phenotype for 4 days. The control group of tadpoles was not exposed to a predation threat. Four replicate groups were used for each treatment; tadpoles were sampled on day 8. Tail tissues from the tadpoles were used for RNA extraction for the microarray analysis. The microarray analysis was performed in triplicate. Abbreviations: Cont, control; Drago, 8 day dragonfly exposure; Salam, 8 day salamander exposure; âDrago, 4 day exposure to dragonfly threat and 4 day recovery; âSalam, 4 day exposure to salamander threat and 4 day recovery.
	Figure 2. Discriminant analysis using Xenopus genome array. (a) Success of hybridization was checked using control genes spotted on the Xenopus genome array. AFFX-BioB to AFFX-r2-P1-cre are internal positive controls of Xenopus genome array. The analysis was performed using array chips that were hybridized using the same conditions. (b) The territorial map based on canonical discriminant functions.
	Figure 3. The nine genes selected by discriminant analysis. (a) The hierarchical clustering of the nine genes was created using single linkage with Euclidean distance. Numbers 1â3 indicate array chip number. Abbreviations as in FigureÂ 1. (b) Averaged gene expression profile obtained by the discriminant analysis.
	Figure 4. Pathway analysis of nine genes selected by discriminant analysis.
	Figure 5. Screening of predator-induced genes showing a greater than 5 fold difference compared to control. The selected genes are depicted by volcano plotting, and the threshold change for gene screening was set as âmore than 5 fold change compared to controlâ. In total, 316 and 301 genes respectively were identified as induced by dragonfly larvae (a) and larval salamanders (b). Fold change is expressed as log2X in the X axis.
	Figure 6. Hierarchical clustering of 80 known genes showing greater than 5 fold difference compared to control that were induced by dragonfly larvae, and selection of dragonfly specific genes. (a) Expression profiles of the genes using hierarchical clustering by single linkage with Euclidean distance. (b) Expression profiles of the 80 genes and (c) procedure used for selection of predation-threat responsive genes. Genes enclosed by pink boxes are dragonfly-specific, and those enclosed in green boxes are those commonly observed after the salamander treatment.
	Figure 7. Hierarchical clustering of 81 known genes showing greater than 5 fold difference to control that were induced by larval salamanders, and the selection of salamander-specific genes. (a) Expression profiles of the genes using hierarchical clustering by single linkage with Euclidean distance. (b) Expression profiles of the 81 genes and (c) procedure for selection of predation-threat responsive genes. Genes surrounded by blue boxes are salamander-specific and genes surrounded by green boxes are commonly observed after the dragonfly treatment.
	Figure 8. Hierarchical clustering analysis of common and specific genes induced by predators. Expression profiles of common and specific genes are depicted by hierarchical clustering using single linkage with Euclidean distance for the five treatment groups. (a) Commonly expressed genes selected as showing greater than 5 fold difference to control. The numbers in the gene title (from left to right) in common genes indicate dragonfly and salamander, respectively. (b) Salamander specific genes. The numbers in the gene title (from left to right) indicate salamander and dragonfly, respectively. (c) Dragonfly specific genes. The numbers in the gene title (from left to right) indicate dragonfly and salamander, respectively.

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