Data from: Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish
| Main Authors: | Gunter, Helen M., Fan, Shaohua, Xiong, Fan, Franchini, Paolo, Fruciano, Carmelo, Meyer, Axel |
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| Format: | info dataset Journal |
| Terbitan: |
, 2013
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4978554 |
Daftar Isi:
- Adaptive phenotypic plasticity, the ability of an organism to change its phenotype to match local environments, is increasingly recognized for its contribution to evolution. However, few empirical studies have explored the molecular basis of plastic traits. The East African cichlid fish Astatoreochromis alluaudi displays adaptive phenotypic plasticity in its pharyngeal jaw apparatus, a structure that is widely seen as an evolutionary key innovation that has contributed to the remarkable diversity of cichlid fishes. It has previously been shown that in response to different diets, the pharyngeal jaws change their size, shape and dentition: hard diets induce an adaptive robust molariform tooth phenotype with short jaws and strong internal bone structures, while soft diets induce a gracile papilliform tooth phenotype with elongated jaws and slender internal bone structures. To gain insight into the molecular underpinnings of these adaptations and enable future investigations of the role that phenotypic plasticity plays during the formation of adaptive radiations, the transcriptomes of the two divergent jaw phenotypes were examined. Our study identified a total of 187 genes whose expression differs in response to hard and soft diets, including immediate early genes, extracellular matrix genes and inflammatory factors. Transcriptome results are interpreted in light of expression of candidate genes—markers for tooth size and shape, bone cells and mechanically sensitive pathways. This study opens up new avenues of research at new levels of biological organization into the roles of phenotypic plasticity during speciation and radiation of cichlid fishes.
- geometric morphometric landmarks of A_alluaudi LPJsThis file contains x and y co-ordinates of A. alluaudi lower pharyngeal jaws (LPJ) used in geometric morphometrics analyses, and calculations of area and centroid size (Figure 3a-c, Table S3). Co-ordinates are in millimeter scale, as set using the 'scale' function in ImageJ. Specimen names correspond those assigned in Table S1.geometric morphometrics data.txtlinear morphometric measurements of A_alluaudi LPJsThis file describes the linear measurements, and weight measurements made of lower pharyngeal jaws (LPJ), and standard lengths of the A. alluaudi specimens, as used in statistical analyses of LPJ size (Figure 3a-b, Table S3). Linear measurements are in mm and weight measurements are in mg. Specimen names correspond those assigned in Table S1.linear morphometrics data.xlsxCandidate gene expression using qRT-PCR on A_alluaudi LPJsThis file contains the relative expression values of candidate genes, amplifying cDNA from lower pharyngeal jaws (LPJ) of the A. alluaudi specimens. The reported values have been scaled against normalisation factors (NF) that were calculated from 2 housekeeeping genes. These expression values were subjected to statistical analyses that are reported in Figure 4 a-c and Table S4. Specimen names correspond those assigned in Table S1.qRT-PCR results.xlsFasta files of RNA-seq contigs generated from A_alluaudi LPJsThis file contains .fasta files, generated through assembly of RNA-seq transcripts, derived from A. alluaudi specimens used in our study. These .fasta files were used for differential expression (DE) analyses and BLAST queries, the results of which are depicted in Figure 5 and Tables S5. In tables S6 and S7, these .fasta sequences were used as queries against the human genome, and significant hits were then used for relative enrichment analyses in DAVID.RNA-seq transcripts.fasta