Gene expression patterns associated with caudal fin shape in the cichlid Lamprologus tigripictilis

Abstract

Variation in fin shape is one of the most prominent features of morphological diversity among fish. Regulation of fin growth has mainly been studied in zebrafish, and it is not clear whether the molecular mechanisms underlying shape variation are equally diverse or rather conserved across species. In the present study, expression levels of 37 candidate genes were tested for association with fin shape in the cichlid fish Lamprologus tigripictilis. The tested genes included members of a fin shape-associated gene regulatory network identified in a previous study and novel candidates selected within this study. Using both intact and regenerating fin tissue, we tested for expression differences between the elongated and the short regions of the spade-shaped caudal fin and identified 20 genes and transcription factors (including angptl5, cd63, csrp1a, cx43, esco2, gbf1, and rbpj), whose expression patterns were consistent with a role in fin growth. Collated with available gene expression data of two other cichlid species, our study not only highlights several genes that were correlated with fin growth in all three species (e.g., angptl5, cd63, cx43, and mmp9), but also reveals species-specific gene expression and correlation patterns, which indicate considerable divergence in the regulatory mechanisms of fin growth across cichlids.

Supplementary information: The online version contains supplementary material available at 10.1007/s10750-022-05068-4.

Keywords: Cichlidae; Fin growth; Fin morphogenesis; Fin regeneration; Lamprologini; Morphological diversity.

Fig. 1

The caudal fin of L. tigripictilis. A Caudal fins were amputated along the dashed red line, and tissue samples representing the short dorsal (dS), the short ventral (vS), and the elongated medial (mL) regions of the dorsal fin were taken as indicated. B Biopsies were taken from the original fin tissue (day 0, representing stage 0) and from regenerating tissue at day 20 (representing stage 1) and day 40 (representing stage 2) after the preceding amputation. C Length of fin ray segments in the three regions of the caudal fin. Different box colors indicate significant differences in segment length

Fig. 2

Expression levels of candidate genes selected based on already identified GRN in N. brichardi. Means and standard deviations of RQ in three biological replicates are shown for the elongated and short regions of the caudal in original (stage 0) and regenerating tissue. See Fig. 1A for fin region codes; numbers 0 to 2 identify regeneration stages. Circles above bars indicate significantly elevated expression (P < 0.05 in paired t-tests; Supplementary data 2, Table S3) in comparisons between elongated and short fin region samples (i.e., compared to the bar matching the shade of the circle)

Fig. 3

Expression levels of candidate genes selected based on co-expression with csrp1a, angptl5, and cd63. Means and standard deviations of RQ in three biological replicates are shown for the elongated and short regions of the caudal in original (stage 0) and regenerating tissue. See Fig. 1A for fin region codes; numbers 0 to 2 identify regeneration stages. Circles above bars indicate significantly elevated expression (P < 0.05 in paired t-tests; Supplementary data 2, Table S3) in comparisons between elongated and short fin region samples (i.e., compared to the bar matching the shade of the circle)

Fig. 4

Expression levels of predicted upstream regulators. Means and standard deviations of RQ in three biological replicates are shown for the elongated and short regions of the caudal in original (stage 0) and regenerating tissue. See Fig. 1A for fin region codes; numbers 0 to 2 identify regeneration stages. Circles above bars indicate significantly elevated expression (P < 0.05 in paired t-tests; Supplementary data 2, Table S3) in comparisons between elongated and short fin region samples (i.e., compared to the bar matching the shade of the circle)

Fig. 5

Correlation analysis reveals significant positive or negative co-expression of the candidate genes. Pearson correlation coefficient (r) was used to assess the pairwise expression similarity between the candidate genes during craniofacial development. Blue represents positive and red represents negative expression correlation. *P < 0.05; **P < 0.01; ***P < 0.001