Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris

Abstract

Background Teleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniofacial morphologies, but less is known about soft craniofacial phenotypes. Here we focus on an example of lip hypertrophy in the benthivorous Lake Tangnayika cichlid, Gnathochromis permaxillaris, considered to be a morphological adaptation to extract invertebrates out of the uppermost layer of mud bottom. We investigate the molecular and regulatory basis of lip hypertrophy in G. permaxillaris using a comparative transcriptomic approach. Results We identified a gene regulatory network involved in tissue overgrowth and cellular hypertrophy, potentially associated with the formation of a locally restricted hypertrophic lip in a teleost fish species. Of particular interest were the increased expression level of apoda and fhl2, as well as reduced expression of cyp1a, gimap8, lama5 and rasal3, in the hypertrophic lip region which have been implicated in lip formation in other vertebrates. Among the predicted upstream transcription factors, we found reduced expression of foxp1 in the hypertrophic lip region, which is known to act as repressor of cell growth and proliferation, and its function has been associated with hypertrophy of upper lip in human. Conclusion Our results provide a genetic foundation for future studies of molecular players shaping soft and exaggerated, but locally restricted, craniofacial morphological changes in fish and perhaps across vertebrates. In the future, we advocate integrating gene regulatory networks of various craniofacial phenotypes to understand how they collectively govern trophic and behavioural adaptations.

Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes

“…Interestingly, we also found enrichment of genes involved in musculoskeletal formation which are known to shape craniofacial phenotypes in cichlids (Gunter et a. 2013;Schneider et al 2014;Hulsey et al 2016;Singh et al 2021), as well as processes involved in the regulation of cell junction assembly which are implicated in lip morphogenesis linked to foraging strategy in a Lake Tanganyika cichlid (Lecaudey et al 2021). We further identified 4,634 cis-sQTLs associated with ecomorph-specific regulation of excision ratios in one or more intron clusters in 2,143 genes (11.1% of the total expressed genes; FDR-corrected P < 0.05; Supplementary Table 9).…”

Parallel molecular mechanisms underlie convergent evolution of the exaggerated snout phenotype in East African cichlids

“…Furthermore, deletion of Bmp2 in human has been reported to cause a range of facial deformities including shortened nose, anteverted nares, elongation of the philtrum and changes in the thickness of lips (Tan et al 2017). Taken together, these findings suggest was recently identified as a key upstream regulator of genes involved in the formation of the hypertrophic lip in another East African cichlid species from Lake Tanganyika (Lecaudey et al 2021). None of the predicted FOX members (foxd3, foxj1 and foxp1) displayed consistent differential expression across both comparisons, but interestingly, the consensus binding site for FOX transcription factor family was also among the predicted binding sites.…”

“…In addition, both foxf1 and foxa2 displayed consistently increased expression in the flapped snout in both comparisons, and are also implicated in the nose morphogenesis in mammals (Dines et al 2019;Kucharczyk et al 2014). We have recently found foxf1 among the regulators of lip hypertrophy in an East African cichlid species as well (Lecaudey et al 2021), suggesting a potentially important and general role of foxf1 in soft tissues exaggeration in cichlids, and given the potential role of foxd3 and foxp1 in cichlid fin exaggeration, FOX genes may play a more general role in tissue elaboration in vertebrates. Among the other predicted TF binding site we found overrepresentation of binding motif for tcf12, a transcription factor with known roles in cranio-skeletal development; particularly in the morphogenesis of the frontal bone and cranial vault thickening in mammals (Piard et al 2015;Sharma et al 2013).…”

“…Convergent evolution of phenotypes, reflecting particular ecological specializations, is a ubiquitous characteristic of adaptive radiations (Schluter & Nagel 1995;Losos et al 1998;Rundle et al 2000;Rüber et al 1999). Cichlid adaptive radiations from the East African Great lakes display an impressive array of repeated morphological traits (Kocher et al 1993), including a few dramatic examples such as nuchal humps and hypertrophied lips (Machado-Schiaffino et al 2014;Manousaki et al 2013;Colombo et al 2013;Baumgarten et al 2015;Lecaudey et al 2019Lecaudey et al , 2021. However, the evolution of such phenotypic novelties is not well understood, but a comparative approach can shed light on the genetic and developmental mechanisms that reconfigure the body plan and give rise to complex traits.…”

Gene expression patterns associated with fin shape differ between two lamprologine cichlids

“…We detected no significant expression differences among fin regions for egr2 and foxd3 in L. tigripictilis and only a weak signal for foxp1 , which matched the pattern in N. brichardi (Table 2). This may suggest transcriptional repressor activity of foxp1 which is also implicated as the main potential repressor TF involved in formation of lip hypertrophy (Lecaudey et al, 2021) and exaggerated snout in two other East African cichlid species. The absence of significant expression differences in two of the proposed upstream regulators of the N .…”