Investigation of gene family evolution and the molecular basis of shell formation in molluscs

Abstract

Since the emergence of shell-bearing molluscs in the Early Cambrian, diverse shell forms have evolved. Modern molluscs are renowned for a highly complex and robust shell, which is the product of the orchestrated expression of genes and secretion of a large number of proteins and other macromolecules from the epithelium of a specialised organ called the mantle. Molluscan shells display remarkable morphological diversity, structure and ornamentation, however the molecular mechanisms underlying the evolution and formation of the shell remain largely unknown. In this thesis, I seek to investigate the nature of the mantle transcriptome focussing on the timing of origin of genes expressed in the mantle and the evolutionary history of gene families that encode secreted proteins in representatives of bivalve and gastropod species.First, by comparative transcriptomics of the mantle, I determined the origin and evolution of gene families expressed in this organ. Gene origin analyses show that most genes expressed in the mantle are taxon-restricted innovations (i.e. unique to a particular species), although a large number of genes arose along the stems leading to the bilaterian and molluscan last common ancestors. Focussing on gene families that encode secreted proteins that are likely to be embedded within the shell and/or to regulate shell construction, I found that these are comprised of both ancient and lineage-specific gene families. The evolution of these gene families is highly dynamic with prolific gene family gains and losses over evolutionary time. By comparing sequences, I also detected indications of positively selected gene families over molluscan evolution. These gene families show unique patterns of enrichment of protein domains, and presumably molecular functions, that are taxa-specific, suggesting that bivalves and gastropods use almost completely different secretory repertoire to construct their shells.I then focused on an ancient gene family expressed in the molluscan mantles -the tyrosinase gene family -to understand how a conserved gene family has been co-opted into the biomineralisation pathway. I found no evidence of large-scale expansion of tyrosinase genes in gastropods, whereas tyrosinase genes in bivalves have undergone substantial independent gene expansions in at least two lineages (Pinctada spp. and Crassostrea gigas), and that the resulting gene duplicates have been co-opted into the mantle gene regulatory network. Many of the tyrosinase genes are found in clusters within the genomes and are expressed at relatively high levels in the mantle. Detailed 3 comparisons of tyrosinase gene expression in different regions of the mantle in two closely related pearl oysters, P. maxima and P. margaritifera, reveal that recently evolved orthologous genes have unique expression profiles across the mantle with high expression levels at the distal mantle edge, suggesting roles in colouration and/or prismatic shell layer construction. Differences in expression levels are consistent with the rapid evo...

Comparative transcriptomic analysis revealed dynamic changes of distinct classes of genes during development of the Manila clam (Ruditapes philippinarum)

“…In mussels Mytilus edulis, chitinrelated enzymes have been shown to play an important role in biochemical defense processes [46]. In a study on mollusk biomineralization, it was reported that there are many tyrosinase genes in the genome of bivalves and qPCR results showed high expression of tyrosinase genes in the mantle tissue of the Pacific oyster C. gigas [47]. In the present study, 15 tyrosinase genes were upregulated during Manila clam D, U, S, J and shell morphology was altered from D to U in Manila clam (Fig.…”

Developing Perspectives on Molluscan Shells, Part 1: Introduction and Molecular Biology

“…Much of our knowledge on chitin in mollusc shells is thanks to transcriptomic and proteomic approaches. In an attempt to understand the molecular basis underlying shell formation, Aguilera (2014) analyzed the mantle transcriptome of eight bivalve and three gastropod species. This study found over-representation of proteins with polysaccharide-binding domains within the mantle transcriptomes.…”

“…However, genomic resources will continue to provide profound insight into physiological processes such as biomineralization. There is a growing need for implementation of advanced analytical techniques looking at gene family evolution (Aguilera, 2014;De Bie et al, 2006;Domazet-Lošo et al, 2007) and gene networks (Shannon et al, 2003;Smoot et al, 2011). Further, more "traditional" techniques with a much longer history of use in the field of physiology (see Simkiss Chapter 2 of this volume) should not be forgotten in the "-omics" era.…”