Identifying putative calcification and decalcification genes in the geniculate coralline alga, <i>Calliarthron tuberculosum</i>

Coralline algae form highly calcified thalli, creating key substrate that promotes biodiversity in nearshore marine environments. Although calcification and decalcification are critical for coralline growth and ecological function, their underlying mechanisms are not fully understood. We capitalized on the unique morphology of articulated coralline algae, assembling tissue-specific transcriptomes for calcified (intergenicular), uncalcified (genicular), and actively decalcifying (young genicular) tissues in the coralline alga Calliarthron tuberculosum and compared gene expression to identify putative calcification and decalcification genes. We captured the greatest differences in gene expression between calcified and uncalcified tissue, with 17.7% (5238 genes) of the genes in the transcriptome differentially expressed, the majority of which (10.9%) were upregulated in calcified tissue. There were also significant differences between decalcifying and uncalcified tissue, with 14.3% (4420 genes) of the genes in the transcriptome differentially expressed. We used functional gene annotation to identify 18 putative calcification genes and 10 putative decalcification genes. Results showed calcium-binding proteins, a vacuolar calcium transporter, and a calcium ATPase may be important for transporting calcium ions during calcification, whereas a proton ATPase may be important for maintaining pH homeostasis in calcified tissue. Additional genes for hydrogen ion transport were highly expressed in uncalcified tissues, including a sodium/hydrogen exchanger and hydrogen pump, which may be important for accumulating hydrogen ions to maintain uncalcified tissues. Differential expression of carbonic anhydrases and aquaporins indicated potential mechanisms for dissolved inorganic carbon transport in calcified and uncalcified tissues. This study has created valuable molecular resources for coralline algae and lent new insights on mechanistic details surrounding calcification and decalcification.