Characterization of the hidden break in giant clam 28S ribosomal RNA
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Abstract
The molluscan 28S ribosomal RNA (rRNA) naturally cleaves into two fragments of similar size as 18S rRNA. This phenomenon, known as the hidden break, has been described in many other protostome species. Here, we characterize the 28S rRNA hidden break region in seven giant clam species, Tridacna gigas, T. derasa, T. maxima, T. noae, T. crocea, Hippopus hippopus and H. porcellanus. We confirm that the break consistently occurs in giant clams and is observed in all tissues and developmental stages. The region of the giant clam 28S rRNA break is located at a position homologous to the well-characterized 28S rRNA break in insects. High AU content and a stem–loop secondary structure in the region may contribute to fragmentation of the 28S rRNA molecule. An awareness of the existence of the hidden break in molluscs, such as the giant clams, which are emerging systems for understanding how environmental change affects life in the ocean, will facilitate progress of RNA sequencing-based analyses that currently rely on standard RNA profiles as a measure of sample integrity.
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The authors would like to thank Dr Ronnie Estrellada of the Semirara Marine Laboratory and Hatchery for generously providing giant clam samples, the Bolinao Marine Laboratory for providing access to the Silaqui Island Giant Clam Ocean Nursery and Niño Dan Posadas for sharing sponge RNA. This work was supported by a grant to C.C. from the Philippine Council for Agriculture, Aquaculture and Natural Resources Research and Development of the Department of Science and Technology (grant no. QMSR-MRRD-MEC-314-1545).
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Contributes to SDGs
Addresses Ocean Decade Challenges
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Tan, K., & Conaco, C. (2021). Characterization of the hidden break in giant clam 28S ribosomal RNA. Journal of Molluscan Studies, 87(3), Article eyab029.