RNA preservation & RNA extraction protocol suitable for field collection of coral samples

The ability to collect samples suitable for RNA extraction in remote field settings is typically hampered by the need for immediate processing or freezing of samples in liquid nitrogen for preservation of nucleic acid integrity. To this end, a range of RNA preservation buffers are available, compatible with ambient temperature transport and subsequent RNA extraction. Here we tested two commonly available RNA storage buffers, RNAlater from Thermo Fisher Scientific and DNA/RNA Shield from Zymo Research, with subsequent RNA extraction using the RNeasy Mini Kit from Qiagen. We assessed three common coral genera (Acropora, Pocillopora, Porites) reported to yield different levels of RNA quality and quantity, partially due to varying levels of mucus that co-purifies with RNA. All samples were collected in the field and preserved at site (on the boat) with storage at ambient temperature, followed by +4°C and -20°C storage, before subsequent RNA extraction. We found DNA/RNA Shield in combination with the RNeasy Mini Kit to yield non-degraded high quality total RNA. The lytic activity of the DNA/RNA Shield buffer facilitates the separation of the coral tissue from the skeleton. At the same time, minimizing the amount of storage buffer is important to obtain sufficiently concentrated RNA for direct use in downstream applications (e.g., RNA-Seq). In summary, we developed a protocol for coral RNA preservation and RNA extraction suitable for application in remote field settings that yield sufficiently concentrated, high quality RNA for direct use in downstream molecular applications.