Preparing Montipora capitata Sample for Shipping to Dovetail Genomics for PacBio Sequencing and Genome Assembly

Goal: Prepare coral sample M1312 for shipping to Dovetail by clipping on dry ice to remove algae (potential contamination) and save some sample (1/3) for storage here just in case we need to use this sample.
Results: It was difficult to clip this sample because of it’s roundness, but the algae is completely removed for the piece sent to Dovetail and a portion is saved at URI as well.
Major Takeaways: We probably need better tool/methods for clipping large chunks off our flash frozen samples. Using a chisel doesn’t work because the sample is not secured in one spot. Our current clippers don’t open wide enough for rounder samples, so we should look into purchasing more.

Sample info

Sample M1312 from the Holobiont Integration project was chose as an ideal sample for sequencing for genome building because the sample is highly bleached, meaning that there are few symbiont cells and not a lot of symbiont DNA that would “contaminate” the genome sequencing. While there is some algal growth on the sample, it hadn’t spread to the whole coral, suggesting that there was still some alive coral tissue at the time of sampling. The coral outlined in the image below is the coral just before flash freezing.

Sample Preparation for Shipping

• Tools that came in contact with the sample were cleaned with 10% bleach, DI water, and 70% ethanol before use
• The sample after storage in the freezer looked relatively identical to the image in the tank
• The sample was clipped on a bed of foil in a cooler full of dry ice to stay frozen. Wire clippers were used to cut off the algal section
• The sample was further clipped (somewhat successfully) to leave a portion of the bleached part at URI and send the rest to Dovetail. Unfortunately most of the clipping resulted in scrapping instead of chunks, so a nice 2/3 to 1/3 clipping ratio was not achieved. About 1/4 of the bleached section came of and was saved along with the algae portion in the original whirl pack for sample M1312
• The remaining 3/4 of the nubbin was placed in a pre-chilled 50mL conical for shipping. The label on the tube is Montipora capitata RUT2303, the LIMS ID-Sample Name for shipping and sequencing
• The tube was placed in a ziploc bag labeled with the same ID and buried in a cooler with dry ice, and shipped overnight to Dovetail Genomics in Scott Valley, CA