Our goal is to quantify the differences in gene expression and identity generated by library preparation methods for the coral holobiont. To this end we examined two coral species from HI, Montipora capitata and Pocillopora acuta, using both a PolyA enrichment method and a rRNA depletion method. We used two dominant, local coral species that vary in their environmental tolerance, the environmentally tolerant Montipora capitata and the more environmentally sensitive Pocillopora acuta (Gibbin et al. 2015; Bahr et al. 2016). Coral samples (one ~5x5cm fragment per colony) were collected from six colonies (3 per species) from the patch reefs of Kāneʻohe Bay, Oʻahu Hawaiʻi under Hawaiʻi Department of Aquatic Resources Special Activity Permit 2019-60 in September 2018. Corals were affixed in an upright position to individually numbered plastic coral fragment mounting plugs by hot-gluing the base of the skeleton to the plug. Coral fragments were allowed to acclimate in outdoor mesocosm tanks (122 cm x 122 cm x 30 cm; 510 L). Coral fragments were snap frozen and stored at -80 °C until extraction.
| Plug_ID | Collection Date | Species |
|---|---|---|
| 1041 | 20180922 | Pocillopora acuta |
| 1471 | 20180922 | Pocillopora acuta |
| 1637 | 20180922 | Pocillopora acuta |
| 1101 | 20180922 | Montipora capitata |
| 1548 | 20180922 | Montipora capitata |
| 1628 | 20180922 | Montipora capitata |
Zymo-Seq RiboFree Total RNA Library Prep Kit Sequenced by Zymo
Prepared using polyA enrichment with the Illumina TruSeq Stranded mRNA Sample Preparation Protocol by Genewiz and sequenced by Genewiz
| Plug_ID | Ribofree_ID | NCBI PolyA | Raw Reads PolyA | PolyA trimmomatic | PolyA fastp | NCBI RiboFree | Raw Reads RiboFree | Ribofree trimmomatic | Ribofree fastp |
|---|---|---|---|---|---|---|---|---|---|
| 1041 | Sample1 | SRR15089756 | 18637582 | 11415345 | 16139150 | SRR15089763 | 16487768 | 15373749 | 13708087 |
| 1471 | Sample2 | SRR15089755 | 16990028 | 8494238 | 14192707 | SRR15089762 | 10755630 | 9639555 | 10040582 |
| 1637 | Sample3 | SRR15089764 | 16853810 | 9124785 | 14370470 | SRR15089761 | 13534820 | 9665261 | 12530595 |
| 1101 | Sample4 | SRR15089760 | 21636831 | 14279432 | 20516377 | SRR15089757 | 10275396 | 21636831 | 9444420 |
| 1548 | Sample5 | SRR15089759 | 17651137 | 11642352 | 16664623 | SRR15089754 | 16601774 | 17651137 | 15532372 |
| 1628 | Sample6 | SRR15089758 | 21647915 | 20490065 | 21647915 | SRR15089765 | 13440121 | 12585896 | 11273035 |