RNA-Seq of Acropora cervicornis: branch tip
The apical tip of a single branch, approximately 1 cm in length, was collected from each of four spatially isolated A. cervicornis colonies located in a backreef habitat at Blackbird Caye. All samples were collected in November 2017 in the early morning hours (0600-0730) to avoid diel variation in gene expression  andpreserved in 95% ethanol immediately following collection and stored at -20 C. One cm3 of skeletal tissue was crushed using a razor blade and combined with acid-washed 425-600 m glass beads in Lysis/Binding solution from the RNAqueous Total RNA Isolation Kit (ThermoFisher Scientific). The resulting mixture was then agitated in a Fisherbrand Bead Mill 24 Homogenizer for 1 minute to remove tissue from skeletal fragments. Total RNA from four colonies was extracted using the RNAqueous kit and sent to Novogene for library preparation and sequencing. Libraries were created by Novogene using the NEBNext Ultra DNA LibraryPrep Kit (New England Biolabs), and were sequenced on the Illumina Novaseq6000 platform using paired-end, 150-bp reads. Novogene removed adaptors before delivery of raw data. Raw fastq files were quality assessed using FastQC [30]. The sequencing reads were trimmed and quality filtered using Cutadapt [31] according to the following specifications. The first 15 base pairs were trimmed from both forward and reverse reads because they exhibited a biased nucleotide composition according to FastQC. Reads with phred scores less than q=30 and reads shorter than 20 base pairs in length were then discarded. Both members of a read-pair were discarded if either the forward or reverse read failed to reach the quality control thresholds. Forward and reverse reads were shuffled to produce a single sequence file for each sample.