Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances

Using transcriptomics, we show that Symbiodinium acclimation to elevated temperature involves up-regulated expression of meiosis genes followed by up-regulated expression of numerous reactive oxygen species scavenging genes and molecular chaperone genes. Our study connects Symbiodinium transcriptional regulation with physiological heat stress responses as well as known bleaching responses of corals harboring these same Symbiodinium. By uncovering these critical links, we greatly advance understanding of the bleaching susceptibility of corals, which is a key process responsible for global coral reef health. We analyzed gene regulation in response to heat stress by two Symbiodinium C1 populations with contrasting thermal tolerances and bleaching thresholds. The thermo-sensitive South Molle (SM) Symbiodinium population and thermo-tolerant Magnetic Island (MI) Symbiodinium population were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). Light was provided at an intensity of 30 µmol quanta m^-2 s^-1 (Crompton 36W cool white fluorescent tubes, 4000 K) with a 12:12 h light:dark cycle. For this study, 50 ml (~1 x 10^6 cells/ml) of each population were added to eight replicate culture flasks per population (n=4 for each temperature treatment). Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C. After 10 days of acclimation, fresh media was supplied to the cultures. After an additional four days of acclimation (two weeks of acclimation total), two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C. Temperature and light intensity in the incubators were monitored with HOBO data loggers. Cultures remained in exponential growth phase, determined by the average of three replicate haemocytometer counts for each sample measured throughout the experiment. Transcriptomes were sampled on day -1 (pre-heating), 9, and 13. SM_min250_nr.fasta: South Molle population de novo transcriptome, non-redundant transcripts (min transcript length 250 bp) SM_transcriptome.fasta: preliminary South Molle population de novo transcriptome (min transcript length 150 bp) MI_min250_nr.fasta: Magnetic Island population de novo transcriptome, non-redundant transcripts (min transcript length 250 bp) MI_transcriptome.fasta: preliminary Magnetic Island population de novo transcriptome (min transcript length 150 bp) Trinity_SM_min250nr_annotation_report.complete.5.xls: SM transcriptome annotation spreadsheet Trinity_MI_min250nr_annotation_report.complete.5.xls: MI transcriptome annotation spreadsheet day*nr.counts.txt: gene count matrix across samples

本研究通过转录组学（transcriptomics）分析，证实虫黄藻（Symbiodinium）对高温的适应过程涉及减数分裂基因表达上调，随后大量活性氧清除基因与分子伴侣基因的表达亦出现上调。
本研究将虫黄藻的转录调控与生理热应激响应，以及携带同种虫黄藻的珊瑚已知的白化响应关联起来。通过揭示这些关键关联，我们极大地推进了对珊瑚白化易感性的认知，而珊瑚白化是影响全球珊瑚礁健康的核心过程。
本研究针对两个具有显著耐热性与白化阈值差异的虫黄藻C1类群，分析其响应热应激的基因调控模式。
分别为热敏性的南莫尔岛（South Molle, SM）虫黄藻种群与耐热性的磁岛（Magnetic Island, MI）虫黄藻种群，将其接种于添加了Daigo IMK培养基（和光纯药工业株式会社，Wako Pure Chemical Industries, Ltd.）的过滤海水中进行培养。光照采用30 μmol quanta m^-2 s^-1的强度（Crompton 36W冷白色荧光灯管，色温4000K），光暗周期设置为12:12小时。
本研究中，每个种群取50 ml（细胞密度约1×10^6 cells/ml）接种至8个重复培养瓶中（每个温度处理组n=4）。每个种群的两个培养瓶被随机分配至4个实验培养箱，于27℃下预适应培养。
预适应10天后更换新鲜培养基；再经过4天预适应（总预适应时长为两周）后，其中两个培养箱以0.5℃/h的速率升温至32℃以实施热应激处理，另外两个培养箱维持27℃不变。
培养箱内的温度与光照强度通过HOBO数据记录仪进行监测。实验全程中，通过对每个样本进行三次重复血细胞计数板计数确认，培养物始终处于指数生长期。分别于第-1天（热应激前）、第9天与第13天采集转录组样本。
本次研究附带的数据集文件说明如下：
SM_min250_nr.fasta：南莫尔种群从头组装转录组，非冗余转录本（转录本最小长度250 bp）
SM_transcriptome.fasta：南莫尔种群初步从头组装转录组（转录本最小长度150 bp）
MI_min250_nr.fasta：磁岛种群从头组装转录组，非冗余转录本（转录本最小长度250 bp）
MI_transcriptome.fasta：磁岛种群初步从头组装转录组（转录本最小长度150 bp）
Trinity_SM_min250nr_annotation_report.complete.5.xls：南莫尔种群转录组注释表格
Trinity_MI_min250nr_annotation_report.complete.5.xls：磁岛种群转录组注释表格
day*nr.counts.txt：样本间基因计数矩阵