Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances. Cladocopium sp. C1

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. Overall design: 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显著上调。本研究将虫黄藻的转录调控与生理热应激响应，以及携带该类虫黄藻的珊瑚已知的白化响应建立了关联。通过揭示这些关键关联，我们大幅加深了对珊瑚白化易感性的理解——而珊瑚白化是影响全球珊瑚礁健康的核心过程之一。
整体实验设计：我们针对两个具有不同耐热性与白化阈值的虫黄藻C1种群，分析其响应热应激的基因调控模式。受试种群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，二者均在添加了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。光照强度设置为30 µmol quanta m^-2 s^-1，由Crompton 36W冷白色荧光灯管提供，色温为4000 K，光暗周期为12:12小时。
本实验中，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，每个温度处理组设置4个重复（n=4）。每个种群的两个培养瓶被随机分配至4个实验培养箱中的一个，于27℃下进行预适应培养。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，剩余两个培养箱维持27℃恒温。培养箱内的温度与光照强度通过HOBO数据记录仪进行实时监测。实验全程确保培养物处于指数生长阶段，该状态通过实验期间对每个样本三次重复血细胞计数的平均值确定。分别在第-1天（加热前）、第9天与第13天采集转录组样本。
相关数据文件说明如下：
SM_min250_nr.fasta：南莫尔种群的从头转录组，包含非冗余转录本（转录本最小长度为250 bp）
SM_transcriptome.fasta：南莫尔种群的初步从头转录组（转录本最小长度为150 bp）
MI_min250_nr.fasta：磁岛种群的从头转录组，包含非冗余转录本（转录本最小长度为250 bp）
MI_transcriptome.fasta：磁岛种群的初步从头转录组（转录本最小长度为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：样本间的基因计数矩阵