Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals

Data from the National Center for Biolotechnology Information, Gene Expression Omnibus GEO accession: GSE96916
Organism: Acropora Millepora
Experiment type: Expression profiling by high throughput sequencing
Summary:
Purpose: Corals are major sources of dimethylsulphoniopropionate (DMSP), a compound that plays a central role in the global sulphur cycle. While DMSP biosynthesis pathways have been investigated in plants and algae, the molecular basis for its production by corals is unknown. Given its potential role as an osmolyte, the effect of salinity stress on levels of DMSP was investigated in both adults and juveniles (lacking photosynthetic symbionts) of the coral Acropora millepora. This study used transcriptomic data to analyse the effects of salinity over the coral A. millepora and to identify coral genes likely to be involved in DMSP biosynthesis.Methods: Adults coral transcriptomic libraries were constructed from samples exposed during 1 and 24 hours of salinity treatment (25 PSU) and control (35 PSU) conditions (n=5 per condition). Juveniles coral transcriptomic libraries were constructed from samples exposed to 24 and 48 hours of salinity treatment (28 PSU) and control (35 PSU) conditions (n=6 per condition). All libraries were sequenced by 100 bp paired-end in a HiSeq 2000. Reads were mapped onto the Acropora millepora genome using TopHat2 to produce a count data gene expression matrix for subsequent gene expression analysis using DESeq2 package.Results: In adult coral samples, 5.5 - 10.2 million RNAseq reads were obtained for each treatment sampling time while 3.4 - 8.8 million reads were obtained for each juvenile coral sample. The count matrix of the 26,622 A. millepora gene predictions were generated using htseq-count workflow. BlastP analysis of the A. millepora gene predictions led to the identification of coral members of gene families implicated in DMSP biosynthesis in other organisms, while RNA-seq data was used to identify the differentially expressed ones in response to hyposaline stress and on this basis were considered to be candidates for roles in DMSP biosynthesis in corals.Conclusions: Hyposaline stress increased DMSP production in both adults and aposymbiotic juvenile corals, and transcriptomic analyses highlighted the potential involvement of specific candidate genes in the production of DMSP via an alga-like pathway. The biochemistry of DMSP production is not well established for any eukaryotic system and, as the first animals in which it has been demonstrated, this is particularly true in the case of corals. Our RNA-seq results enabled the identification of candidates for roles in DMSP biosynthesis in corals but, given its critical roles in diverse biological processes, a thorough investigation of the molecular mechanisms leading to its production by corals is required.
Overall design: RNA-seq profiles of Acropora millepora coral adults (n=18) and juveniles (n=23) under hyposaline stress were generated by 100 bp paired-end sequencing using HiSeq 2000.

数据来源于美国国家生物技术信息中心（National Center for Biotechnology Information）基因表达综合数据库（Gene Expression Omnibus，GEO），收录号为GSE96916。
实验生物：鹿角杯形珊瑚（Acropora millepora）。
实验类型：基于高通量测序的表达谱分析。
研究概述：
研究背景与目的：珊瑚是二甲基巯基丙酸内盐（dimethylsulphoniopropionate，DMSP）的主要来源，该化合物在全球硫循环中发挥核心作用。目前已在植物与藻类中解析了DMSP的生物合成通路，但珊瑚产生DMSP的分子基础仍未明确。鉴于DMSP作为渗透压调节剂的潜在功能，本研究探究了盐度胁迫对鹿角杯形珊瑚成体及幼体（无光合共生体）体内DMSP水平的影响。本研究通过转录组数据，分析盐度胁迫对鹿角杯形珊瑚的调控作用，并筛选出可能参与DMSP生物合成的珊瑚候选基因。
实验方法：
成体珊瑚转录组文库：取自经盐度处理（25 PSU）及对照（35 PSU）条件分别暴露1小时、24小时的样本，每组设置5个生物学重复。
幼体珊瑚转录组文库：取自经盐度处理（28 PSU）及对照（35 PSU）条件分别暴露24小时、48小时的样本，每组设置6个生物学重复。
所有文库均采用HiSeq 2000平台进行100 bp双端测序。使用TopHat2将测序reads比对至鹿角杯形珊瑚参考基因组，生成基因表达计数矩阵，后续采用DESeq2软件包进行差异基因表达分析。
实验结果：
成体珊瑚样本中，各处理采样时间点的RNA测序reads数为550万至1020万；幼体珊瑚样本的测序reads数为340万至880万。通过htseq-count流程生成了26622个鹿角杯形珊瑚基因预测结果的计数矩阵。对鹿角杯形珊瑚基因预测结果进行BlastP分析，鉴定出其他生物中参与DMSP生物合成的基因家族的珊瑚同源基因；结合RNA-seq数据筛选出响应低盐胁迫的差异表达基因，据此将其列为珊瑚中参与DMSP生物合成的候选基因。
研究结论：
低盐胁迫可提升成体及无共生体幼体珊瑚的DMSP产生量，转录组分析表明特定候选基因可能通过类藻类通路参与DMSP的生物合成。目前尚未在任何真核生物系统中明确DMSP产生的完整生化机制，而作为首个被证实可产生DMSP的动物类群，珊瑚的相关分子机制尤为亟待阐明。本研究的RNA-seq结果筛选出了珊瑚中参与DMSP生物合成的候选基因，但鉴于DMSP在多种生物学过程中的关键作用，仍需开展深入研究以解析珊瑚产生DMSP的分子机制。
实验整体设计：
本研究采用HiSeq 2000平台进行100 bp双端测序，获取了低盐胁迫下鹿角杯形珊瑚成体（n=18）及幼体（n=23）的RNA-seq表达谱。