海洋生物分类与系统演化实验室知识库

相较于浅海环境，深海热液、冷泉环境不仅黑暗、高压、低氧、寡营养，
还富含甲烷、硫化物及重金属等有毒物质，通过细菌等化能自养微生物将化学
能转化为生物质，维系着整个生态系统的运转。热液和冷泉虽然同为深海化能
生态系统，但因其成因和分布等不同，环境特征也有较大差别。 尽管如此，大
型生物却能在如此极端环境中生存并形成群落，它们经过长期的适应与历史进
化过程，形成了独特的生命特征和环境适应机制。 拟刺铠虾科中的劳盆拟刺铠
虾(Munidopsis lauensis)和威氏拟刺铠虾(Munidopsis verrilli)是深海化能生态系统
底栖生物类群的优势物种之一，可作为探究深海化能极端环境大型生物适应性
机制的优良材料。
为探究拟刺铠虾适应深海化能极端环境的分子基础， 本研究首先使用
Pacbio和 Illumina测序平台分别对劳盆拟刺铠虾和威氏拟刺铠虾及其浅海近缘种
美丽异铠虾(Allogalathea elegans)进行了三代全长转录组及二代普通转录组测定
与比较分析。 结果发现， 深海物种的高表达基因中与免疫相关的通路显著富集，
与先天免疫、抗氧化、低温适应以及硫代谢等相关的基因发生了显著扩张，与
免疫、解毒和抗环境压力等相关的基因受到了正选择。 这些特征可能在拟刺铠
虾适应低温、富含有毒物质、 微生物组成复杂等的深海化能极端环境过程中发
挥重要作用。
聚焦深海热液与冷泉生物群落对环境适应机制是否存在差异这一科学问题，
本研究以深海热液、冷泉共有种劳盆拟刺铠虾为研究对象，比较了其在热液和
冷泉不同深海化能环境中的转录组差异。为此，对采集自马努斯热液和南海冷
泉的劳盆拟刺铠虾的肝胰腺和肌肉组织分别进行了转录组测序与分析。 两组织
共有的差异表达转录本呈现出环境相关的聚类模式，暗示了环境介导的基因表
达模式。进一步分析发现大多数与抗氧化、解毒、 DNA 损伤修复以及先天免疫
相关的大多数基因在热液个体中表达上调。考虑到马努斯热液和南海冷泉环境
中的硫化氢浓度差异以及硫化氢的细胞毒性，进一步对参与硫化氢代谢与解毒
的基因进行了筛选与分析，发现线粒体硫化氢氧化、内源性硫化氢合成及氧化
磷酸化相关的基因均发生显著的差异表达，且大部分基因在热液个体中表达上
调。 研究结果揭示出劳盆拟刺铠虾可能会通过调节环境适应性的关键基因表达
模式以适应不同的深海化能环境，如不同的硫化氢、重金属浓度与微生物组成
等。此外， 相对于冷泉环境而言，劳盆拟刺铠虾在热液环境中受到的环境胁迫
可能更大，这也与热液较冷泉环境更极端相一致。
深海化能环境中甲壳动物具有橙眼和白眼两种表型。为探究威氏拟刺铠虾两种眼睛表型产生的分子基础， 本研究开展了其橙眼(OE)和白眼(WE)的比较转
录组分析。分析发现许多差异转录本的功能与先天免疫、氧化应激和解毒等生
物过程相关。 此外， 发现与眼睛色素合成途径关键酶的编码基因 OE 和 WE 中的
表达量存在差异。 与同样具有两种眼睛表型的长角阿尔文虾(Alvinocaris
longirostris)的眼睛转录组数据进行了联合分析，结果发现与免疫、蝶啶色素及
眼黄素合成途径的关键基因在两种虾橙眼与白眼中的表达趋势一致。由此推测
深海化能生态系统中微环境变化(如微生物、有毒物质等)引起眼组织产生生理
响应，可能影响了眼睛色素的合成，造成了眼睛两种颜色表型的产生。
综上，本研究利用二代和三代转录组测序技术， 通过与浅海近缘种的比较
分析，探究了拟刺铠虾对深海化能环境的适应机制； 首次对深海热液和冷泉的
共有优势物种劳盆拟刺铠虾开展了多组织的比较分析； 同时对威氏拟刺铠虾两
种眼睛性状差异的分子基础进行了初步探究，相关研究结果将从转录组层面拓
展人们对大型生物如何适应深海极端环境以及如何响应不同的深海化能生境的
理解。 本研究丰富了深海极端化能生境大型底栖生物的转录组数据，也为探究
深海化能生态系统甲壳动物的适应性进化及新基因资源的开发提供了数据支撑。

Compared to shallow marine environments, deep-sea hydrothermal vent and cold seep environments are not only dark, high-pressure, low-oxygen and oligotrophic, but also rich in toxic substances such as methane, sulphur and hydrogen sulfide, etc., which are converted into biomass by chemoautotrophic microorganisms, sustaining the entire ecosystem. Despite sharing similar processes of chemosynthesis, deep-sea vents and seeps are assumed to different in tectonic settings and physicochemical properties. Nevertheless, animals have evolved a series of survival strategies to thrive in such extreme deep-sea environments. The munidopsid squat lobsters, Munidopsis lauensis and Munidopsis verrilli are among the dominant species in the benthic communities of deep-sea chemosynthetic ecosystems, and can serve as excellent materials for exploring the mechanisms underlying adaptation of macrofauna to deep-sea chemosynthetic extreme environments.

To providing insights into adaptations of munidopsid squat lobsters to deep-sea chemosynthetic environments, full-length transcriptomes of M. lauensis, M. verrilli and their shallow-sea relative Allogalathea elegans were generated using a combination of single-molecule real-time and Illumina RNA-seq technology. The analysis revealed a significant enrichment of immune-related pathways in the highly expressed genes of deep-sea squat lobsters. Gene family expansion analysis revealed that genes related to innate immune response, sulfur metabolism, antioxidant defense, and cold tolerance underwent significant expansion in deep-sea squat lobsters. Finally, positively selected genes identified in two deep-sea Munidopsis species were involved in immunity, detoxification and resistance to environmental stress. These genes may play important roles in the adaptation of munidopsid squat lobsters to deep-sea extreme environmental conditions, such as low temperature, complex microbial composition, high concentrations of hydrogen sulfide and heavy metals.

Considering the differences in tectonic settings and physicochemical properties between deep-sea vents and seeps, it is hypothesized that the local animals probably exhibited novel molecular features associated with adaptation to their respective habitats. In this study, comparative transcriptome analysis was applied to characterize gene expression profiles of hepatopancreas and muscles of M. lauensis from a methane seep in the South China Sea (CS) and a hydrothermal vent in the Manus back-arc Basin (HV). A heatmap based on the expression levels of 1,017 common differentially expressed transcripts (DETs) to hepatopancreas and muscle indicated remarkably different expression patterns between HV and CS lobsters regardless of sampled tissues, suggesting an environmentally mediated pattern of gene expression. Functional annotation and enrichment analyses indicated most of the shared DETs involved in detoxification, oxidative stress resistance and innate immune response were consistently up-regulated in HV lobsters. At the same time, there was clear evidence for the upregulation of genes associated with hydrogen sulfide (H2S) oxidation, endogenous H2S production and mitochondrial oxidative phosphorylation in HV lobsters. It is hypothesized that the M. lauensis may have adapted to different deep-sea chemosynthetic environments by regulating the expression patterns of key genes related to environmental adaptation. Moreover, overexpression of a battery of environmental response-related genes in HV might suggest hydrothermal vents as more extreme deepsea chemoautotrophic environments in comparison with cold seeps.

In deep-sea chemosynthetic environment, it is interesting to find orange-eye (OE) and white-eye (WE) phenotypes in some crustacean species. We performed a comparative transcriptome analysis to investigate the molecular basis for the formation of the two eye phenotypes of M. verrilli. Comparative transcriptome analysis revealed that the functions of many DETs between OE and WE were associated with biological processes such as innate immunity, antioxidation and detoxification. Of note, we found that 23 unigenes associated with ocular pigment synthesis were also significantly differentially expressed between OE and WE. A joint analysis of the eye transcriptomic data of Alvinocaris longirostris, which also has two eye color phenotypes, showed that the expression trends of key genes involved in immune, pteridine pigment synthesis pathways and the ommochrome biosynthesis pathway were consistent in the orange and white eyes of both deep-sea crustacean species. The underlying factors driving different eye color phenotype formation may be related with physical responses of M. verrilli to variable micro-environmental stressors in deep-sea chemosynthetic habitats,which in turn influence pigment synthesis in the eye.

In summary, this study provides the first comparative analysis of deep-sea munidopsid squat lobsters with their shallow-water relatives using second- and thirdgeneration transcriptome sequencing techniques. This study also represents a first step in understanding molecular basis of crustacean adaptation to different types of deep-sea chemosynthetic environments by investigating transcriptional profiling in multiple tissues. These results greatly expand our understanding of how microbenthic crustaceans adapt to deep-sea chemosynthetic extreme environments and respond to different vent and seep environments at the transcriptome level. Furthermore, we provide a preliminary investigation of the molecular basis of differences in the two eye color phenotypes of M. verrilli. In the present study, we enrich the transcriptome data of macrobenthic organisms inhabiting in deep-sea chemosynthetic environments. The results can also provide important datasets for studying adaptive evolution of crustaceans in deep-sea chemosynthetic ecosystems and exploring new genetic resources.