Institutional Repository of Key Laboratory of Marine Ecology & Environmental Sciences, CAS
|Adaptations to deep-sea, insights from omic studies on Bathymodiolus platifrons
|Place of Conferral
|深海偏顶蛤 基因组 转录组 适应性 共生 种群连通性 基因组大小 免疫 抗胁迫
深海因其高压、黑暗以及光合作用来源的有机物匮乏等特征，长期被视为“生命荒漠”，随着海洋研究的发展，人们发现在深海中存在另一种特殊的生态系统，即深海化能合成生态系统。化能自养菌利用氧化环境中CH4、H2S等还原性的物质释放的化学能合成有机物，供养整个生态系统。深海Bathymodiolus属贻贝广泛存在于很多深海化能合成生态系统中，其中，Bathymodiolus platifrons贻贝是西太平洋很多热液和冷泉环境共有的优势种，基于其生态系统中的重要地位以及该系统中多种生物基因组大小的调查结果，选定该物种作为研究模型，采用多组学和生物信息学的研究方法，围绕B. platifrons（深海贝）及其亲缘关系较近的偏顶蛤Modiolus kurilensis（近海贝）开展了比较基因组和比较转录组的测序和分析工作，揭示了B. platifrons在基因组水平以及基因表达水平上对环境的适应性特征。其中，与化能自养菌的共生关系是其适应深海化能还原环境的一个关键因素，本研究也重点探讨了深海贝与其共生菌之间的相互作用关系。此外，深海生物的起源问题一直饱受争议，本研究基于线粒体基因组的测序结果，重建了已有数据的所有贻贝的系统发育树，以探讨深海贝的起源，同时比较了B. platifrons热液群体和冷泉群体，以探讨不同群体之间的连通性。获得的主要结论如下：
基于流式细胞术测定了所研究区域多种优势生物的基因组大小，选定深海B. platifrons作为研究模型开展基因组测序，流式细胞术测定基因组大小约为2.4 Gb,基因组survey评估结果约为2.2 Gb。
基于线粒体基因组开展的系统发育分析结果表明，所有的Bathymodiolus贻贝聚在一起，以M. kurilensis贻贝作为姐妹枝。深海Bathymodiolus贻贝较近期分化时间（37.4 Mya）以及其位于系统进化树远离根节点的末端节点的位置，都支持深海贝并不是古老物种，而是不晚于白垩纪中期的时候从近海向深海演化而来。因此，这些深海贝不属于“活化石”。
热液区和冷泉区的深海贝基因组相似度很高，且在群体水平上，基因组大小和线粒体基因组分析的结果都显示，两个群体没有发生分化，相距甚远（> 980 km） 的南海冷泉区和冲绳海槽热液区的B. platifrons贻贝不同群体间具有较好的连通性。
The deep-sea has been considered as a biological desert for marine animals due to its harsh conditions including complete darkness, low temperature and oligotrophic conditions. However, with more and more investigation of deap-sea, it is found that there are numerous flourished ecosystems scattered all around the deap-sea and called as deap-sea chemosythetic ecosystems, which are powered by chemosynthetic bacteria. Over past decades, the topic about how these species adapt to such “hash” habitats has drawn continuous attentions, but remains as an open question. Genome sequencing is a powerful method to study none-model species, and the knowledge of genome size is an important prerequisite. Mussels of subfamily Bathymodiolinae have been found to be one of the dominant species in diverse chemosynthetic ecosystems, among them, Bathymodiolus platifrons has been found to be common in the West-pacfic Ocean. Based on the genome size investigation of a wide range of invertebrates in sampling area, and considering the ecological importance, we choose B. platifrons as model species to study the adaptation to deep-sea. In order to identify the linaege-specific adaptive characteristics of B. platifrons, we conducted genome sequencing and RNA-seq of the mussel in a comparative frame with its costal relative Modiolus kurilensis. Compared with coastal mussels, one of the most extraordinary traits of Bathymodiolus mussels is their endosymbiosis. Based on the multi-omic analysis, we also disscussed the interaction relationship of this symbiotic system. Besides, there are debates about the origin of deep-sea life all these years. We also explored the phylogenetic interactions of mussels based on mitochondrial genomes sequencing and analysis, trying to understand the evolutionary transmission of the taxa. Meanwhile, we compared 20 complete mitogenomes of B. platifrons from a vent and a seep to explore the population connectivity. The main results are as follows:
1. Genome size and features
The genome size of B. platifrons was about 2.4 Gb and 2.2 Gb estimated by flow cytometry and genome survey respectively. Compared with other genomes of Lophotrochozoa species, the transposon elements were expanded in B. platifrons, especially the helitron elements, which could induce changes in genome, so it might play a role in the genomic rearrangement during the evolution.
In addition, the numbers and length of introns in three mussels were higher than those in other mollusks, with the increasing of numbers of alternative splicing, these might be the special features shared in mussels.
Both the deep-sea Bathymodiolus mussels and costal mussels possess diverse gene families related to stress responses, there were no specific or significantly expanded families in Bathymodiolus mussels, indicating that all mussels might possess the potential to cope with diverse stresses, but prefering different gene members of the same gene family in different species.
Compared with coastal relatives, the symbiotic relationship in deep-sea mussels are one of the most obvious and important difference. From the genomic insight, many gene families related to endocytosis, transporters, glycosylation were expanded or positively selected in deep-sea mussels, which indicated that the symbiotic relationship might have be a selective driver for the evolution of B. platifrons.
In deep-sea chemosynthetic ecosystems, many symbiotic invertebrates rely on the chemoautotrophic bacteria for nutrients, with the reduction of their digestive systems. We compared the number of digestion-related genes and expression pattern of different tissues between B. platifrons with other mollusks, the results indicated that B. platifrons mussels still have the potential of digestion, which might be good for the mussels to live in more diverse habitats and adapt to the unstable conditions.
3. The origin of deep-sea mussels
Combining evidence of the shallow divergence (37.4 Mya), the tip positioning in the phylogenetic trees as well as published fossil records, a recent invasion no older than the mid-cretaceous of Bathymodiolus spp. from shallow water to the deep-sea chemosynthetic ecosystem was supported. Hence, these deep-sea mussels are not living fossils.
4. Interactions between B. platifrons and its symbionts
Based on the comparative transcriptomic analysis, we identified several candidate pattern recognition receptors (PRRs) such as TLRs, C1qDC proteins, which might play a role in host-symbiont recognition. However, the results of statistics of representative PRR numbers using either genomic data or RNA-seq data all indicated that PRRs seemed to be globally reduced in B. platifrons, which might facilitate the infection and maintenance of their symbionts. Phagocytosis or endocytosis might be the routes for their entrance, after that, the symbionts were restricted in host-dedrived membrane and dwelled in host cell. Our results highlighted the lysosomal activities in deep-sea mussels, indicating that nutrients might be absorbed from the symbionts by cellular digestion. Meanwhile, diverse transporters were also identified to be positively selected or more highly expressed in the deep-sea mussels, which could provide more effective exchange of nutrients and intermediate metabolites.
To maintain a sustainale symbiotic relationship between Bathymodiolus mussels and their symbionts, related physiological processes such as lysosome activity, autophagy and apoptosis are need to be regulated coordinately, but the mechanisms remains unclear.
5. Population connectivity
According to the genome sequencing and analysis, the two genomes of B. platifrons from the studied hydrothermal vent and cold seep were highly similar. Besides, even with our hypervariable molecular marker, no structured genetic differentiation can be detected for B. platifrons from the seep and vent. The two populations were well connected, possibly by a strong Kuroshio Current during prolonged planktonic larvae stages.
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|郑平. 深海偏顶蛤（Bathymodiolus platifrons）对深海环境的适应性机制[D]. 中国科学院海洋研究所. 中国科学院大学,2018.
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