Genomics of two scyphozoan jellyfish

M.Phil.Jellyfish are free-swimming medusa form of individuals of the phylum Cnidaria, which is the closest sister group to the Bilateria. Jellyfish are of economic and ecological importance but understanding of their biology and evolution has been hindered by a lack of genomic resources. Here we report the genomes of two species of the class Scyphozoa, Sanderia malayensis and Rhopilema esculentum, sequenced using both next generation and third generation sequencing technologies. We have designed assembly pipelines for each jellyfish depending on their respective genome characteristics as well as data coverages of different sequencing platforms. Highquality reference assemblies and gene annotations have been achieved for both species. Comparative analyses revealed unique genomic features of jellyfish. These included intact Parahox clusters identified for the first time in cnidarians, indicating that an intact Parahox cluster was already present in the common ancestor of cnidarians and bilaterians. Comprehensive survey of Parahox genes in cnidarians revealed a correlation between cnidarian life cycles/body plans and their Parahox gene contents. Differential gain and loss of homeobox genes in different lineages of cnidarians was found, which further contributes to the understanding of the molecular basis for the diversity of cnidarians. The data reported here further provide new resources for studying cnidarians.The high throughput sequencing data also enable us to investigate the genomics of jellyfish mitochondrial genomes and jellyfish-associated bacteria. We have assembled the complete linear mitochondrial genomes for both jellyfish species but identified no NUMTs in the two j ellyfish genomes, indicating that linear mitochondrial genomes do not necessarily cause high NUMTs contents. The complete genome of jellyfish endosymbiont M. sp. I associated with S. malayensis was also assembled and further analysis showed that this bacterium or its close relatives are widely associated with scyphozoans. This Mycoplasma endosymbiont belongs to a novel group of symbiotic bacteria, which probably protect their hosts against invading viruses. Further studies are needed to fully uncover the biological roles of this bacterium in symbiosis with its jellyfish host.刺胞動物是跟兩側對稱動物親緣關{系最近的動物分支，而刺胞動物常見的能夠自由游泳的形態就是水母。水母對生態系統和社會經濟都很重要，但是人們對它們的暸解因為基因組資料的缺乏而受到喂制。我們於是利用二代測序和三代測序技術測了天草水母和海蜜的基因組。根據每種水母的基因組特性和獲得的測序數據，我們設計了合理的組裝流程，最終得到了高品質的基因組和注釋。利用比較基因組學，我們發現這兩種水母有著跟其他已經測序的刺胞動物不同的基因組特性，比如完整的Parahox 基因簇。水母中保留著的完整Parahox 基因簇說明在刺胞動物和兩側對稱動物的共同祖先中就已經存在了完整Parahox基因簇。我們也調查了其他各種刺胞動物的Parah ox 基因， 發現Parahox 基因簇可能和刺胞動物的生活史/身體構造有著某種相關性。我們也發現在不同劇胞動物支系中都存在著各自同源異型盒基因的獲得和丟失， 這可能有助於理解刺胞動物多樣性背後的分子機制。我們獲得的基因組資料也為進一步研究刺胞動物提供了新的有價值的資源。高通量數據同時也提供了研究水母線粒體基因組和伴隨的微生物基因組的機會。我們組裝了完整的這兩種水母的線性線粒體基因組，但是卻沒有在核基因為且裡面找到線粒體插入留下的片段。這說明線性的線粒體基因組不一定會導致核基因組中線粒體來源片段的增加。我們在天草水母中發現了一種胞內共生的細菌並且組裝了它的完整的環狀基因組。進一步的分析表明這類細菌廣泛地存在於各種水母之中。這個物種屬於一類之前少有研究的共生細菌，並且它的基因組特性表明它有可能在保護宿主抵抗病毒入侵中起到作用。完全揭示這種共生細菌的生物學角色需要後續進一步的研究。Cao, Jianquan.Thesis M.Phil. Chinese University of Hong Kong 2018.Includes bibliographical references (leaves 111-132).Abstracts also in Chinese.Title from PDF title page (viewed on …)