Marcionetti Anna, Rossier Victor, Bertrand Joris A M, Litsios Glenn, Salamin Nicolas
Department of Computational Biology, Biophore, University of Lausanne, Lausanne, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Mol Ecol Resour. 2018 Feb 17. doi: 10.1111/1755-0998.12772.
Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare groups to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies. This resource is valuable for advancing studies of the particular life history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.
小丑鱼（或海葵鱼）是珊瑚礁鱼类中极具代表性的一类，主要因其与海葵的互利共生关系而闻名。它们具有独特的生活史特征，比如复杂的社会结构和涉及顺序性雌雄同体的交配系统，同时寿命格外长。此外，小丑鱼被认为是在海洋环境中经历适应性辐射的少数类群之一。在此，我们组装并注释了首个小丑鱼物种——番茄小丑鱼（双锯鱼）的基因组。我们获得了17,801个组装好的支架，共包含26,917个基因。组装和注释的完整性令人满意，在双锯鱼的组装中检索到了96.5%的辐鳍鱼超保守直系同源基因（BUSCOs）。所得组装的质量与其他硬骨鱼组装相当。这一资源对于推进小丑鱼独特生活史特征的研究很有价值，也有助于种群遗传学研究和新系统发育标记的开发。它还将为比较基因组学开辟道路。事实上，未来对亲缘关系密切的鱼类进行基因组比较，可能会提供方法来鉴定与适应不同海葵宿主的独特适应性相关的基因，以及更好地描绘适应性辐射的基因组特征。
