Robledo Diego, Hermida Miguel, Rubiolo Juan A, Fernández Carlos, Blanco Andrés, Bouza Carmen, Martínez Paulino
Department of Zoology, Genetics and Physical Anthropology, Faculty of Biology (CIBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
Comp Biochem Physiol Part D Genomics Proteomics. 2017 Mar;21:41-55. doi: 10.1016/j.cbd.2016.12.001. Epub 2016 Dec 24.
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.
鲽形目鱼类具有很高的市场接受度，因此代表着一种有利可图的水产养殖产品。主要养殖品种是大菱鲆（Scophthalmus maximus），其次是牙鲆（Paralichthys olivaceous）和半滑舌鳎（Cynoglossus semilaevis），但其他品种如大西洋庸鲽（Hippoglossus hippoglossus）、塞内加尔鳎（Solea senegalensis）和欧洲鳎（Solea solea）也有重要产量，并且在养殖方面非常有前景。对于这些品种中的大多数，都有重要的基因组资源，包括全基因组测序项目、遗传图谱和转录组。在这项工作中，我们将这些品种的所有可用基因组信息整合到一个共同框架内，以大菱鲆和半滑舌鳎的全组装基因组（>210倍覆盖）作为参考。获得了与生产性状遗传基础相关的新见解以及有助于理解该类群进化起源和多样化的新数据。尽管物种之间一般存在1:1的染色体同线性关系，但大菱鲆和半滑舌鳎基因组的比较显示出巨大的染色体内重排。可用图谱信息的整合支持了鲽形目鱼类进化过程中的特定染色体融合，并促进了对先前报道的生产性状遗传关联在不同物种间的比较。在比较这六个物种的转录组资源时，鉴定出了一组约2500个直系同源基因和约150个常见的微小RNA，并且在鲽形目鱼类转录组中检测到了特定的假定缺失基因集，这可能反映了它们的进化多样化。
