Polyploid Genome Organization and Evolution of Sturgeons (Acipenseridae)

背景。脊椎动物基因组的进化以几个古老的全基因组重复（WGD）事件为特征。虽然在大多数现存的动物类群中，再倍化过程已经导致了功能上的二倍体基因组，但在一些鱼类和两栖动物物种中，由于最近的WGDs，这些过程仍在进行中，并为研究多倍体的进化后果提供了方便的模型。鲟鱼代表了这样一种全古多倍体鱼类，在那里有去多倍体的记录。在系统发育上，这些鱼是硬骨鱼的外群，它们表现出许多有趣的生物学特征，包括底栖动物的特化、晚成熟、极端长寿、缓慢的分子进化、类两栖动物的胚胎学特征、种间杂交的倾向以及由此产生的杂种的生育能力。许多与这些专门化有关的重要生物学问题仍未得到解决。由于大多数鲟鱼是极度濒危的物种，其中一些问题不仅具有根本的生物学意义，而且对这些物种的保护生物学也具有重要意义。预期的结果。我们将运用基因组和转录组测序生物信息学、基因表达分析等技术，对小鲟（120条染色体）和西伯利亚鲟（240条染色体）的胚胎和不同生命阶段的组织进行基因表达分析，揭示其基因组结构和基因表达的新特征。东北鲟基因组草图组装和注释的尝试，可为解决进化生物学、生态学、保护和水产养殖等方面的问题提供参考。它将为理解多倍体基因组进化的模式和机制以及这些过程与适应的联系提供新的见解，并与我们正在进行的基因组研究相比较。我们将研究我们之前项目中发现的相似区域，以估计不同倍性水平的鲟鱼物种的再倍化率和模式。我们将集中研究与其他鱼类性别决定有关的基因，并利用RADseq技术寻找雄性和雌性之间的遗传差异。我们的数据将为未来依赖基因组资源的项目提供一个框架，这些项目既可以用于人工饲养鲟鱼的成功繁殖，也可以用于适当的保护管理。

Background. The evolution of vertebrate genomes is characterized by several ancient whole genome duplication (WGD) events. While in most extant animal taxa processes of rediploidization already led to functionally diploid genomes, in some fish and amphibian species due to more recent WGDs these processes are still ongoing and provide convenient models to study the evolutionary consequences of polyploidization. Sturgeons represent such an all-paleopolyploid group of fish, where de-polyploidization is recorded. Phylogenetically these fish are an outgroup to teleosts and they show many interesting biological features including benthic specialization, late maturity, extreme longevity, slow molecular evolution, amphibian-like embryological traits, propensity to interspecific hybridization with fertility of resulting hybrids. Many important biological questions connected to these specialisations remain unresolved. As most sturgeon species are extremely endangered, some of these issues are not only of fundamental biological interest, but are also of importance for conservation biology of these species. Expected Results. We will apply technologies of genome and transcriptome sequencing bioinformatics, gene expression analysis in embryos and tissues of different life stages of sterlet (Acipenser ruthenus, 120 chromosomes) and Siberian sturgeon (A. baerii, 240 chromosomes) to reveal new characteristics of their genome structure and gene expression. The attempted Siberian sturgeon draft genome assembly and annotation can serve as a reference for other acipenserid species to solve problems in evolutionary biology, ecology, conservation and aquaculture. It will provide on its own and in comparison with our ongoing genomic work on sterlet new insights into understanding the modes and mechanisms of polyploid genome evolution and connection of these processes with adaptation. We will study paralogous regions revealed in our previous projects to estimate the rates and modes of rediploidization in sturgeon species with different ploidy level. We will concentrate on genes involved in sex determination in other fish species and employ RADseq technologies to search for genetic differences between males and females. Our data will provide a framework for future projects that rely on genomic resources and can be used both for successful breeding of sturgeons in captivity and proper conservation management.