Animal Breeding and Genomics Group, Wageningen University, Wageningen, The Netherlands.
Experimental Zoology Group, Wageningen University, Wageningen, The Netherlands.
BMC Evol Biol. 2019 Jul 26;19(1):156. doi: 10.1186/s12862-019-1484-2.
The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ's complexity by a tiny amount. This evolutionary process can be studied by comparing closely related species that vary in the presence or absence of their organs. This is the case for the placenta in the live-bearing fish family Poeciliidae, as members of this family vary markedly in their ability to supply nutrients to their offspring via a placenta. Here, we investigate the genomic basis underlying this phenotypic variation in Heterandria formosa, a poeciliid fish with a highly complex placenta. We compare this genome to three published reference genomes of non-placental poeciliid fish to gain insight in which genes may have played a role in the evolution of the placenta in the Poeciliidae.
We sequenced the genome of H. formosa, providing the first whole genome sequence for a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. Using comparative evolutionary analyses, we found 17 genes that were positively selected exclusively in H. formosa, as well as five gene duplications exclusive to H. formosa. Eight of the genes evolving under positive selection in H. formosa have a placental function in mammals, most notably endometrial tissue remodelling or endometrial cell proliferation.
Our results show that a substantial portion of positively selected genes have a function that correlates well with the morphological changes that form the placenta of H. formosa, compared to the corresponding tissue in non-placental poeciliids. These functions are mainly endometrial tissue remodelling and endometrial cell proliferation. Therefore, we hypothesize that natural selection acting on genes involved in these functions plays a key role in the evolution of the placenta in H. formosa.
复杂器官的进化被认为是通过逐步的过程发生的，每个后续步骤都通过微小的增量增加器官的复杂性。这个进化过程可以通过比较密切相关的物种来研究，这些物种在它们的器官存在或不存在方面有所不同。这种情况在胎生鱼类家族 Poeciliidae 的胎盘上就是如此，因为这个家族的成员在通过胎盘向后代提供营养的能力上差异很大。在这里，我们研究了 Heterandria formosa 中这种表型变异的基因组基础，Heterandria formosa 是一种胎盘非常复杂的胎生鱼类。我们将这个基因组与三个已发表的非胎盘胎生鱼类的参考基因组进行比较，以了解哪些基因可能在 Poeciliidae 胎盘的进化中发挥了作用。
我们对 H. formosa 的基因组进行了测序，提供了第一个胎盘胎生鱼类的全基因组序列。我们通过将其基因序列与三个非胎盘胎生鱼类的近亲进行比较，寻找适应性进化的特征。通过比较进化分析，我们发现了 17 个在 H. formosa 中仅受到正选择的基因，以及 5 个仅在 H. formosa 中发生的基因复制。在 H. formosa 中受到正选择进化的 8 个基因在哺乳动物中具有胎盘功能，其中最重要的是子宫内膜组织重塑或子宫内膜细胞增殖。
我们的结果表明，与非胎盘胎生鱼类的相应组织相比，在 H. formosa 中受到正选择的大量基因具有与形成 H. formosa 胎盘的形态变化密切相关的功能。这些功能主要是子宫内膜组织重塑和子宫内膜细胞增殖。因此，我们假设，作用于这些功能相关基因的自然选择在 H. formosa 胎盘的进化中起着关键作用。
