Picolo Floriane, Piégu Benoît, Monget Philippe
PRC, UMR85, INRAE, CNRS, IFCE, Université de Tours, F-37380 Nouzilly, France.
Heliyon. 2023 Sep 16;9(9):e20217. doi: 10.1016/j.heliyon.2023.e20217. eCollection 2023 Sep.
Cell signalling involves a myriad of proteins, many of which belong to families of related proteins, and these proteins display a huge number of interactions. One of the events that has led to the creation of new genes is whole genome duplication (WGD), a phenomenon that has made some major innovations possible. In addition to the two WGDs that happened before gnathostome radiation, teleost genomes underwent one (the 3WGD group) or two (the 4WGD group) extra WGD after separation from the lineage leading to holostei. In the present work, we studied in 63 teleost species whether the orthologues of human genes involved in 47 signalling pathways (HGSP) remain more frequently duplicated, triplicated or in the singleton state compared with the whole genome. We found that these genes have remained duplicated and triplicated more frequently in teleost of the 3WGD and 4WGD groups, respectively. Moreover, by examining pairs of interacting gene products in terms of conserved copy numbers, we found a majority of the 1:1 and 1:2 proportions in the 3WGD group (between 54% and 60%) and of the 2:2 and 2:4 proportions in the 4WGD group (30%). In both groups, we observed the 0:n proportion at a mean of approximately 10%, and we found some pseudogenes in the concerned genomes. Finally, the proportions were very different between the studied pathways. The n:n (i.e. same) proportion concerned 20%-65% of the interactions, depending on the pathways, and the n:m (i.e. different) proportion concerned 34%-70% of the interactions. Among the n:n proportion, the 1:1 ratio is most represented (25.8%) and among the n:m ratios, the 1:2 is most represented (25.0%). We noted the absence of gene loss for the JAK-STAT, FoxO and glucagon pathways. Overall, these results show that the teleost gene orthologues of HGSP remain duplicated (3WGD) and triplicated (4WGD) more frequently than the whole genome, although some genes have been lost, and the proportions have not always been maintained.
细胞信号传导涉及无数蛋白质，其中许多属于相关蛋白质家族，这些蛋白质表现出大量的相互作用。导致新基因产生的事件之一是全基因组复制（WGD），这一现象使一些重大创新成为可能。除了在有颌类辐射之前发生的两次全基因组复制外，硬骨鱼基因组在从导致全骨鱼类的谱系分离后经历了一次（3WGD组）或两次（4WGD组）额外的全基因组复制。在本研究中，我们在63种硬骨鱼物种中研究了参与47条信号通路的人类基因（HGSP）的直系同源基因与全基因组相比，是否更频繁地保持重复、三倍体状态或单拷贝状态。我们发现，这些基因在3WGD组和4WGD组的硬骨鱼中分别更频繁地保持重复和三倍体状态。此外，通过检查相互作用的基因产物对的保守拷贝数，我们发现在3WGD组中大多数是1:1和1:2比例（54%至60%之间），在4WGD组中是2:2和2:4比例（30%）。在两组中，我们观察到0:n比例平均约为10%，并且在相关基因组中发现了一些假基因。最后，所研究的信号通路之间的比例差异很大。n:n（即相同）比例涉及20% - 65%的相互作用，具体取决于信号通路，n:m（即不同）比例涉及34% - 70%的相互作用。在n:n比例中，1:1比例占比最大（25.8%），在n:m比例中，1:2比例占比最大（25.0%）。我们注意到JAK - STAT、FoxO和胰高血糖素信号通路没有基因丢失。总体而言，这些结果表明，HGSP的硬骨鱼基因直系同源基因比全基因组更频繁地保持重复（3WGD）和三倍体状态（4WGD），尽管一些基因已经丢失，并且比例并不总是保持不变。
