Department of Biology, Ochanomizu University, Tokyo, Japan.
The Laboratory, Marine Biological Association of the UK, Plymouth, UK.
BMC Ecol Evol. 2022 Apr 28;22(1):53. doi: 10.1186/s12862-022-02006-9.
Canalization, or buffering, is defined as developmental stability in the face of genetic and/or environmental perturbations. Understanding how canalization works is important in predicting how species survive environmental change, as well as deciphering how development can be altered in the evolutionary process. However, how developmental gene expression is linked to buffering remains unclear. We addressed this by co-expression network analysis, comparing gene expression changes caused by heat stress during development at a whole-embryonic scale in reciprocal hybrid crosses of sibling species of the ascidian Ciona that are adapted to different thermal environments.
Since our previous work showed that developmental buffering in this group is maternally inherited, we first identified maternal developmental buffering genes (MDBGs) in which the expression level in embryos is both correlated to the level of environmental canalization and also differentially expressed depending on the species' gender roles in hybrid crosses. We found only 15 MDBGs, all of which showed high correlation coefficient values for expression with a large number of other genes, and 14 of these belonged to a single co-expression module. We then calculated correlation coefficients of expression between MDBGs and transcription factors in the central nervous system (CNS) developmental gene network that had previously been identified experimentally. We found that, compared to the correlation coefficients between MDBGs, which had an average of 0.96, the MDBGs are loosely linked to the CNS developmental genes (average correlation coefficient 0.45). Further, we investigated the correlation of each developmental to MDBGs, showing that only four out of 62 CNS developmental genes showed correlation coefficient > 0.9, comparable to the values between MDBGs, and three of these four genes were signaling molecules: BMP2/4, Wnt7, and Delta-like.
We show that the developmental pathway is not centrally located within the buffering network. We found that out of 62 genes in the developmental gene network, only four genes showed correlation coefficients as high as between MDBGs. We propose that loose links to MDBGs stabilize spatiotemporally dynamic development.
canalization 或缓冲作用被定义为在遗传和/或环境干扰下的发育稳定性。了解 canalization 的工作原理对于预测物种如何在环境变化中生存以及破译进化过程中发育如何改变都很重要。然而，发育基因表达与缓冲作用之间的联系尚不清楚。我们通过共表达网络分析来解决这个问题，比较了在适应不同热环境的棘皮动物海鞘的姐妹种的正反杂交中，整个胚胎尺度上发育过程中热应激引起的基因表达变化。
由于我们之前的工作表明，该组中的发育缓冲作用是母系遗传的，我们首先在杂交中识别了母系发育缓冲基因（MDBGs），其表达水平既与环境 canalization 的水平相关，又根据物种在杂交中的性别角色而不同。我们只发现了 15 个 MDBGs，它们的表达与大量其他基因的相关系数值都很高，其中 14 个属于一个单一的共表达模块。然后，我们计算了先前通过实验确定的中枢神经系统（CNS）发育基因网络中 MDBGs 与转录因子之间的表达相关性系数。与 MDBGs 的平均相关系数 0.96 相比，我们发现 MDBGs 与 CNS 发育基因的相关性较弱（平均相关系数 0.45）。此外，我们研究了每个发育基因与 MDBGs 的相关性，结果表明，在 62 个 CNS 发育基因中，只有 4 个基因的相关性系数大于 0.9，与 MDBGs 的值相当，其中 3 个基因是信号分子：BMP2/4、Wnt7 和 Delta-like。
我们表明，发育途径不在缓冲网络的中心位置。我们发现，在发育基因网络的 62 个基因中，只有 4 个基因的相关性系数与 MDBGs 一样高。我们提出，与 MDBGs 的松散联系稳定了时空动态发育。
