Co-expression network analysis of environmental canalization in the ascidian Ciona.
Co-expression network analysis of environmental canalization in the ascidian Ciona.
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DOI：
10.1186/s12862-022-02006-9
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发表时间：
2022-04-28
影响因子：
2.2
通讯作者：
中科院分区：
文献类型：
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渠化，或缓冲，被定义为面对遗传和/或环境扰动的发育稳定性。了解渠化是如何工作的，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如何改变发育非常重要。然而，发育基因表达如何与缓冲作用联系起来仍不清楚。我们通过共表达网络分析解决了这一问题，比较了海鞘玻璃海鞘适应不同热环境的同胞物种在互惠杂交中在全胚胎规模发育过程中热应激引起的基因表达变化。由于我们以前的工作表明，在这个组中的发育缓冲是母系遗传，我们首先确定了母系发育缓冲基因（MDBG），其中在胚胎中的表达水平既与环境渠化的水平，也差异表达取决于物种的性别角色在杂交。我们发现只有15 MDBG，所有这些都表现出高相关系数值与大量的其他基因的表达，其中14个属于一个单一的共表达模块。然后，我们计算了MDBG和转录因子在中枢神经系统（CNS）发育基因网络，以前已被实验确定的表达之间的相关系数。我们发现，与MDBG之间的相关系数平均为0.96相比，MDBG与CNS发育基因的相关性较弱（平均相关系数为0.45）。此外，我们研究了每种发育与MDBG的相关性，表明62个CNS发育基因中只有4个显示相关系数> 0.9，与MDBG之间的值相当，并且这4个基因中的3个是信号分子：BMP 2/4、Wnt 7和Delta样。我们发现，发展途径是不是位于中心的缓冲网络。我们发现，在发育基因网络中的62个基因中，只有4个基因的相关系数与MDBG之间的相关系数一样高。我们建议，松散的联系MDBG稳定时空动态发展。在线版本包含补充材料，可通过10.1186/s12862-022-02006-9获得。
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. The online version contains supplementary material available at 10.1186/s12862-022-02006-9.
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DOI：
10.1016/j.jembe.2017.09.019
发表时间：
2017-12-01
影响因子：
2
作者：
Malfant, Marine;Coudret, Jerome;Viard, Frederique
通讯作者：
Viard, Frederique
影响因子：
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作者：
Imai, Kaoru S.;Stolfi, Alberto;Satou, Yutaka
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Satou, Yutaka
影响因子：
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影响因子：
9.8
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Levy, Sasha F.;Siegal, Mark L.
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Siegal, Mark L.
影响因子：
64.8
作者：
Queitsch, C;Sangster, TA;Lindquist, S
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Lindquist, S