Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
BMC Genomics. 2012 Sep 21;13:501. doi: 10.1186/1471-2164-13-501.
Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization).
Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate.
The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.
珊瑚礁属于地球上生态和经济最重要的生态系统之一。然而，由于海水表面温度升高、疾病和污染，它们在全球范围内持续减少。了解这些压力源对不同珊瑚物种的分子影响对于预测珊瑚种群如何应对这种持续的干扰至关重要。使用分子工具，如微阵列，已经深入了解珊瑚的分子应激反应。在这里，我们对不同的珊瑚物种进行了比较基因组杂交（CGH），与包含 13546 个 cDNA 克隆的 Acropora palmata 微阵列平台杂交，以鉴定潜在的快速进化基因，并确定现有的微阵列平台是否适合用于基因表达研究（通过异源杂交）。
我们的结果表明，当前用于 A. palmata 的微阵列平台能够为广泛的珊瑚物种提供生物学相关信息，涵盖了复杂的进化枝和强健的进化枝。对高度分化基因的分析表明，没有注释的基因数量显著增加，这证实了先前的发现，即分类限制基因的分化速度更高。在有注释的基因中，我们发现许多线粒体基因在 M. faveolata 中与 A. palmata 相比高度分化，而大多数核编码基因保持平均分化率。
在不同的珊瑚物种中使用现有的微阵列平台进行转录分析将极大地提高我们对压力和健康的分子基础的理解，并突出石珊瑚物种之间的进化差异。从基因组的角度来看，我们表明 cDNA 阵列可用于识别分化模式。在强健的珊瑚中，线粒体编码基因似乎比核编码基因分化得更快。因此，在使用线粒体标记进行石珊瑚系统发育时需要考虑到这一点。
