Huth Troy J, Place Sean P
Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
BMC Genomics. 2013 Nov 20;14:805. doi: 10.1186/1471-2164-14-805.
The notothenioids comprise a diverse group of fishes that rapidly radiated after isolation by the Antarctic Circumpolar Current approximately 14-25 million years ago. Given that evolutionary adaptation has led to finely tuned traits with narrow physiological limits in these organisms, this system provides a unique opportunity to examine physiological trade-offs and limits of adaptive responses to environmental perturbation. As such, notothenioids have a rich history with respect to studies attempting to understand the vulnerability of polar ecosystems to the negative impacts associated with global climate change. Unfortunately, despite being a model system for understanding physiological adaptations to extreme environments, we still lack fundamental molecular tools for much of the Nototheniidae family.
Specimens of the emerald notothen, Trematomus bernacchii, were acclimated for 28 days in flow-through seawater tanks maintained near ambient seawater temperatures (-1.5°C) or at +4°C. Following acclimation, tissue specific cDNA libraries for liver, gill and brain were created by pooling RNA from n = 5 individuals per temperature treatment. The tissue specific libraries were bar-coded and used for 454 pyrosequencing, which yielded over 700 thousand sequencing reads. A de novo assembly and annotation of these reads produced a functional transcriptome library of T. bernacchii containing 30,107 unigenes, 13,003 of which possessed significant homology to a known protein product. Digital gene expression analysis of these extremely cold adapted fish reinforced the loss of an inducible heat shock response and allowed the preliminary exploration into other elements of the cellular stress response.
Preliminary exploration of the transcriptome of T. bernacchii under elevated temperatures enabled a semi-quantitative comparison to prior studies aimed at characterizing the thermal response of this endemic fish whose size, abundance and distribution has established it as a pivotal species in polar research spanning several decades. The comparison of these findings to previous studies demonstrates the efficacy of transcriptomics and digital gene expression analysis as tools in future studies of polar organisms and has greatly increased the available genomic resources for the suborder Notothenioidei, particularly in the Trematominae subfamily.
南极鱼亚目包含多种鱼类，大约在1400万至2500万年前被南极绕极流隔离后迅速辐射演化。鉴于进化适应已使这些生物形成了生理极限狭窄的精细调节性状，该系统为研究生理权衡以及对环境扰动的适应性反应极限提供了独特机会。因此，在试图了解极地生态系统对全球气候变化相关负面影响的脆弱性方面，南极鱼亚目有着丰富的研究历史。不幸的是，尽管它是理解对极端环境生理适应的模型系统，但对于南极鱼科的许多种类，我们仍然缺乏基本的分子工具。
将宝石南极鱼（Trematomus bernacchii）的样本在接近环境海水温度（-1.5°C）或+4°C的流通海水箱中驯化28天。驯化后，通过汇集每个温度处理下n = 5个个体的RNA，创建了肝脏、鳃和脑的组织特异性cDNA文库。对这些组织特异性文库进行条形码标记并用于454焦磷酸测序，产生了超过70万个测序读数。对这些读数进行从头组装和注释，生成了一个包含30107个单基因的宝石南极鱼功能转录组文库，其中13003个与已知蛋白质产物具有显著同源性。对这些极端适应寒冷的鱼类进行数字基因表达分析，强化了诱导性热休克反应的丧失，并允许对细胞应激反应的其他要素进行初步探索。
对宝石南极鱼在高温下的转录组进行初步探索，使得能够与先前旨在表征这种特有鱼类热反应的研究进行半定量比较，这种鱼类的大小、丰度和分布已使其在数十年的极地研究中成为关键物种。将这些发现与先前的研究进行比较，证明了转录组学和数字基因表达分析作为未来极地生物研究工具的有效性，并大大增加了南极鱼亚目，特别是南极鱼亚科可用的基因组资源。
