Transcrintomic and genomic evolution under constant cold in Antarctic notothenioid fish
Transcrintomic and genomic evolution under constant cold in Antarctic notothenioid fish
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DOI：
10.1073/pnas.0802432105
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发表时间：
2008-09-02
影响因子：
11.1
通讯作者：
Chen, Liangbiao
中科院分区：
文献类型：
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作者：
Chen, Zuozhou;Cheng, C. -H. Christina;Chen, Liangbiao
抗冻糖蛋白强化的南极notothenioid鱼包括在孤立的寒冷的南大洋的主要鱼类亚目。它们在生态上的成功，无疑意味着它们在进化过程中获得了除防冻保护之外的一整套冷稳定功能。以前的研究，这些硬骨鱼的适应性变化，一般检查一个单一的基因型或表型。我们在这里报告的转录和基因组变化与南极notothenioid冷适应的全基因组调查。我们对南极鱼Dissostichus mawsoni的4种组织中的33，560个EST进行了测序和特征分析，获得了3，114个非冗余蛋白质基因家族及其表达谱。通过比较分析D. mawsoni和温带/热带硬骨鱼，我们鉴定了177个notothenioid蛋白家族，其表达比后者高出许多倍，表明与冷相关的上调。这些上调的基因家族在蛋白质生物合成、蛋白质折叠和降解、脂质代谢、抗氧化、抗凋亡、先天免疫、绒毛膜发生等方面起作用，所有这些都在减轻拟银鱼生活史中冷冻温度下的压力方面具有公认的功能重要性。我们进一步研究了这种表达上调的基因组和进化基础，通过比较基因组杂交的DNA从四对南极和基础非南极的notothenioids到10,700 D。mawsoni cDNA探针，发现了118个蛋白质编码基因的显著至惊人的（3至>300倍，P < 0.05）舌特异性重复，其中许多对应于上调基因家族。我们的综合三方研究的结果强烈表明，在恒定的寒冷下的进化导致了显着的特定蛋白质基因家族的基因组扩增，增强基因表达和基因功能，有助于南极鱼在冰冻极地条件下的生理适应性。
The antifreeze glycoprotein-fortified Antarctic notothenioid fishes comprise the predominant fish suborder in the isolated frigid Southern Ocean. Their ecological success undoubtedly entailed evolutionary acquisition of a full suite of cold-stable functions besides antifreeze protection. Prior studies of adaptive changes in these teleost fishes generally examined a single genotype or phenotype. We report here the genome-wide investigations of transcriptional and genomic changes associated with Antarctic notothenioid cold adaptation. We sequenced and characterized 33,560 ESTs from four tissues of the Antarctic notothenioid Dissostichus mawsoni and derived 3,114 nonredundant protein gene families and their expression profiles. Through comparative analyses of same-tissue transcriptome profiles of D. mawsoni and temperate/tropical teleost fishes, we identified 177 notothenioid protein families that were expressed many fold over the latter, indicating cold-related up-regulation. These up-regulated gene families operate in protein biosynthesis, protein folding and degradation, lipid metabolism, antioxidation, antiapoptosis, innate immunity, choriongenesis, and others, all of recognizable functional importance in mitigating stresses in freezing temperatures during notothenioid life histories. We further examined the genomic and evolutionary bases for this expressional up-regulation by comparative genomic hybridization of DNA from four pairs of Antarctic and basal non-Antarctic notothenioids to 10,700 D. mawsoni cDNA probes and discovered significant to astounding (3-to >300-fold, P < 0.05) Antarctic-specific duplications of 118 protein-coding genes, many of which correspond to the up-regulated gene families. Results of our integrative tripartite study strongly suggest that evolution under constant cold has resulted in dramatic genomic expansions of specific protein gene families, augmenting gene expression and gene functions contributing to physiological fitness of Antarctic notothenioids in freezing polar conditions.