Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors
Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors
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新模型原生生物 Euplotes vannus 的基因组分析，重点关注基因组重排和对环境压力的抵抗力
DOI：
10.1111/1755-0998.13023
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发表时间：
2019-09-01
影响因子：
7.7
通讯作者：
Song, Weibo
中科院分区：
文献类型：
--
作者：
Chen, Xiao;Jiang, Yaohan;Song, Weibo
作为细胞和环境生物学研究的模式生物，自由生活和世界性纤毛虫vannus表现出有趣的特征，如双基因组结构(即每个细胞/有机体中分离的生殖线和体细胞核)、“基因大小”的染色体、停止密码子重新分配、程序性核糖体移码(PRF)和对环境应激源的强大抵抗力。然而，解释这些显著特征的分子机制在很大程度上仍不清楚。在这里，我们报告了一个联合分析的重新组装的高质量大核(MAC；即，体细胞)和部分微核(MIC；即，生殖系)的基因组序列，以及不同条件下的转录组图谱数据。结果表明：(A)MAC基因组包含超过25000条完整的“基因大小”的纳米染色体(~85Mb单倍体基因组大小)，N50~2.7kb；(B)尽管在终止密码子UAA和UAG处有很高的移码频率，但我们没有观察到该物种由于PRF而导致的转录丰度下降；(C)MIC基因组中几乎所有内消减序列(IES)的5‘-TA-3’序列基序保守，染色体断裂位点(CBSS)重复并保留在MAC基因组中；(D)通过分析不同环境应激源(包括营养稀缺、极端温度、盐度和氨的存在)下MAC中基因的加权相关网络，我们确定了对这些外部物理或化学刺激做出反应的基因簇，以及(E)我们观察到HSP70基因在盐分和化学胁迫下转录急剧增加，但令人惊讶的是，在温度变化下没有；我们将这种温度抗性与调节区温度胁迫敏感元件的进化丢失联系起来。与这项研究中产生的基因组资源一起，这些数据为理解高度适应微生物的独特生物学提供了分子证据。
As a model organism for studies of cell and environmental biology, the free-living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), "gene-sized" chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high-quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete "gene-sized" nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5 '-TA-3 ' is conserved at nearly all internally-eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature-resistance to the evolved loss of temperature stress-sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online at Euplotes vannus Genome Database (), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.