The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology.
The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology.
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DOI：
10.7554/elife.31628
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发表时间：
2018-01-29
期刊：
影响因子：
7.7
通讯作者：
Zamore PD
中科院分区：
文献类型：
--
作者：
Fu Y;Yang Y;Zhang H;Farley G;Wang J;Quarles KA;Weng Z;Zamore PD
我们报告了鳞翅目昆虫害虫粉纹夜蛾Hi5细胞基因组的组装草案，将90.6%的碱基分配给28条染色体中的一条，并预测了14，037个蛋白质编码基因。化学感受和解毒基因家族揭示了T. ni特异性基因扩展可以解释其广泛分布和对杀虫剂的快速适应。来自胸部、卵巢、睾丸和种系来源的Hi5细胞系的转录组和小RNA数据显示295个microRNA和>393个piRNA产生基因座以及39个编码小RNA途径蛋白的基因的不同表达谱。几乎所有的W染色体都致力于皮尔纳的产生，而T. ni siRNA不是2 ′-O-甲基化的。为了能够使用Hi5细胞作为模型系统，我们已经建立了基因组编辑和单细胞克隆方案。霸王ni基因组提供了对害虫控制的见解，并使Hi5细胞成为离体研究小RNA的新工具。一种被称为卷心菜尺蠖的普通蛾与科学界的关系越来越密切。它的毛虫对卷心菜、花椰菜和花椰菜作物构成严重威胁，它们已经开始抵抗通常用于控制它们的杀虫剂。此外，这种昆虫的生殖细胞--产生精子和卵子的细胞--在实验室中被用作人工生产感兴趣的蛋白质的“工厂”。生殖细胞还具有一组称为RNA沉默的遗传机制。其中一个过程被称为皮尔纳，它保护基因组免受“跳跃基因”的侵害。这些遗传元件可以通过在DNA中从一个地方移动到另一个地方来引起突变：在生殖细胞中，皮尔纳在遗传信息传递给下一代之前抑制它们。并不是所有的生殖细胞在实验条件下都能同样良好地生长，或者很容易在实验室中用于检查皮尔纳机制。另一方面，来自卷心菜尺蠖的生殖细胞具有某些特性，使其成为研究昆虫中皮尔纳的理想选择。然而，飞蛾的基因组尚未完全解析。这阻碍了对控制害虫的新方法，如何使用生殖细胞来生产更有用的蛋白质或皮尔纳的研究。解码基因组需要几个步骤。首先，整个遗传信息被分解成可以破译的短片段。接下来，这些片段需要被“组装”--按照正确的顺序放在一起，以重建整个基因组。基因组的某些部分由相同部分的重复形成，可能难以组装。最后，基因组必须被注释：不同的区域--比如基因--需要被识别和标记。在这里，Fu等人组装并注释了卷心菜尺蠖的基因组，并在此过程中开发了可用于基因组中具有大量重复序列的其他物种的策略。有机会获得的全部遗传信息，使人们有可能使用他们的生殖细胞，以产生新类型的蛋白质，例如用于制药目的。Fu等人继续通过改进方案使这些细胞的工作变得更加容易，以便现代研究技术，如基因编辑技术CRISPR-Cas9，可以用于Looper生殖系细胞。基因组图谱还显示，参与从昆虫体内清除毒素的基因正在迅速进化，这可能解释了为什么飞蛾很容易对杀虫剂产生抗药性。这些知识可以帮助找到控制害虫的新方法。最后，参与RNA沉默的基因被标记：结果表明整个染色体是piRNA的来源。结合Fu等人开发的新方案，这可能使卷心菜尺蠖生殖系细胞成为任何皮尔纳机制研究的默认选择。皮尔纳在蛾中的作用方式可以为人类皮尔纳的研究提供信息，因为这些过程在动物王国中高度相似。
We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2´-O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo. A common moth called the cabbage looper is becoming increasingly relevant to the scientific community. Its caterpillars are a serious threat to cabbage, broccoli and cauliflower crops, and they have started to resist the pesticides normally used to control them. Moreover, the insect’s germline cells – the ones that will produce sperm and eggs – are used in laboratories as ‘factories’ to artificially produce proteins of interest. The germline cells also host a group of genetic mechanisms called RNA silencing. One of these processes is known as piRNA, and it protects the genome against ‘jumping genes’. These genetic elements can cause mutations by moving from place to place in the DNA: in germline cells, piRNA suppresses them before the genetic information is transmitted to the next generation. Not all germline cells grow equally well under experimental conditions, or are easy to use to examine piRNA mechanisms in a laboratory. The germline cells from the cabbage looper, on the other hand, have certain characteristics that would make them ideal to study piRNA in insects. However, the genome of the moth had not yet been fully resolved. This hinders research on new ways of controlling the pest, on how to use the germline cells to produce more useful proteins, or on piRNA. Decoding a genome requires several steps. First, the entire genetic information is broken in short sections that can then be deciphered. Next, these segments need to be ‘assembled’ – put together, and in the right order, to reconstitute the entire genome. Certain portions of the genome, which are formed of repeats of the same sections, can be difficult to assemble. Finally, the genome must be annotated: the different regions – such as the genes – need to be identified and labeled. Here, Fu et al. assembled and annotated the genome of the cabbage looper, and in the process developed strategies that could be used for other species with a lot of repeated sequences in their genomes. Having access to the looper’s full genetic information makes it possible to use their germline cells to produce new types of proteins, for example for pharmaceutical purposes. Fu et al. went on to make working with these cells even easier by refining protocols so that modern research techniques, such as the gene-editing technology CRISPR-Cas9, can be used on the looper germline cells. The mapping of the genome also revealed that the genes involved in removing toxins from the insects’ bodies are rapidly evolving, which may explain why the moths readily become resistant to insecticides. This knowledge could help finding new ways of controlling the pest. Finally, the genes involved in RNA silencing were labeled: results show that an entire chromosome is the source of piRNAs. Combined with the new protocols developed by Fu et al., this could make cabbage looper germline cells the default option for any research into the piRNA mechanism. How piRNA works in the moth could inform work on human piRNA, as these processes are highly similar across the animal kingdom.