Genome streamlining in a minute herbivore that manipulates its host plant.
Genome streamlining in a minute herbivore that manipulates its host plant.
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基因组在一分钟内流线型的食草动物操纵它的宿主植物。
DOI：
10.7554/elife.56689
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发表时间：
2020-10-23
期刊：
影响因子：
7.7
通讯作者：
Kant MR
中科院分区：
文献类型：
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作者：
Greenhalgh R;Dermauw W;Glas JJ;Rombauts S;Wybouw N;Thomas J;Alba JM;Pritham EJ;Legarrea S;Feyereisen R;Van de Peer Y;Van Leeuwen T;Clark RM;Kant MR
番茄赤霉病螨（Aculops lycopersici）是地球上最小的动物之一。它是番茄上的一种世界性害虫，能有效地抑制寄主的自然抗性。我们对其基因组进行了测序，这是第一个绒螨，并探索是否有与螨的微小尺寸和生活方式相关的基因组特征。只有32.5 Mb，基因组是迄今为止报道的任何节肢动物中最小的，让人想起微生物真核生物，异常精简。它具有很少的转座因子，微小的基因间区域，并且是显着的内含子贫乏，因为超过80%的编码基因是无内含子的。此外，根据生态专业化理论，这种防御抑制草食动物具有非常少的环境反应基因家族，如参与化学感受和解毒的基因家族。其他损失与该物种高度衍生的身体计划有关。我们的研究结果加速了对后生动物生命在小的物理和基因组大小的限制下的进化力量的理解。节肢动物是一组无脊椎动物，包括昆虫-如苍蝇或甲虫-蜘蛛类-如蜘蛛或蝎子-和甲壳类-包括虾和木虱。最小的节肢动物之一，测量不到0.2毫米，是番茄赤霉病螨Aculops lycopersici。这种蛛形纲动物是地球上最小的动物之一，甚至比一些单细胞生物还小，而且只有四条腿，不像其他蛛形纲动物。它是番茄植物上的主要害虫，对许多其他动物有毒，它以茎和叶的顶部细胞层为食。番茄种植者需要一种方法来识别和治疗番茄赤霉病，但这种微小的物种仍然是一个谜。解决这种害虫的一种方法可能是仔细研究它的基因组，因为这可以揭示螨虫使用什么基因来解毒它的饮食。研究螨的基因组还可以揭示进化如何处理生物变小的信息。一个特别感兴趣的领域是其基因组的整体大小。基因组中并非所有的DNA都是编码蛋白质的基因的一部分;还有所谓的“非编码”DNA。这些序列在控制细胞如何以及何时使用它们的基因方面发挥着重要作用。在人类基因组中，只有1%的DNA编码蛋白质。事实上，大多数人类蛋白质编码基因被称为内含子的非编码DNA序列中断。在这里，Greenhalgh，Dermauw等人对整个番茄赤霉病螨基因组进行了测序，并揭示了这种螨不仅体型微小：这些微小的动物拥有迄今为止报道的最小的节肢动物基因组，几乎比人类基因组小一百倍。这种基因小型化的部分原因似乎是非编码DNA的大量丢失。螨基因组中约40%编码蛋白质，80%的蛋白质编码基因不含内含子。剩下的小型化过程涉及到基因本身的丢失。这些螨已经失去了一些决定身体结构的基因，这可以解释为什么它们的腿比其他蛛形纲动物少。此外，它们只携带一小部分参与感知化学物质和清除毒素的基因，这可以解释为什么它们主要存在于番茄植物中。Greenhalgh，Dermauw et al.的发现揭示了在大小进化的极端情况下基因组可能发生的变化。对其他螨类的基因组进行测序可以揭示这种遗传小型化在进化史上何时发生。此外，更好地了解番茄赤螨基因组可能会导致更早地检测植物侵染的方法的发展，并对番茄农业非常有益。
The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host’s natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite’s minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species’ highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size. Arthropods are a group of invertebrates that include insects – such as flies or beetles – arachnids – like spiders or scorpions – and crustaceans – including shrimp and woodlice. One of the tiniest species of arthropods, measuring less than 0.2 millimeters, is the tomato russet mite Aculops lycopersici. This arachnid is among the smallest animals on Earth, even smaller than some single-celled organisms, and only has four legs, unlike other arachnids. It is a major pest on tomato plants, which are toxic to many other animals, and it feeds on the top cell layer of the stems and leaves. Tomato growers need a way to identify and treat tomato russet mite infestations, but this tiny species remains something of a mystery. One way to tackle this pest may be to take a closer look at its genome, as this could reveal what genes the mite uses to detoxify its diet. Examining the mite’s genome could also reveal information about how evolution handles creatures becoming smaller. An area of particular interest is the overall size of its genome. Not all of the DNA in a genome is part of genes that code for proteins; there are also sections of so-called ‘non-coding’ DNA. These sequences play important roles in controlling how and when cells use their genes. In the human genome, for example, just 1% of the DNA codes for protein. In fact, most human protein-coding genes are interrupted by sequences of non-coding DNA, called introns. Here, Greenhalgh, Dermauw et al. sequence the entire tomato russet mite genome and reveal that not only is the mite's body size miniature: these tiny animals have the smallest arthropod genome reported to date, almost a hundred times smaller than the human genome. Part of this genetic miniaturization seems to be down to massive loss of non-coding DNA. Around 40% of the mite genome codes for protein, and 80% of its protein coding genes contain no introns. The rest of the miniaturization involves loss of genes themselves. The mites have lost some of the genes that determine body structure, which could explain why they have fewer legs than other arachnids. Additionally, they only carry a small set of genes involved in sensing chemicals and clearing toxins, which could explain why they are mostly found on tomato plants. Greenhalgh, Dermauw et al.’s findings shed light on what may happen to the genome at the extremes of size evolution. Sequencing the genomes of other mites could reveal when in evolutionary history this genetic miniaturization occurred. Furthermore, a better understanding of the tomato russet mite genome could lead to the development of methods to detect the infestation of plants earlier and be highly beneficial for tomato agriculture.