The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion.
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion.
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DOI：
10.7554/elife.20062
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发表时间：
2016-11-16
期刊：
影响因子：
7.7
通讯作者：
Aboobaker A
中科院分区：
文献类型：
--
作者：
Kao D;Lai AG;Stamataki E;Rosic S;Konstantinides N;Jarvis E;Di Donfrancesco A;Pouchkina-Stancheva N;Sémon M;Grillo M;Bruce H;Kumar S;Siwanowicz I;Le A;Lemire A;Eisen MB;Extavour C;Browne WE;Wolff C;Averof M;Patel NH;Sarkies P;Pavlopoulos A;Aboobaker A
夏威夷扇形甲壳动物是研究发育机制和新近再生的一个很有前途的模式系统。我们已经对基因组进行了测序，可以对所有关键的信号通路、转录因子和非编码RNA进行注释，这将加强正在进行的功能研究。Parhyale是包括甲壳类粮食作物物种在内的马拉科分支的成员。我们分析了Parhyale的免疫相关基因，将其作为这些物种的重要比较系统，这些物种的免疫相关水产养殖问题随着养殖的加强而增加。我们还发现，Parhyale和多角类动物中的其他物种含有进行木质纤维素消化所需的酶组(“吃木头”)，这表明这种能力可能早于这种谱系的多样化。我们的数据为进一步发展Parhyale作为实验模型提供了必要的资源。第一个软体动物基因组将支持正在进行的粮食作物物种比较工作和研究木质纤维素作为能源的研究。Http://dx.doi.org/10.7554/eLife.20062.001是一种海洋甲壳类动物，被称为夏威夷甲壳类，与对虾、虾和螃蟹有亲缘关系，分布在世界各地的热带海岸线上。这个物种最近吸引了科学兴趣，因为它可能是一个新的模型，研究动物胚胎在出生前是如何发育的，以及因为Parhyale可以迅速再生失去的四肢，组织和器官如何再生。事实上，Parhyale具有许多特征，使其成为一种很好的模式生物，它体积小，生长快，易于在实验室中饲养和照料。已经开发了几种研究工具，以使研究Parhyale变得更容易。这包括创建一种系统，在这种动物中使用流行的基因编辑技术CRISPR。然而，大多数模式生物可用的一个关键资源缺失了；这种甲壳类动物的所有遗传信息，也就是它的基因组，都没有完整的序列。Kao，Lai，Stamataki等人。他们现在编辑了Parhyale基因组--比人类基因组略大--并研究了它的遗传学。分析表明，Parhyale拥有能够完全消化植物物质的基因。这是不寻常的，因为大多数这样做的动物都依赖于细菌的帮助。Kao，Lai，Stamataki等人。还识别了一些基因，这些基因为甲壳类动物的免疫系统提供了一些最早的见解，该系统保护这些生物免受疾病的侵袭。Kao，Lai，Stamataki等人。提供了一个资源和发现，可以帮助建立Parhyale作为一个流行的模式生物，用于研究生物学中的几个概念，包括器官再生和胚胎发育。例如，了解Parhyale如何消化植物物质，可以推动生物燃料行业朝着高效生产更绿色能源的方向发展。对其免疫系统的洞察也可以被调整，以使养殖的对虾和对虾更耐感染，从而提高海产品产量。DOI：http://dx.doi.org/10.7554/eLife.20062.002
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source. DOI: http://dx.doi.org/10.7554/eLife.20062.001 The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory. Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available. Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases. Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production. DOI: http://dx.doi.org/10.7554/eLife.20062.002