Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics
Diversity within diversity: Parasite species richness in poison frogs assessed by transcriptomics
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多样性中的多样性：通过转录组学评估毒蛙寄生虫物种丰富度
DOI：
10.1016/j.ympev.2018.03.015
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发表时间：
2018
影响因子：
4.1
通讯作者：
Coloma, Luis A.
中科院分区：
文献类型：
--
作者：
Santos, Juan C.;Tarvin, Rebecca D.;O'Connell, Lauren A.;Blackburn, David C.;Coloma, Luis A.
共生体（如内寄生虫和共生体）在寄主生态中发挥着不可或缺的作用，但在许多情况下，它们的多样性可能被低估了。虽然传统上使用形态学、保守基因序列和散弹枪宏基因组学来表征内寄生虫，但宿主转录组是鉴定这些生物多样性的未充分利用的资源。通过从宿主转录组中分离非宿主转录本，单个宿主组织现在可以同时揭示其内寄生虫物种丰富度（即不同分类群的数量），并提供对寄生虫基因表达的见解。这些方法可以用于宿主分类群，其内寄生虫大多是未知的，如热带两栖动物。在这里，我们把重点放在毒蛙（石蛙科）作为宿主，这是一个新热带分支，以其明亮的颜色和防御性生物碱而闻名。这些毒素是防止脊椎动物捕食者（如蛇和鸟）、细菌和咬皮肤的体外寄生虫（如蚊子）的有效保护；然而，对它们对真核内寄生虫的威慑作用知之甚少。利用树线虫的新转录组，我们开发了一个生物信息学管道，用于鉴定内寄生虫，该管道使用宿主注释RNA-seq数据和一组优先寄生虫分类术语，用于挖掘特定的内寄生虫。我们发现了一个大的蠕虫和原生动物群落，它们大多局限于消化道和一些全身寄生虫（如锥虫）。与我们的预期相反，所有的石斛蛙，无论是否存在生物碱防御，都有内寄生虫，其物种丰富度最高的地方是青蛙的消化道。其中一些生物（如蛔虫）可能被证明是多面手，因为它们没有被发现与它们的青蛙宿主共同多样化。我们提出，体内寄生虫可能通过在生物碱含量比青蛙皮肤少的组织中定居，从而逃脱毒蛙的化学防御，而青蛙皮肤是储存大多数毒素的地方。
Symbionts (e.g., endoparasites and commensals) play an integral role in their host's ecology, yet in many cases their diversity is likely underestimated. Although endoparasites are traditionally characterized using morphology, sequences of conserved genes, and shotgun metagenomics, host transcriptomes constitute an underused resource to identify these organisms’ diversity. By isolating non-host transcripts from host transcriptomes, individual host tissues can now simultaneously reveal their endoparasite species richness (i.e., number of different taxa) and provide insights into parasite gene expression. These approaches can be used in host taxa whose endoparasites are mostly unknown, such as those of tropical amphibians. Here, we focus on the poison frogs (Dendrobatidae) as hosts, which are a Neotropical clade known for their bright coloration and defensive alkaloids. These toxins are an effective protection against vertebrate predators (e.g., snakes and birds), bacteria, and skin-biting ectoparasites (e.g., mosquitoes); however, little is known about their deterrence against eukaryotic endoparasites. Withde novotranscriptomes of dendrobatids, we developed a bioinformatics pipeline for endoparasite identification that uses host annotated RNA-seq data and set ofa prioriparasite taxonomic terms, which are used to mine for specific endoparasites. We found a large community of helminths and protozoans that were mostly restricted to the digestive tract and a few systemic parasites (e.g.,Trypanosoma). Contrary to our expectations, all dendrobatid frogs regardless of the presence of alkaloid defenses have endoparasites, with their highest species richness located in the frog digestive tract. Some of these organisms (e.g., roundworms) might prove to be generalists, as they were not found to be co-diversifying with their frog hosts. We propose that endoparasites may escape poison frogs’ chemical defenses by colonizing tissues with fewer alkaloids than the frog’s skin, where most toxins are stored.