The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition.
The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition.
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DOI：
10.1038/s41598-021-03642-9
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发表时间：
2022-01-07
影响因子：
4.6
通讯作者：
Griffiths-Jones S
中科院分区：
文献类型：
--
作者：
Calvo L;Birgaoanu M;Pettini T;Ronshaugen M;Griffiths-Jones S
Parhyale hawaiensis已成为甲壳类动物的首选模型，这是由于其易处理性，易于成像，测序基因组以及CRISPR/Cas9基因组编辑工具的开发。然而，缺乏跨越胚胎发育的转录组数据集，并且几乎没有非蛋白质编码RNA的注释，包括microRNA。我们在Parhyale中使用配对大小选择的RNA-seq文库在7个时间点对microRNA，mRNA和长非编码RNA进行了测序，涵盖了胚胎发育中的重要转变。针对microRNA，我们在Parhyale中注释了175个位点，其中88个没有已知的同源物。我们使用这些数据来注释37个甲壳动物基因组的microRNAome，并提出了一个核心甲壳动物microRNA集约61个序列家族。我们研究的动态表达的microRNA和mRNA在母合子过渡。我们的数据表明，合子基因组激活发生在两个波Parhyale与microRNA转录几乎完全在第二波。与其他节肢动物的研究结果相反，我们没有预测microRNA在清除母体转录物中的一般作用。这些数据显着扩展了Parhyale可用的转录组学资源，并促进其作为模式生物的研究过程中的小RNA从胚胎发育到再生。
Parhyale hawaiensis has emerged as the crustacean model of choice due to its tractability, ease of imaging, sequenced genome, and development of CRISPR/Cas9 genome editing tools. However, transcriptomic datasets spanning embryonic development are lacking, and there is almost no annotation of non-protein-coding RNAs, including microRNAs. We have sequenced microRNAs, together with mRNAs and long non-coding RNAs, in Parhyale using paired size-selected RNA-seq libraries at seven time-points covering important transitions in embryonic development. Focussing on microRNAs, we annotate 175 loci in Parhyale, 88 of which have no known homologs. We use these data to annotate the microRNAome of 37 crustacean genomes, and suggest a core crustacean microRNA set of around 61 sequence families. We examine the dynamic expression of microRNAs and mRNAs during the maternal-zygotic transition. Our data suggest that zygotic genome activation occurs in two waves in Parhyale with microRNAs transcribed almost exclusively in the second wave. Contrary to findings in other arthropods, we do not predict a general role for microRNAs in clearing maternal transcripts. These data significantly expand the available transcriptomics resources for Parhyale, and facilitate its use as a model organism for the study of small RNAs in processes ranging from embryonic development to regeneration.
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