Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation.
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation.
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DOI：
10.1186/s13059-018-1498-x
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发表时间：
2018-08-24
期刊：
影响因子：
12.3
通讯作者：
Parkinson J
中科院分区：
文献类型：
--
作者：
Swapna LS;Molinaro AM;Lindsay-Mosher N;Pearson BJ;Parkinson J
在Lophotrochozoa/Spiralia superphylum中，很少有生物具有像淡水真涡虫那样高的快速检测基因功能和单细胞转录组学的能力。特别是Schmidtea medialacea物种已成为研究成体干细胞生物学和再生机制的有力模型。尽管如此，缺乏系统的尝试来定义基因互补及其注释，限制了比较分析，详细说明了生物化学途径的保护和识别谱系特异性创新。在这项研究中，我们比较了几个转录组，并定义了一个强大的35，232个转录本。由此，我们进行系统的功能注释，并进行基因组规模的代谢重建的S。地中海。跨物种的基因内容比较确定保守的，特定的谱系，和扩大的基因家族，这可能有助于再生性能的涡虫。特别是，我们发现TRAF基因家族在真涡虫中得到了极大的扩展。我们进一步提供了2000个细胞的单细胞RNA测序分析，揭示了由基因表达的独特特征定义的已知和新型细胞类型。其中包括一种新的间充质细胞群以及一种参与眼睛再生的细胞类型。我们的代谢重建的整合进一步揭示了给定细胞类型适应能量和核苷酸生物合成途径以支持其专门作用的程度。总的来说，S.与其他模型系统相比，medicleea显示出高水平的基因和途径保守性，使其成为研究这些途径在干细胞生物学和再生中的作用的可行模型。本文的在线版本（10.1186/s13059-018-1498-x）包含补充材料，可供授权用户使用。
In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic functional annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that the TRAF gene family has been greatly expanded in planarians. We further provide a single-cell RNA sequencing analysis of 2000 cells, revealing both known and novel cell types defined by unique signatures of gene expression. Among these are a novel mesenchymal cell population as well as a cell type involved in eye regeneration. Integration of our metabolic reconstruction further reveals the extent to which given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles. In general, S. mediterranea displays a high level of gene and pathway conservation compared with other model systems, rendering it a viable model to study the roles of these pathways in stem cell biology and regeneration. The online version of this article (10.1186/s13059-018-1498-x) contains supplementary material, which is available to authorized users.
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影响因子：
14.9
作者：
NCBI Resource Coordinators
通讯作者：
NCBI Resource Coordinators
DOI：
10.1016/j.cbpb.2017.07.001
发表时间：
2017-11
期刊：
Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology
影响因子：
--
作者：
El Kouni MH
通讯作者：
El Kouni MH
DOI：
10.1093/database/bar068
发表时间：
2012
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Burge S;Kelly E;Lonsdale D;Mutowo-Muellenet P;McAnulla C;Mitchell A;Sangrador-Vegas A;Yong SY;Mulder N;Hunter S
通讯作者：
Hunter S
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
4.6
作者：
Currie, Ko W.;Pearson, Bret J.
通讯作者：
Pearson, Bret J.