A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology-猫眼课题宝

DOI：

10.1093/dnares/dsz003

发表时间：

2018-09

期刊：

DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

M. Matsunami;Miyuki Suzuki;Yoshikazu Haramoto;A. Fukui;Takeshi Inoue;K. Yamaguchi;I. Uchiyama;Kazuki Mori;K. Tashiro;Yuzuru Ito;T. Takeuchi;Ken-ichi T. Suzuki;K. Agata;S. Shigenobu;Toshinori Hayashi

有尾目两栖类蝾螈具有独特的生物学特性，特别是具有突出的再生能力。伊比利亚棱纹蝾螈（Pleurodeles waltl）是一种很有前途的模式蝾螈沿着其成功开发了简单的育种系统和高效的转基因和基因组编辑方法。然而，目前对华岗菇的遗传信息了解有限。在本研究中，我们进行了一个密集的转录组分析，利用RNA测序建立基因模型和注释。我们从胚胎发育过程中的11种不同组织和9个时间点的各种样品中产生了12亿个Illumina读数。它们被组装成202，788个非冗余重叠群，这些重叠群似乎覆盖了几乎完整（约98%）的P. waltl蛋白编码基因。使用基因集作为参考，我们的基因网络分析确定再生，发育阶段，和组织特异性共表达基因模块。与其他脊椎动物的同源分析揭示了两栖动物的基因库进化，包括有尾两栖类特有的bmp 4缺失和wnt 11b重复。我们的转录组资源将加强未来的研究，采用这种新兴的模式动物再生研究以及其他领域，如发育生物学，干细胞生物学，癌症研究，行为学和毒理基因组学。这些数据可通过我们的门户网站iNewt（http：//www.nibb.ac.jp/imori/main/）查阅。

Urodele amphibian newts have unique biological properties, notably including prominent regeneration ability. Iberian ribbed newt, Pleurodeles waltl, is a promising model newt along with the successful development of the easy breeding system and efficient transgenic and genome editing methods. However, genetic information of P. waltl was limited. In the present study, we conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build gene models and annotate them. We generated 1.2 billion Illumina reads from a wide variety of samples across 11 different tissues and 9 time points during embryogenesis. They were assembled into 202,788 non-redundant contigs that appear to cover nearly complete (~98%) P. waltl protein-coding genes. Using the gene set as a reference, our gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Ortholog analyses with other vertebrates revealed the gene repertoire evolution of amphibians which includes urodele-specific loss of bmp4 and duplications of wnt11b. Our transcriptome resource will enhance future research employing this emerging model animal for regeneration research as well as other areas such as developmental biology, stem cell biology, cancer research, ethology and toxico-genomics. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/).

A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology

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