Medaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high-quality genome sequence and a variety of genetic tools are available for this model organism. However, existing genome annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long-read RNA-seq, short-read RNA-seq, and ATAC-seq. By integrating these data sets, we constructed a much-improved gene model set including about 17,000 novel isoforms and identified 1600 transcription factors, 1100 long noncoding RNAs, and 150,000 potential cis-regulatory elements as well. Time-series data sets provided another dimension of information. With the expression dynamics of genes and accessibility dynamics of cis-regulatory elements, we investigated isoform switching, as well as regulatory logic between accessible elements and genes, during embryogenesis. We built a user-friendly medaka omics data portal to present these data sets. This resource provides the first comprehensive omics data sets of medaka embryogenesis. Ultimately, we term these three assays as the minimum ENCODE toolbox and propose the use of it as the initial and essential profiling genomic assays for model organisms that have limited data available. This work will be of great value for the research community using medaka as the model organism and many others as well.

中文翻译：

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花aka胚胎发生的动态转录和染色质可及性景观。

Medaka（Oryzias latipes）已经成为重要的脊椎动物模型，广泛用于遗传学，发育生物学，环境科学和许多其他领域。该模型生物可使用高质量的基因组序列和多种遗传工具。但是，现有的基因组注释仍然是基本的，因为它主要基于计算预测和短读RNA-seq数据。在这里，我们报告了由长读RNA-seq，短读RNA-seq和ATAC-seq构成的花aka胚发生的动态转录组景观。通过整合这些数据集，我们构建了一个经过大量改进的基因模型集，包括大约17,000个新的同工型，并鉴定了1600个转录因子，1100个长非编码RNA和15万个潜在的顺-调节元素。时间序列数据集提供了信息的另一个方面。利用基因的表达动力学和顺式调控元件的可及性动态，我们研究了胚胎发生过程中同工型转换以及可及性元件与基因之间的调控逻辑。我们建立了一个用户友好的medaka omics数据门户来展示这些数据集。该资源提供了medaka胚胎发生的第一个综合组学数据集。最终，我们将这三种测定法称为最小的ENCODE工具箱，并建议将其用作数据有限的模型生物的初始和基本分析基因组测定法。这项工作对于使用medaka作为模型生物的研究界以及其他许多领域将具有重大价值。