Yang Kevin Yi, Chen Yuan, Zhang Zuming, Ng Patrick Kwok-Shing, Zhou Wayne Junwei, Zhang Yinfeng, Liu Minghua, Chen Junyuan, Mao Bingyu, Tsui Stephen Kwok-Wing
School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
Sci Rep. 2016 Mar 16;6:23195. doi: 10.1038/srep23195.
Vertebrates diverged from other chordates approximately 500 million years ago and have adopted several modifications of developmental processes. Amphioxus is widely used in evolutionary developmental biology research, such as on the basic patterning mechanisms involved in the chordate body plan and the origin of vertebrates. The fast development of next-generation sequencing has advanced knowledge of the genomic organization of amphioxus; however, many aspects of gene regulation during amphioxus development have not been fully characterized. In this study, we applied high-throughput sequencing on the transcriptomes of 13 developmental stages of Chinese amphioxus to gain a comprehensive understanding of transcriptional processes occurring from the fertilized egg to the adult stage. The expression levels of 3,423 genes were significantly changed (FDR ≤ 0.01). All of these genes were included in a clustering analysis, and enrichment of biological functions associated with these clusters was determined. Significant changes were observed in several important processes, including the down-regulation of the cell cycle and the up-regulation of translation. These results should build a foundation for identifying developmentally important genes, especially those regulatory factors involved in amphioxus development, and advance understanding of the developmental dynamics in vertebrates.
脊椎动物大约在5亿年前从其他脊索动物分化而来，并对发育过程进行了多种修饰。文昌鱼广泛应用于进化发育生物学研究，例如关于脊索动物身体结构的基本模式形成机制以及脊椎动物的起源。下一代测序技术的快速发展推动了对文昌鱼基因组组织的认识；然而，文昌鱼发育过程中基因调控的许多方面尚未得到充分表征。在本研究中，我们对中国文昌鱼13个发育阶段的转录组进行了高通量测序，以全面了解从受精卵到成体阶段发生的转录过程。3423个基因的表达水平发生了显著变化（FDR≤0.01）。所有这些基因都纳入了聚类分析，并确定了与这些聚类相关的生物学功能富集情况。在几个重要过程中观察到了显著变化，包括细胞周期的下调和翻译的上调。这些结果应为鉴定发育重要基因，特别是参与文昌鱼发育的调控因子奠定基础，并促进对脊椎动物发育动态的理解。
