背景:鳗鱼的幼体时期是钩头幼虫,具有独特而特殊的身体形态,具有叶状和透明的特征,它们经历了巨大的变态,变成了幼年的玻璃鳗鱼。关于钩头症向玻璃鳗鱼阶段的过渡知之甚少,因为在公海中很难捕捉变态幼虫。然而,日本鳗鱼饲养技术的最新进展使研究鳗鱼的幼虫变态成为可能。在本研究中,我们使用RNA测序研究了日本鳗鱼小脑变态过程中基因表达的动态。
结果:在变态过程中,日本鳗鱼根据形态特征分为7个发育阶段,RNA测序用于收集每个阶段的基因表达数据。身体总共产生了3.548亿次清洁读数,头部产生了3.655亿次清洁读数,在处理原始读取之后。为了过滤表征发育阶段的基因,建立了随机森林算法的分类模型。使用从创建的模型获得的解释变量特征的重要性,我们确定了在鳗鱼变态过程中,在体内选择的46个基因和在头部选择的169个基因,这些基因被定义为“最具特征的基因”。接下来,使用最具特征的基因及其相关基因进行网络分析和随后的基因聚类,然后构建了体内6个簇和头部5个簇。然后,通过基因本体论(GO)富集分析揭示了簇的特征。在日本鳗鱼幼虫变态过程中,每个阶段的表达模式和GO术语与先前的观察和实验一致。
结论:已经产生了变态日本鳗鱼的基因组和转录组资源。通过随机森林算法通过统计建模鉴定了表征日本鳗鱼变态的基因。这些基因的功能与以前在鳗鱼变态过程中的观察和实验一致。
BACKGROUND: Anguillid eels spend their larval period as leptocephalus larvae that have a unique and specialized body form with leaf-like and transparent features, and they undergo drastic metamorphosis to juvenile glass eels. Less is known about the transition of leptocephali to the glass eel stage, because it is difficult to catch the metamorphosing larvae in the open ocean. However, recent advances in rearing techniques for the Japanese eel have made it possible to study the larval metamorphosis of anguillid eels. In the present study, we investigated the dynamics of gene expression during the metamorphosis of Japanese eel leptocephali using RNA sequencing.
RESULTS: During metamorphosis, Japanese eels were classified into 7 developmental stages according to their morphological characteristics, and RNA sequencing was used to collect gene expression data from each stage. A total of 354.8 million clean reads were generated from the body and 365.5 million from the head, after the processing of raw reads. For filtering of genes that characterize developmental stages, a classification model created by a Random Forest algorithm was built. Using the importance of explanatory variables feature obtained from the created model, we identified 46 genes selected in the body and 169 genes selected in the head that were defined as the \"most characteristic genes\" during eel metamorphosis. Next, network analysis and subsequently gene clustering were conducted using the most characteristic genes and their correlated genes, and then 6 clusters in the body and 5 clusters in the head were constructed. Then, the characteristics of the clusters were revealed by Gene Ontology (GO) enrichment analysis. The expression patterns and GO terms of each stage were consistent with previous observations and experiments during the larval metamorphosis of the Japanese eel.
CONCLUSIONS: Genome and transcriptome resources have been generated for metamorphosing Japanese eels. Genes that characterized metamorphosis of the Japanese eel were identified through statistical modeling by a Random Forest algorithm. The functions of these genes were consistent with previous observations and experiments during the metamorphosis of anguillid eels.