Single-molecule long-read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis)
Single-molecule long-read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis)
复制标题
单分子长读长测序揭示了玉米及其野生近缘类蜀黍（Zea mays ssp. parviglumis）之间广泛的基因组和转录组变异
DOI：
10.1111/1755-0998.13454
复制
发表时间：
2021
影响因子：
7.7
通讯作者：
Li Lin
中科院分区：
文献类型：
--
作者：
Li Zhao;Han Linqian;Luo Zi;Li Lin
玉米（Zea maysssp.parviglumis）的野生祖先大刍草（Teosinte），是现代玉米品系改良的重要种质资源。然而，我们关于大刍草的遗传和基因组信息有限，并且缺乏最先进的工具来注释在没有参考基因组的情况下通过单分子长读段测序组装的转录组。在这里，我们对来自大刍草近交系TIL11的五种组织的cDNA文库进行了单分子长读序测序，并鉴定了70，044种非冗余转录异构体。我们设计了一个最先进的、基于机器学习的生物信息学管道DenovoAS_blog，在没有完整参考基因组的情况下注释TIL11转录组，准确率高达91%，为复杂基因组提供了一个强大的基因分类器。此外，我们通过Nanopore测序构建了具有16，633个高质量重叠群和112 kb的N50的TIL11基因组草案。来自从大刍草扩展到玉米的家族的基因在基因本体（GO）术语“RNA修饰途径”中显著富集，并且在TIL11中比在玉米自交系B73中具有更多的转录异构体。TIL11和B73之间的基因表现出共线性，并且基因间区域被转座因子广泛改变。本研究加深了对玉米驯化的认识，并为玉米野生种质资源的利用提供了参考。
Teosinte (Zea maysssp.parviglumis), the wild progenitor of maize (Zea maysL.), is an important germplasm resource for improvement of modern maize lines. However, we have limited genetic and genomic information about teosinte and lack state‐of‐the‐art tools to annotate transcriptomes assembled by single‐molecule long‐read sequencing without a reference genome. Here, we employed single‐molecule long‐read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 nonredundant transcript isoforms. We devised a state‐of‐the‐art, machine learning‐based bioinformatics pipeline DenovoAS_Finder to annotate the TIL11 transcriptome without a complete reference genome with an accuracy of up to 91%, providing a robust gene classifier of complex genomes. Additionally, we constructed a draft TIL11 genome with 16,633 high‐quality contigs and a N50 of 112 kb by Nanopore sequencing. Genes from families that expanded from teosinte to maize were significantly enriched in the gene ontology (GO) term “RNA modification pathway” and had more transcript isoforms in TIL11 than in the maize inbred line B73. Genes showed collinearity between TIL11 and B73, and intergenic regions were extensively altered by transposable elements. Our study furthers the understanding of maize domestication and provides a resource for the utilization of wild germplasm in maize breeding.