Institute for Data Science and Informatics, University of Missouri, Columbia, USA.
Division of Plant Science and Technology, University of Missouri, Columbia, USA.
Sci Rep. 2023 Feb 3;13(1):1960. doi: 10.1038/s41598-023-29115-9.
Certain cultivars of maize show increased tolerance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaptation, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697-specific RNA-Seq datasets were generated and used for a de novo transcriptome assembly to characterize any genotype-specific genetic features. The assembly was aided by an Iso-Seq library of transcripts generated from various FR697 plant tissue samples. The Necklace pipeline was used to combine a Trinity de novo assembly along with a reference guided assembly and the Viridiplantae proteome to generate an annotated consensus "SuperTranscriptome" assembly of 47,915 transcripts with a N50 of 3152 bp in length. The results were compared by Blastn to maize reference genes, a Benchmarking Universal Single-Copy Orthologs (BUSCO) genome completeness report and compared with three maize reference genomes. The resultant 'SuperTranscriptome' was demonstrated to be of high-quality and will serve as an important reference for analysis of the maize nodal root transcriptomic response to environmental perturbations.
某些玉米品种通过维持根系生长来提高对水分亏缺条件的耐受性。为了更好地理解与这种适应相关的分子机制，从参考自交系 B73 和自交系 FR697 中收集了节根生长区样本，FR697 在水分亏缺下保持根系伸长的能力相对较强。在田间和控制环境条件下，对植物进行了不同的水分胁迫水平处理。生成了 FR697 特异性 RNA-Seq 数据集，并用于从头转录组组装，以表征任何基因型特异性的遗传特征。组装得到了来自不同 FR697 植物组织样本的转录物 Iso-Seq 文库的帮助。使用 Necklace 管道将 Trinity 从头组装与参考引导组装以及 Viridiplantae 蛋白质组结合起来，生成了一个注释共识“SuperTranscriptome”组装，包含 47,915 个转录本，长度为 3152 bp，N50 为 3152 bp。通过 Blastn 将结果与玉米参考基因进行比较，报告了基准通用单拷贝同源物（BUSCO）基因组完整性，并与三个玉米参考基因组进行了比较。结果表明，生成的“SuperTranscriptome”质量很高，将作为分析玉米节根转录组对环境扰动响应的重要参考。
