从超深度测序揭示了玉米近乎完整的玉米苗转录组快照

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评论作者：Candice Hirsch

新一代测序已扩大生物学家能够问的问题的广度和深度。下一代测序已经被用来研究玉米和其他物种基因组、转录组和表观遗传组。然而，与任何技术一样，了解下一代测序方法的优点和局限性是很重要的。在本文中，使用B73幼苗转录组极深测序的RNA测序（RNA-SEQ ），作者解决了与测序深度后果的一个重要问题。在本文的研究结果中，作者显示相对于模拟的浅测序（2000万读取），他们能平均检测多于7,444个5b转录段，并表明许多缺失的转路段与转录因子的活动有关。他们还能够改善目前B73的结构注解，包括扩大基因模型和辨识未注解的基因。本文为序列的深度提供了重要见解，这在一定程度上取决于该研究的科学目标。

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing

Abstract: RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.