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Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica

文献类型： 外文期刊

作者： Guan, Jin 1 ; Yin, Shuxia 2 ; Yue, Yuesen 1 ; Liu, Lingyun 1 ; Guo, Yidi 1 ; Zhang, Hui 1 ; Fan, Xifeng 1 ; Teng, Ke 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Inst Grassland Flowers & Ecol, Beijing 100097, Peoples R China

2.Beijing Forestry Univ, Sch Grassland Sci, Beijing 100083, Peoples R China

关键词： Zoysia japonica; Full-length transcriptome; Alternative splicing; Fusion transcripts; Transcription factors; Senescence

期刊名称：BMC PLANT BIOLOGY （ 影响因子：5.26； 五年影响因子：5.761 ）

ISSN： 1471-2229

年卷期： 2022 年 22 卷 1 期

页码：

收录情况： SCI

摘要： Background Zoysia japonica is an important warm-season turfgrass used worldwide. Although the draft genome sequence and a vast amount of next-generation sequencing data have been published, the current genome annotation and complete mRNA structure remain incomplete. Therefore, to analyze the full-length transcriptome of Z. japonica, we used the PacBio single-molecule long-read sequencing method in this study. Results First, we generated 37,056 high-confidence non-redundant transcripts from 16,005 gene loci. Next, 32,948 novel transcripts, 913 novel gene loci, 8035 transcription factors, 89 long non-coding RNAs, and 254 fusion transcripts were identified. Furthermore, 15,675 alternative splicing events and 5325 alternative polyadenylation sites were detected. In addition, using bioinformatics analysis, the underlying transcriptional mechanism of senescence was explored based on the revised reference transcriptome. Conclusion This study provides a full-length reference transcriptome of Z. japonica using PacBio single-molecule long-read sequencing for the first time. These results contribute to our knowledge of the transcriptome and improve the knowledge of the reference genome of Z. japonica. This will also facilitate genetic engineering projects using Z. japonica.

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