PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome
文献类型： 外文期刊
作者： Teng, Ke 1 ; Teng, Wenjun 1 ; Wen, Haifeng 1 ; Yue, Yuesen 1 ; Guo, Weier 2 ; Wu, Juying 1 ; Fan, Xifeng 1 ;
作者机构： 1.Beijing Acad Agr & Forestry Sci, Beijing Res & Dev Ctr Grass & Environm, Beijing 100097, Peoples R China
2.Univ Calif Davis, Dept Plant Biol, Davis, CA 95616 USA
关键词： Carex breviculmis; SMRT sequencing; Alternative splicing events; LncRNA; Transcription factors
期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）
ISSN： 1471-2164
年卷期： 2019 年 20 卷 1 期
页码：
收录情况： SCI
摘要： Background: Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing ( NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts. Results: In this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing. Conclusions: This study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis.
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