Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing.
Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing.
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通过单分子长读长测序分析红三叶草（Trifolium pratense L.）的转录本和剪接亚型
DOI：
10.1186/s12870-018-1534-8
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发表时间：
2018-11-26
影响因子：
5.3
通讯作者：
Xu L
中科院分区：
文献类型：
--
作者：
Chao Y;Yuan J;Li S;Jia S;Han L;Xu L
背景：红三叶草（Trifolium pratense L.）是一种重要的冷季型豆科植物，是继苜蓿之后种植最广泛的饲用豆科植物。结果：本研究利用单分子长片段测序技术对三叶草转录组进行了全序列测定，共鉴定出29,730个已知基因的新剪接异构体和2194个新基因的新剪接异构体。总共鉴定了5492个可变剪接事件，并且红三叶草中的大多数可变剪接事件被校正为内含子保留。此外，在SMRT检测的15，229个基因中，8719个（包括186，517个转录本）具有至少一个poly（A）位点。此外，我们确定了4333长的非编码RNA和3762融合transcripts.Conclusions：我们分析了全长转录组的红三叶草与PacBio SMRT。这些新发现为完善红三叶草基因组草图注释和全面表征红三叶草转录组提供了重要信息。
Background:Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. Although a draft genome sequence was published already, the sequences and completed structure of mRNA transcripts remain unclear, which limit further explore on red clover.Results:In this study, the red clover transcriptome was sequenced using single-molecule long-read sequencing to identify full-length splice isoforms, and 29,730 novel isoforms from known genes and 2194 novel isoforms from novel genes were identified. A total of 5492 alternative splicing events was identified and the majority of alter spliced events in red clover was corrected as intron retention. In addition, of the 15,229 genes detected by SMRT, 8719 including 186,517 transcripts have at least one poly(A) site. Furthermore, we identified 4333 long non-coding RNAs and 3762 fusion transcripts.Conclusions:We analyzed full-length transcriptome of red clover with PacBio SMRT. Those new findings provided important information for improving red clover draft genome annotation and fully characterization of red clover transcriptome.
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