Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China.
BMC Plant Biol. 2018 Nov 26;18(1):300. doi: 10.1186/s12870-018-1534-8.
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.
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.
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.
红车轴草（Trifolium pratense L.）是一种重要的冷季豆科植物，是继紫花苜蓿之后种植最广泛的饲料豆科植物。尽管已经公布了基因组草图，但 mRNA 转录本的序列和完整结构仍不清楚，这限制了对红车轴草的进一步研究。
本研究利用单分子长读测序技术对红车轴草转录组进行测序，以鉴定全长剪接异构体，从已知基因中鉴定出 29730 个新的异构体和 2194 个新基因的新异构体。共鉴定出 5492 个可变剪接事件，红车轴草中大多数可变剪接事件被校正为内含子保留。此外，在 SMRT 检测到的 15229 个基因中，包括 186517 个转录本在内的 8719 个基因至少有一个 poly(A) 位点。此外，我们还鉴定出 4333 个长非编码 RNA 和 3762 个融合转录本。
我们利用 PacBio SMRT 分析了红车轴草的全长转录组。这些新发现为改进红车轴草基因组草图注释和全面表征红车轴草转录组提供了重要信息。
