Abstract
BackgroundRed 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.ResultsIn 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.ConclusionsWe 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.
Highlights
Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa
The sorghum transcriptome was analyzed by the 3rd sequencing technology and results showed that sequencing data uncovered over 7000 novel alternative splicing events, about 11,000 novel splice isoforms, over 2100 novel genes and several thousand transcripts that differ in 3′ untranslated regions due to alternative polyadenylation (APA) [9]
The results showed that more than 42,280 distinct splicing isoforms were derived from 128,667 intron-containing full-length non-chimeric (FLNC) reads and 25,069 polyadenylation sites from 11,450 genes, 6311 of which have APA sites [12]
Summary
Red clover (Trifolium pratense L.) is an important cool-season legume plant, which is the most widely planted forage legume after alfalfa. The sorghum transcriptome was analyzed by the 3rd sequencing technology and results showed that sequencing data uncovered over 7000 novel alternative splicing events, about 11,000 novel splice isoforms, over 2100 novel genes and several thousand transcripts that differ in 3′ untranslated regions due to APA [9]. The results showed that more than 42,280 distinct splicing isoforms were derived from 128,667 intron-containing full-length non-chimeric (FLNC) reads and 25,069 polyadenylation sites from 11,450 genes, 6311 of which have APA sites [12]. 867 novel high-confidence lncRNAs were identified and had a much longer mean length than those identified by Illumina short-read sequencing [10] Those works provided useful information of transcriptomes and served as valuable resources for further research
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