A Comprehensive View Of Brachypodium Distachyon Transcriptome By Using Single Molecular Real-Time Sequencing

Brachypodium distachyon,as a model plant of monocot grasses,has a compact genome and high co-linearity with important grass crop,such as wheat,barely,rice and sorghum,providing a great reference to Wheat,Barley and various important forage grass crops.However,due to the limitation of the technology,the post-transcriptional mechanism of B.distachyon has not been fully resolved with good coverage and precision.In this study,we pooled together high-quality RNA of leaf,root and rhizome of B.distachyon,which was sequenced using Pacific Biosciences(PacBio)single-molecule real-time sequencing technology which shown no GC bias and able to produce full length transcript.After quality control,filtering,error-correction and clustering,we finally obtained 32,833 full-length high quality isoforms with an average length 2055bp,covering-47%genes from B.distachyon genome.We also detected 4394 genes which shown mis-annotated in the current release of gene annotation and 1010 potentially novel genes.Additionally,we identified 75 high-confidence fusion genes based on RNAseq data.Besides,we also compared advantage of PacBio isoforms and RNAseq reads and showed that PacBio reads have helped in improving the structure of the reference transcripts while less desirable in gene expression quantification due to their relatively low sequencing depth compared to the short-read Illumina sequencing.We also identified 3800 genes exhibited alternative splicing(AS)and 10109 genes show alternative polyadenylation(APA)which accounting for?11%and?30%annotated genes respectively.Finally,we identified likely miRNA targets and high quality lncRNAs.These results revealed that these target and lncRNAs were related to AS and APA regulation.In summary,our results not only showed that we are able to reconstruct B.distachyon transcriptome with better coverage and precision than previous studies which potentially could lead to much better gene annotations,but also revealed that post transcriptional regulation is sophisticated and massive of AS and APA genes were found would contribute to a better understanding of the post transcriptional mechanism inside B.distachyon.