The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts

Abstract

Background High-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the generation of full-length sequences revealing splice variants that may be important in regulating gene action. Investigation of the diversity of transcripts in the rice transcriptome including splice variants was conducted using PacBio long-read sequence data to improve the annotation of the rice genome. Results A cDNA library was prepared from RNA extracted from leaves, roots, seeds, inflorescences, and panicles of O. sativa ssp. japonica var Nipponbare and sequenced on a PacBio Sequel platform. This produced 346,190 non-redundant full-length non-chimeric reads (FLNC) resulting in 33,504 high-quality transcripts. Half of the transcripts were multi-exonic and entirely matched with the reference transcripts. However, 14,874 novel isoforms were also identified resulting predominantly from intron retention and at least one novel splice site. Intron retention was the prevalent alternative splicing event and exon skipping was the least observed. Of 73,659 splice junctions, 12,755 (17%) represented novel splice junctions with canonical and non-canonical intron boundaries. The complexity of the transcriptome was examined in detail for 19 starch synthesis-related genes, defining 276 spliced isoforms of which 94 splice variants were novel. Conclusion The data reveal the great complexity of the rice transcriptome. The novel transcripts provide new insights that may be a key input in future research to improve the annotation of the rice genome.

The Landscape of Fusion Transcripts in Plants: A New Insight into Genome Complexity

“…Transcription-mediated gene fusion in plants was thought to be extremely rare for a long time. However, as the last decade unfolded, genome-wide surveys unveiled a multitude of transcription-induced chimeras [25][26][27]74]. Nevertheless, the functional and evolutionary potential, as well as the emergence of these fusion transcripts in plants, remains relatively uncharted territory.…”

“…in Oryza, it was estimated that fusion gene origination rates, contributing to the emergence of new genes, are notably high (63 fusion genes per species per million years) [24,30]. Another study conducted on rice reported that 6.8% of the total spliced isoforms were fusion transcripts [27]. Zhang et al identi ed that approximately 50% of novel genes on the short arm of chromosome 3 in rice have emerged through chimeric mechanisms [75].…”

“…This led to the revelation of fusion transcripts in plant genomes. Over the past decade, there has been substantial progress in identifying FTs in various plant species, including [24][25][26] red clover (Trifolium pratense L.) [26], Oryza [25,27], Arabidopsis thaliana [28], Camellia sinensis [29], and Zea mays [30]. These plant-speci c fusion transcripts contribute to the complexity of plant transcriptome, potentially playing roles in stress responses, morphological alterations, or gene silencing [31][32][33][34][35][36].…”

Development of CRISPR/Cas9 Construct in Rice (Oryza sativa subsp. indica) Using Golden Gate Cloning Method Towards Drought Tolerance

“…Then, homology search was conducted with BLAST DIAMOND and proceeded with the BLAST2GO tool by utilising OmicsBox. The OmicsBox software allows for functional gene annotation utilities such as high throughput BLAST, Mapping, InterProScan, and Gene Ontology (GO) annotation [23,24].…”

SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

“…This approach has been used to profile complex transcriptomes from neural tissues [2], tumor cells [3], T-cell receptors [4], and multiple plant tissues [5]. In addition, lrRNA-seq has been used to study allele-specific gene expression [6], circular RNAs [7], functional pseudogenes [8], and single-cell isoform diversity [9] [4].…”