Full-length transcriptome reconstruction reveals genetic differences in hybrids of Oryza sativa and Oryza punctata with different ploidy and genome compositions

Abstract

Background Allopolyploid breeding is an efficient technique for improving the low seed setting rate of autotetraploids in plant breeding and one of the most promising breeding methods. However, there have been few comprehensive studies of the posttranscriptional mechanism in allopolyploids. Results By crossing cultivated rice (Oryza sativa, genome AA) with wild rice (Oryza punctata, genome BB), we created hybrid rice lines with different ploidy and genome compositions [diploid hybrid F01 (AB), allotetraploid hybrid F02 (AABB) and F03 (AAAB)]. The genetic differences of the hybrids and the mechanism of allopolyploid breeding dominance were revealed through morphological and cytological observations and single molecule real-time sequencing techniques. The tissues and organs of allotetraploid hybrid F02 exhibited "gigantism" and the highest levels of fertility. The numbers of non-redundant transcripts, gene loci and new isoforms in the polyploid rice lines were higher and the isoform lengths greater than those of the diploid line. Moreover, alternative splicing (AS) events occurred twice as often in the polyploid rice lines than the diploid line. During these events, intron retention dominated. Furthermore, a large number of new genes and isoforms specific to the lines of different ploidy were discovered. Conclusions The results indicated that alternative polyadenylation (APA) and AS events contributed to the complexity and superiority of polyploids in the activity of translation regulators, nucleic acid binding transcription factor activities and the regulation of molecular function. Therefore, these APA and AS events in allopolyploid rice were found to play a role in regulation. Our study provides new germplasm for polyploid rice breeding and reveals complex regulatory mechanisms that may be related to heterosis and fertility.

High-quality reference transcriptome construction improves RNA-seq quantification in Oryza sativa indica

“…The quality of the transcriptome annotation could help with fast and accurate estimation of transcript expression and AS events using the RNA-seq data with the help of the 3DRNA-seq tool ( Chaudhary and Kalkal, 2021 ; Guo et al, 2021 ; Vitoriano et al, 2021 ; Escudero-Martinez et al, 2022 ). Despite rice being an important crop plant and several attempts being made in the past to improve its transcriptome annotation and AS diversity, IndicaRTD contains a significantly higher number of transcript isoforms ( Lu et al, 2010 ; Zhang et al, 2010 ; Zhang H. et al, 2019 ; Schaarschmidt et al, 2020 ; Wang S. et al, 2022 ; Hasan et al, 2022 ; He et al, 2022 ). Several single gene studies have identified the role of AS transcript isoforms in the eukaryotic system including the plant system specifically in rice ( Ganie and Reddy, 2021 ; Singh and Ahi, 2022 ; Wright et al, 2022 ).…”

“…Equivalent and upgraded strategies can also be employed to improve IndicaRTD quality. Other reports have shown that long-read sequencing has been performed for rice plants and several novel AS transcripts were found, but none of them discussed comprehensive transcriptome annotation ( Schaarschmidt et al, 2020 ; Wang X. et al, 2022 ; Hasan et al, 2022 ; He et al, 2022 ). Some drawbacks of the current IndicaRTD are a lack of information to identify TSS, transcription end (polyadenylation) sites (TES), alternative polyadenylation (APA), and the right combination of different TSS, TES, and SJs using the short-read RNA-seq data ( Zhang et al, 2017a ; Zhang et al, 2022 ).…”

“…The Ensembl deposited transcriptome annotation for the indica variety was created with publicly available sequence tagged sites (STSs), full-length cDNAs, and expressed sequence tags (ESTs) ( Yu et al, 2002 ; Cunningham et al, 2019 ). However, studies have reported AS transcripts in the indica and japonica varieties, which do not mention the high-quality transcriptome data ( Lu et al, 2010 ; Zhang et al, 2010 ; Zhang G. et al, 2019 ; Schaarschmidt et al, 2020 ; Wang X. et al, 2022 ; Hasan et al, 2022 ; He et al, 2022 ). The approximate size of the rice diploid genome is 500 MB compared to the 135 MB of A. thaliana , which recently reported 82,190 non-redundant transcripts from 34,212 genes in the AtRTD2 database (db) ( Brown et al, 2017 ; Zhang et al, 2015 , 2017).…”

Full‐length transcriptome sequencing reveals extreme incomplete annotation of the goat genome

“…The full‐length transcriptome provides an important way to improve the quality of genome annotation, which has been studied in a variety of plant and animal species (Ali et al, 2021; Feng et al, 2019; Zhang et al, 2022). Recent studies have shown that a full‐length transcriptome enables the identification of novel genes and lncRNAs, the identification of full‐length splice isoforms and the detection of novel alternative splicing (AS) and alternative polyadenylation events (Grabherr et al, 2011; He et al, 2022).…”

“…| Yanhong Cao 2 Feng et al, 2019;. Recent studies have shown that a full-length transcriptome enables the identification of novel genes and lncRNAs, the identification of full-length splice isoforms and the detection of novel alternative splicing (AS) and alternative polyadenylation events (Grabherr et al, 2011;He et al, 2022).…”