Plant ISOform sequencing database (PISO): a comprehensive repertory of full‐length transcripts in plants

Feng, Jia-Wu; Huang, Shanshan; Guo, Yi-Xiong; Li, Dongxu; Song, Jia‐Ming; Gao, Junxiang; Li, Huan

doi:10.1111/pbi.13076

Cited by 4 publications

(2 citation statements)

References 10 publications

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“…2A). Our results showed that IR is the predominant mode of AS, which is consistent with most land plants in the PISO database, including Arabidopsis, sorghum, and maize [10,12,31]. It has been reported that IR events are regulated in the nucleus and may be widespread as storage form of precursor RNA [12].…”

Section: Discussionsupporting

confidence: 87%

A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing

et al. 2022

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Background Posttranscriptional processing of precursor mRNAs contributes to transcriptome and protein diversity and gene regulatory mechanisms in eukaryotes. However, this posttranscriptional mechanism has not been studied in the marine macroalgae Gracilariopsis lemaneiformis, which is the most cultivated red seaweed species in China. Results In the present study, third-generation sequencing (Pacific Biosciences single-molecule real-time long-read sequencing, SMRT-Seq) was used to sequence the full-length transcriptome of G. lemaneiformis to identify alternatively spliced transcripts and alternative polyadenylation (APA) sites in this species. RNAs were isolated from G. lemaneiformis under various treatments including abiotic stresses and exogenous phytohormones, and then equally pooled for SMRT-Seq. In summary, 346,544 full-length nonchimeric reads were generated, from which 13,630 unique full-length transcripts were obtained in G. lemaneiformis. Compared with the known splicing events in the gene models, more than 3000 new alternative splicing (AS) events were identified in the SMRT-Seq reads. Additionally, 810 genes were found to have poly (A) sites and 91 microRNAs (miRNAs), 961 long noncoding RNAs and 1721 novel genes were identified in G. lemaneiformis. Moreover, validation experiments showed that abiotic stresses and phytohormones could induce some specific AS events, especially intron retain isoforms, cause some alterations to the relative ratios of transcripts annotated to the same gene, and generate novel 3′ ends because of differential APA. The growth of G. lemaneiformis was inhibited by Cu stress, while this inhibition was alleviated by ACC treatment. RNA-Seq analysis further revealed that 211 differential alternative splicing (DAS) events and 142 DAS events was obtained in CK vs Cu and Cu vs Cu + ACC, respectively, suggesting that AS of functional genes could be regulated by Cu stress and ACC. Compared with Cu stress, the expression of transcripts with DAS events mainly involved in the carbon fixation in photosynthetic organisms and oxidative phosphorylation pathway was upregulated in Cu + ACC treatment, revealing that ACC alleviated the growth inhibition by Cu stress by increasing carbon fixation and oxidative phosphorylation. Conclusions Our results provide the first comprehensive picture of the full-length transcriptome and posttranscriptional mechanism in red macroalgae, including transcripts that appeared in the presence of common abiotic stresses and phytohormones, which will improve the gene annotations of Gracilariopsis and contribute to the study of gene regulation in this important cultivated seaweed.

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Section: Discussionsupporting

confidence: 87%

A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing

et al. 2022

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“…At present, PacBio and ONT deep sequencing are increasingly used for genome annotation, identification of co/post-transcriptional events and fusion transcripts. Recently, several studies collected and reanalyzed long reads from Iso-Seq into comprehensive databases such as Plant ISOform sequencing database (PISO) (Feng et al, 2019) and ISOdb (Xie et al, 2018). ISOdb and PISO deposited 8 and 19 species, respectively.…”

Section: Applications and Bioinformatics Tools For Iso-seq And Nanopomentioning

confidence: 99%

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

et al. 2019

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Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.

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A new mechanism of flowering regulation by the competition of isoforms in Osmanthus fragrans

Li,

Xia,

Cushman

et al. 2023

Annals of Botany

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The regulation of flowering time is typically governed by transcription factors or epigenetic modifications. Transcript isoforms can play important roles in flowering regulation. Recently, transcript isoforms were discovered in the key genes, OfAP1 and OfTFL1, of the flowering regulatory network in Osmanthus fragrans. OfAP1-b generates a full-length isoform of OfAP1-b1 as well as an isoform of OfAP1-b2 that lacks the C-terminal domain. Although OfAP1-b2 does not possess an activation domain, it has a complete K domain that allows it to form heterodimers. OfAP1-b2 competes with OfAP1-b1 by binding with OfAGL24 to create non-functional and functional heterodimers. As a result, OfAP1-b1 promotes flowering while OfAP1-b2 delays flowering. OfTFL1 produces two isoforms located in different areas: OfTFL1-1 in the cytoplasm and OfTFL1-2 in the nucleus. When combined with OfFD, OfTFL1-1 does not enter the nucleus to repress AP1 expression, leading to early flowering. Conversely, when combined with OfFD, OfTFL1-2 enters the nucleus to repress AP1 expression, resulting in later flowering. Tissue-specific expression and functional conservation testing of OfAP1 and OfTFL1 support the new model’s effectiveness in regulating flowering. Overall, this study provides new insights into regulating flowering time by the competition of isoforms.

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Plant ISOform sequencing database (PISO): a comprehensive repertory of full‐length transcripts in plants

Cited by 4 publications

References 10 publications

A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing

A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

A new mechanism of flowering regulation by the competition of isoforms in Osmanthus fragrans

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