Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

Tardáguila, Manuel; Fuente, Lorena de la; Martí, Cristina; Pereira, Cécile; Pardo-Palacios, Francisco; Risco, Héctor del; Ferrell, Marc; Mellado-López, Maravillas; Macchietto, Marissa; Verheggen, Kenneth; Edelmann, Mariola J.; Ezkurdia, Iakes; Vázquez, Jesús; Tress, Michael L.; Mortazavi, A; Martens, Lennart; Rodrı́guez-Navarro, Susana; Moreno‐Manzano, Victoria; Conesa, Ana

doi:10.1101/gr.239137.118

Cited by 66 publications

(32 citation statements)

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“…Then, the collapsed transcripts were corrected using Illumina data with LoRDEC (Salmela and Rivals, 2014). Non-canonical splicing junctions caused by reverse-transcription artifacts were detected by applying the SQUANTI tool (Tardaguila et al, 2018).…”

Section: Pipeline For Iso-seq Analysismentioning

confidence: 99%

A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

et al. 2020

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SUMMARY Brassica napus is a recent allopolyploid derived from the hybridization of Brassica rapa (ArAr) and Brassica oleracea (CoCo). Because of the high sequence similarity between the An and Cn subgenomes, it is difficult to provide an accurate landscape of the whole transcriptome of B. napus. To overcome this problem, we applied a single‐molecule long‐read isoform sequencing (Iso‐Seq) technique that can produce long reads to explore the complex transcriptome of B. napus at the isoform level. From the Iso‐Seq data, we obtained 147 698 non‐redundant isoforms, capturing 37 403 annotated genes. A total of 18.1% (14 934/82 367) of the multi‐exonic genes showed alternative splicing (AS). In addition, we identified 549 long non‐coding RNAs, the majority of which displayed tissue‐specific expression profiles, and detected 7742 annotated genes that possessed isoforms containing alternative polyadenylation sites. Moreover, 31 591 AS events located in open reading frames (ORFs) lead to potential protein isoforms by in‐frame or frameshift changes in the ORF. Illumina RNA sequencing of five tissues that were pooled for Iso‐Seq was also performed and showed that 69% of the AS events were tissue‐specific. Our data provide abundant transcriptome resources for a transcript isoform catalog of B. napus, which will facilitate genome reannotation, strengthen our understanding of the B. napus transcriptome and be applied for further functional genomic research.

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Section: Pipeline For Iso-seq Analysismentioning

confidence: 99%

A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

et al. 2020

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“…( E ) Distribution of de novo transcriptome assembly transcripts among different structural categories when compared to NCBI predicted gene models. ( C – E ) Generated using SQANTI 21 . FSM full splice match, ISM incomplete splice match, NIC novel in catalogue, NNC novel not in catalogue (see Table S1 for explanation).…”

Section: Resultsmentioning

confidence: 99%

“…To derive the final transcriptome assembly, 3.9 million reads among all error corrected reads that were aligned at least 99% in length and with at least 95% identity were used. The de novo assembled transcriptome was analyzed using SQANTI 21 and PRAPI 22 . The transcriptome assembly contained a total of 10,840 genes of which 9072 genes matched the NCBI annotated genes, while 1768 genes were new, hereafter referred to as novel genes (Supplementary Table S6 ).…”

Section: Resultsmentioning

confidence: 99%

Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest

Bayega

Oikonomopoulos

Gregoriou

et al. 2021

Sci Rep

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The olive fruit fly, Bactrocera oleae, is the most important pest for the olive fruit but lacks adequate transcriptomic characterization that could aid in molecular control approaches. We apply nanopore long-read RNA-seq with internal RNA standards allowing absolute transcript quantification to analyze transcription dynamics during early embryo development for the first time in this organism. Sequencing on the MinION platform generated over 31 million reads. Over 50% of the expressed genes had at least one read covering its entire length validating our full-length approach. We generated a de novo transcriptome assembly and identified 1768 new genes and a total of 79,810 isoforms; a fourfold increase in transcriptome diversity compared to the current NCBI predicted transcriptome. Absolute transcript quantification per embryo allowed an insight into the dramatic re-organization of maternal transcripts. We further identified Zelda as a possible regulator of early zygotic genome activation in B. oleae and provide further insights into the maternal-to-zygotic transition. These data show the utility of long-read RNA in improving characterization of non-model organisms that lack a fully annotated genome, provide potential targets for sterile insect technic approaches, and provide the first insight into the transcriptome landscape of the developing olive fruit fly embryo.

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“…However, in the present investigation, due to cost, we decided to pool RNAs from a variety of tissues and used a strategy that would ensure some long reads. Also, we wanted to enhance sequences that may lead to the identification of splice variants, as the PacBio is the ideal Next Gen sequencer for this purpose ( 48 ). For this work, we used a single adult male FHM, to prevent confounding by single polymorphic sequences from a population of fish (Manuscript in preparation).…”

Section: Resultsmentioning

confidence: 99%

Tissue-Based Mapping of the Fathead Minnow (Pimephales promelas) Transcriptome and Proteome

et al. 2018

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Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The fathead minnow (Pimephales promelas) is a widely used small fish model for aquatic toxicology and regulatory testing, particularly in North America. A draft genome has been published, but the amount of available genomic or transcriptomic information is still far behind that of other more broadly studied species, such as the zebrafish. Here, we used a proteogenomics approach to survey the tissue-specific proteome and transcriptome profiles in adult male fathead minnow. To do so, we generated a draft transcriptome using short and long sequencing reads from liver, testis, brain, heart, gill, head kidney, trunk kidney, and gastrointestinal tract. We identified 30,378 different putative transcripts overall, with the assembled contigs ranging in size from 264 to over 9,720 nts. Over 17,000 transcripts were >1,000 nts, suggesting a robust transcriptome that can be used to interpret RNA sequencing data in the future. We also performed RNA sequencing and proteomics analysis on four tissues, including the telencephalon, hypothalamus, liver, and gastrointestinal tract of male fish. Transcripts ranged from 0 to 600,000 copies per gene and a large portion were expressed in a tissue-specific manner. Specifically, the telencephalon and hypothalamus shared the most expressed genes, while the gastrointestinal tract and the liver were quite distinct. Using protein profiling techniques, we identified a total of 4,045 proteins in the four tissues investigated, and their tissue-specific expression pattern correlated with the transcripts at the pathway level. Similarly to the findings with the transcriptomic data, the hypothalamus and telencephalon had the highest degree of similarity in the proteins detected. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.

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Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

Abstract: et al. quality control in full-length transcriptome identification and quantification SQANTI: extensive characterization of long-read transcript sequences for

Cited by 66 publications

References 0 publications

A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest

Tissue-Based Mapping of the Fathead Minnow (Pimephales promelas) Transcriptome and Proteome

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