A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon

A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic Salmon

Atlantic salmon (Salmo salar) is a major species produced in world aquaculture and an important vertebrate model organism for studying the process of rediploidization following whole genome duplication events (Ss4R, 80 mya). The current Salmo salar transcriptome is largely generated from genome sequ...

Full description

Bibliographic Details
Main Authors:	Sigmund Ramberg, Bjørn Høyheim, Tone-Kari Knutsdatter Østbye, Rune Andreassen
Format:	Article
Language:	English
Published:	Frontiers Media S.A. 2021-04-01
Series:	Frontiers in Genetics
Subjects:	Atlantic salmon transcriptome full-length mRNA hybrid error correction PacBio Iso-seq Illumina sequencing
Online Access:	https://www.frontiersin.org/articles/10.3389/fgene.2021.656334/full

Similar Items

De novo high-accuracy transcriptomes from long-read sequencing reveals a wide variety of novel splice variants in copepodids and adult female salmon lice (Lepeophtheirus salmonis)
by: Sine Alise Hartvigsen Hansen, et al.
Published: (2023-07-01)

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms
by: Yongli Wang, et al.
Published: (2021-09-01)

Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in human microbiome samples
by: Elena Buetas, et al.
Published: (2024-03-01)

Combined PacBio Iso-Seq and Illumina RNA-Seq Analysis of the <i>Tuta absoluta</i> (Meyrick) Transcriptome and Cytochrome P450 Genes
by: Min Liu, et al.
Published: (2023-04-01)

Accurate characterization of the IFITM locus using MiSeq and PacBio sequencing shows genetic variation in Galliformes
by: Irene Bassano, et al.
Published: (2017-05-01)

HISEA: HIerarchical SEed Aligner for PacBio data
by: Nilesh Khiste, et al.
Published: (2017-12-01)

Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq
by: Eman M. Khalaf, et al.
Published: (2023-12-01)

Gene Expression and Isoform Identification of PacBio Full-Length cDNA Sequences for Berberine Biosynthesis in <i>Berberis koreana</i>
by: Neha Samir Roy, et al.
Published: (2021-06-01)

First whole genome assembly and annotation of a European common bean cultivar using PacBio HiFi and Iso-Seq data
by: Sébastien Carrère, et al.
Published: (2023-06-01)

PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response
by: Xiaojie Liu, et al.
Published: (2021-01-01)

Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing
by: Benjamin D. Young, et al.
Published: (2024-02-01)

Alternative Splicing Regulation of Anthocyanin Biosynthesis in Camellia sinensis var. assamica Unveiled by PacBio Iso-Seq
by: Lijiao Chen, et al.
Published: (2020-08-01)

TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data
by: Guofeng Meng, et al.
Published: (2019-05-01)

Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
by: Sébastien Lhomme, et al.
Published: (2021-12-01)

Chromosome-Level Genome Assembly of Cerasus humilis Using PacBio and Hi-C Technologies
by: Pengfei Wang, et al.
Published: (2020-10-01)

SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
by: Shaya Akbarinejad, et al.
Published: (2021-06-01)

Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing
by: Chunman Zuo, et al.
Published: (2018-06-01)

PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning
by: Haiying Xie, et al.
Published: (2020-09-01)

Chromosome-level genome assembly of Fragaria pentaphylla using PacBio and Hi-C technologies
by: Rui Sun, et al.
Published: (2022-09-01)

SequelTools: a suite of tools for working with PacBio Sequel raw sequence data
by: David E. Hufnagel, et al.
Published: (2020-10-01)

Comparative transcriptome analysis of dioecious floral development in Trachycarpus fortunei using Illumina and PacBio SMRT sequencing
by: Feng Xiao, et al.
Published: (2023-11-01)

Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution
by: Russell J. S. Orr, et al.
Published: (2018-07-01)

PacBio Sequencing Unravels Soil Bacterial Assembly Processes along a Gradient of Organic Fertilizer Application
by: Wenhui Wang, et al.
Published: (2023-07-01)

PaSS: a sequencing simulator for PacBio sequencing
by: Wenmin Zhang, et al.
Published: (2019-06-01)

PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species
by: Jingli Yang, et al.
Published: (2021-10-01)

The complete chloroplast genome of greater duckweed (Spirodela polyrhiza 7498) using PacBio long reads: insights into the chloroplast evolution and transcription regulation
by: Yating Zhang, et al.
Published: (2020-01-01)

Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies
by: Linda Beauclair, et al.
Published: (2019-10-01)

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome
by: Jiawen Cui, et al.
Published: (2020-06-01)

De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome
by: David Ryder, et al.
Published: (2024-03-01)

Iso-seq and RNA-seq profiling of Fenneropenaeus penicillatus: Unravelling the signaling pathway and genes involved in the ovarian development
by: Kianann Tan, et al.
Published: (2023-10-01)

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System
by: Moonsuk Hur, et al.
Published: (2019-09-01)

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
by: Patrick D. Schloss, et al.
Published: (2016-03-01)

Expression Analysis in Atlantic Salmon Liver Reveals miRNAs Associated with Smoltification and Seawater Adaptation
by: Alice Shwe, et al.
Published: (2022-04-01)

High-throughput long paired-end sequencing of a Fosmid library by PacBio
by: Zhaozhao Dai, et al.
Published: (2019-11-01)

Co-Expression Analysis Reveals Differential Expression of Homologous Genes Associated with Specific Terpenoid Biosynthesis in <i>Rehmannia glutinosa</i>
by: Ji-Nam Kang, et al.
Published: (2022-06-01)

Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome
by: Guoshun Xu, et al.
Published: (2022-01-01)

Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade
by: Weian Du, et al.
Published: (2022-07-01)

Chromosome-Level Assembly of the Chinese Hooksnout Carp (Opsariichthys bidens) Genome Using PacBio Sequencing and Hi-C Technology
by: Xiaojun Xu, et al.
Published: (2022-01-01)

Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform
by: Xiaochen eChen, et al.
Published: (2015-02-01)

A new PacBio genome sequence of an Australian Pyrenophora tritici-repentis race 1 isolate
by: Paula Moolhuijzen, et al.
Published: (2019-10-01)