Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell.

Frontiers in Genetics
Michelle M HalsteadPablo J Ross

Abstract

A comprehensive annotation of transcript isoforms in domesticated species is lacking. Especially considering that transcriptome complexity and splicing patterns are not well-conserved between species, this presents a substantial obstacle to genomic selection programs that seek to improve production, disease resistance, and reproduction. Recent advances in long-read sequencing technology have made it possible to directly extrapolate the structure of full-length transcripts without the need for transcript reconstruction. In this study, we demonstrate the power of long-read sequencing for transcriptome annotation by coupling Oxford Nanopore Technology (ONT) with large-scale multiplexing of 93 samples, comprising 32 tissues collected from adult male and female Hereford cattle. More than 30 million uniquely mapping full-length reads were obtained from a single ONT flow cell, and used to identify and characterize the expression dynamics of 99,044 transcript isoforms at 31,824 loci. Of these predicted transcripts, 21% exactly matched a reference transcript, and 61% were novel isoforms of reference genes, substantially increasing the ratio of transcript variants per gene, and suggesting that the complexity of the bovine transcriptome i...Continue Reading

References

Feb 15, 2001·Trends in Genetics : TIG·B R Graveley
Oct 8, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Janine StutterheimGodelieve A M Tytgat
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Dec 17, 2008·Proceedings of the National Academy of Sciences of the United States of America·Auinash KalsotraThomas A Cooper
Jan 30, 2010·Nature Methods·Lira MamanovaDaniel J Turner
Apr 2, 2010·Molecular Ecology·Bettina Harr, Leslie M Turner
Apr 9, 2010·Nature Reviews. Genetics·Hadas KerenGil Ast
May 10, 2011·Molecular Biology and Evolution·Jonathan M MudgeJennifer Harrow
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Nov 15, 2011·Nature Biotechnology·Tim R MercerJohn L Rinn
May 23, 2012·PLoS Biology·Philippe JulienHenrik Kaessmann
Oct 11, 2012·PloS One·Dafne Pérez-MontareloAntonio Reverter
Dec 12, 2012·Genetics, Selection, Evolution : GSE·Mahdi SaatchiDorian J Garrick
Dec 22, 2012·Science·Nuno L Barbosa-MoraisBenjamin J Blencowe
Oct 11, 2013·Nature Biotechnology·Donald SharonMichael Snyder
Nov 5, 2013·Nature Methods·Tamara SteijgerPaul Bertone
Apr 17, 2014·PloS One·Sean ThomasUNKNOWN Bench To Basinet CvDC Informatics Subcommittee
May 31, 2014·PloS One·Timothy P RobinsonMarius Gilbert
Jun 26, 2014·Proceedings of the National Academy of Sciences of the United States of America·Hagen TilgnerMichael P Snyder
Aug 31, 2014·International Review of Neurobiology·Boris Guennewig, Antony A Cooper
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Oct 24, 2014·Frontiers in Immunology·Kathleen Thompson-CrispiBonnie A Mallard
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Nov 7, 2015·Genomics, Proteomics & Bioinformatics·Anthony Rhoads, Kin Fai Au
Feb 3, 2016·F1000Research·Camilla L C IpUNKNOWN MinION Analysis and Reference Consortium
Mar 25, 2016·Nature·Eleonora LeucciJean-Christophe Marine
Jun 30, 2016·Proceedings of the National Academy of Sciences of the United States of America·Adriana García-RuizCurtis P Van Tassell
Oct 1, 2016·Cell Death and Differentiation·Maria Paola ParonettoClaudio Sette
Sep 21, 2017·PloS One·Arnaud UngaroAndré Gilles
Jan 16, 2018·Nature Methods·Daniel R GaraldeDaniel J Turner
May 12, 2018·Bioinformatics·Heng Li
May 17, 2018·Methods in Molecular Biology·Anthony BayegaJiannis Ragoussis
Jun 1, 2018·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yao LiChangchun Li
Jul 28, 2018·Bioinformatics·Ashraful ArefeenTao Jiang

❮ Previous
Next ❯

Software Mentioned

HTSeq
RepeatMasker
guppy
RAMPAGE
BLASTN
Pychopper
Pinfish
GENCODE
DESeq2
ont

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.