Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

Genome Biology
André E MinocheHeinz Himmelbauer

Abstract

We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.

References

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Citations

Apr 20, 2016·Advanced Drug Delivery Reviews·Dmitriy KhodakovDavid Yu Zhang
Aug 5, 2016·Genome Génome / Conseil National De Recherches Canada·Ainong Shi, Beiquan Mou
Dec 21, 2016·The Plant Journal : for Cell and Molecular Biology·Yongping LiChunying Kang
Jun 22, 2016·PloS One·Maria CartolanoKorbinian Schneeberger
Dec 5, 2015·Scientific Reports·Chenxi XuQuanhua Wang
Jun 7, 2017·Nature Communications·Gina G Capistrano-GossmannF J Kopisch-Obuch
Apr 8, 2017·Molecular Genetics and Genomics : MGG·Şurhan GölAnne Frary
Dec 19, 2017·Frontiers in Genetics·Juncheng WangHuajun Wang
Jun 25, 2016·Nature Communications·Salah E Abdel-GhanyAnireddy S N Reddy
Oct 6, 2018·The Plant Journal : for Cell and Molecular Biology·Guoqiang ZhangBing Zhang
Jun 19, 2019·Database : the Journal of Biological Databases and Curation·Keeley CollinsYi Zheng
May 20, 2019·The Plant Journal : for Cell and Molecular Biology·Álvaro Rodríguez Del RíoJuliane C Dohm
Jun 8, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yue ZhangPingfang Yang
Mar 1, 2020·International Journal of Molecular Sciences·Junqin ZhouXiaofeng Tan
Nov 20, 2016·Genome Research·Zheng KuangStefan Canzar
Nov 22, 2018·Frontiers in Endocrinology·Candice LavelleNancy D Denslow
Jul 26, 2019·Nature Reviews. Genetics·Rory StarkJames Hadfield
May 26, 2017·Nature Communications·Chenxi XuQuanhua Wang
Jul 22, 2018·Frontiers in Molecular Biosciences·Markus HaakBoas Pucker
Nov 6, 2018·Nature Communications·Kristoffer SahlinPaul Medvedev
Jun 1, 2018·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yao LiChangchun Li
Sep 9, 2019·GigaScience·Elena BushmanovaAndrey D Prjibelski
Mar 11, 2020·Scientific Data·Ajit Kumar PatraYoungik Yang
Oct 17, 2017·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Yongping LiChunying Kang

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Datasets Mentioned

BETA
AYZS02000000
AYZV02000000
SRX674050
SRX674044

Methods Mentioned

BETA
PCR
chip
ELIP

Software Mentioned

khmer
Perl script
blasr
BLAT
ClustalW
RepeatMasker
proovread
Gmap
AUGUSTUS
randomSplit

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