Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing

被引：36

作者：

Cook, David E. ^{[1
,3
]}

Valle-Inclan, Jose Espejo ^{[1
,4
]}

Pajoro, Alice ^{[2
,5
]}

Rovenich, Hanna ^{[1
,6
]}

Thomma, Bart P. H. J. ^{[1
]}

Faino, Luigi ^{[1
,7
]}

机构：

[1] Wageningen Univ & Res, Lab Phytopathol, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands

[2] Wageningen Univ & Res, Lab Mol Biol, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands

[3] Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66056 USA

[4] Univ Utrecht, Univ Med Ctr Utrecht, Ctr Mol Med, Dept Genet, NL-3584 CX Utrecht, Netherlands

[5] Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, D-50829 Cologne, Germany

[6] Univ Cologne, Bot Inst, Cluster Excellence Plant Sci CEPLAS, D-50674 Cologne, Germany

[7] Univ Roma La Sapienza, Dept Environm Biol, Ple Aldo Moro 5, I-00185 Rome, Italy

来源：

PLANT PHYSIOLOGY | 2019年 / 179卷 / 01期

关键词：

ARABIDOPSIS INFORMATION RESOURCE; RNA-SEQ; PROVIDES INSIGHTS; GENE PREDICTION; TRANSCRIPTOME; CHROMOSOME; EVOLUTION; ORTHOMCL; TOOL;

D O I：

10.1104/pp.18.00848

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current annotation pipelines do not incorporate such information. Here we present long-read annotation (LoReAn) software, an automated annotation pipeline utilizing short-and long-read cDNA sequencing, protein evidence, and ab initio prediction to generate accurate genome annotations. Based on annotations of two fungal genomes (Verticillium dahliae and Plicaturopsis crispa) and two plant genomes (Arabidopsis [Arabidopsis thaliana] and Oryza sativa), we show that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA-sequencing data generated from either the Pacific Biosciences or MinION sequencing platforms, correctly predicting gene structure, and capturing genes missed by other annotation pipelines.

引用

页码：38 / 54

页数：17

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