Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing.
Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation.
School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
Kenneth A
KA
Watanabe
School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
Arielle
A
Homayouni
School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
Tara
T
Tufano
School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
Jennifer
J
Lopez
School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA.
Patricia
P
Ringler
Texas A&M AgriLife Research, 17360 Coit Road, Dallas, TX 75252, USA.
Paul
P
Rushton
School of Life Sciences, University of Nevada Las Vegas, 4505 South Maryland Parkway, Las Vegas, NV 89154, USA jeffery.shen@unlv.edu.
Qingxi J
QJ
Shen
D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D018745:Genome, Plant; D058977:Molecular Sequence Annotation / Q000379:methods*; D016366:Open Reading Frames; D012275:Oryza / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012984:Software; D013728:Terminator Regions, Genetic; D024363:Transcription Initiation Site; D059467:Transcriptome
D018076:DNA, Complementary
Oryza sativa; RNA-sequencing; cufflinks; genome annotation; novel genes; transcript assembly