RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’

BMC Genomics

Research Article

Laszlo G. Kovacs¹  Zachary N. Harris²  Jason P. Londo³ 

[1] Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO, USA;Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO, USA;Present address: Saint Louis University, Department of Biology, 1 N. Grand Blvd, Saint Louis, MO, USA;United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, 630 W. North Street, Geneva, NY, USA;

关键词: Transcriptome;    Genome re-annotation;    RNA-seq;    lncRNA;    Minimum free energy;    Riesling;    Vitis vinifera;   

DOI  :  10.1186/s12864-017-4346-6

 received in 2017-08-25, accepted in 2017-11-22,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar ‘Riesling’ to improve annotation of the grapevine reference genome sequence.ResultsHere we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy.ConclusionsIn grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species.

【 授权许可】

CC BY   
© The Author(s). 2017

【 图 表 】

Fig. 1