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

• Published in: BMC genomics Vol. 18; no. 1; pp. 937 - 12
• Main Authors: Harris, Zachary N., Kovacs, Laszlo G., Londo, Jason P.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 02.12.2017; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Animal Genetics and Genomics; Annotations; Assembly; Biomedical and Life Sciences; Computer applications; Cultivars; Cultivation; Expected values; Free energy; Fruit cultivation; Gene expression; Gene sequencing; Genetic aspects; Genome re-annotation; Genome, Plant; Genomes; Genomics; Grapes; Heterozygosity; High-Throughput Nucleotide Sequencing - methods; Life Sciences; lncRNA; Methods; Microarrays; Microbial Genetics and Genomics; Minimum free energy; Models, Genetic; Molecular Sequence Annotation; Non-coding RNA; Nucleotide sequence; Plant Genetics and Genomics; Plant genomics; Proteins; Proteomics; Quality control; Reference Values; Research Article; Ribonucleic acid; Riesling; RNA; RNA sequencing; RNA, Long Noncoding - genetics; RNA-seq; Software; Transcriptome; Vitis - genetics; Vitis - growth & development; Vitis vinifera; Genome re-annotation; lncRNA; RNA-seq; Riesling; Minimum free energy; Transcriptome; Vitis vinifera
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-017-4346-6

Background The 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. Results Here 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. Conclusions In 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.