RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’
Abstract 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....
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| Format: | Article |
| Language: | English |
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BMC
2017-12-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4346-6 |
| _version_ | 1811229946716094464 |
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| author | Zachary N. Harris Laszlo G. Kovacs Jason P. Londo |
| author_facet | Zachary N. Harris Laszlo G. Kovacs Jason P. Londo |
| author_sort | Zachary N. Harris |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-12T10:21:46Z |
| format | Article |
| id | doaj.art-af676f2a07c947ac9fb37195f5588e36 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T10:21:46Z |
| publishDate | 2017-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-af676f2a07c947ac9fb37195f5588e362022-12-22T03:37:05ZengBMCBMC Genomics1471-21642017-12-0118111210.1186/s12864-017-4346-6RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’Zachary N. Harris0Laszlo G. Kovacs1Jason P. Londo2Missouri State University, Biology DepartmentMissouri State University, Biology DepartmentUnited States Department of Agriculture, Agricultural Research Service, Grape Genetics Research UnitAbstract 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.http://link.springer.com/article/10.1186/s12864-017-4346-6TranscriptomeGenome re-annotationRNA-seqlncRNAMinimum free energyRiesling |
| spellingShingle | Zachary N. Harris Laszlo G. Kovacs Jason P. Londo RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ BMC Genomics Transcriptome Genome re-annotation RNA-seq lncRNA Minimum free energy Riesling |
| title | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
| title_full | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
| title_fullStr | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
| title_full_unstemmed | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
| title_short | RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’ |
| title_sort | rna seq based genome annotation and identification of long noncoding rnas in the grapevine cultivar riesling |
| topic | Transcriptome Genome re-annotation RNA-seq lncRNA Minimum free energy Riesling |
| url | http://link.springer.com/article/10.1186/s12864-017-4346-6 |
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