Towards an improved apple reference transcriptome using RNA-seq

Publication Overview
TitleTowards an improved apple reference transcriptome using RNA-seq
AuthorsBai Y, Dougherty L, Xu K
TypeJournal Article
Journal NameMolecular genetics and genomics : MGG
CitationBai Y, Dougherty L, Xu K. Towards an improved apple reference transcriptome using RNA-seq. Molecular genetics and genomics : MGG. 289(3):427-38


The reference genome of apple (Malus × domestica) has been available since 2010. Despite being a milestone in apple genomics, the reference genome is difficult to be used as a reference in RNA-seq (RNA sequencing) analysis, a widespread technology in transcriptomic studies. One of the major limitations appears to be the low coverage of the reference transcriptome in RNA-seq mapping of reads. To improve the reference transcriptome, we obtained 14 sets of strand-specific RNA-seq data of 168.5 million reads in total from fruit of Golden Delicious (GD, the source of the reference genome) in varying growth and developmental stages. Using a combination of genome-guided assembly and de novo assembly, the apple reference transcriptome was improved to a collection of 71,178 genes or transcripts, which includes 53,654 genes predicted originally (with MDP prefixed in their IDs) and 17,524 novel transcripts. Of these novel transcripts, 8,144 were identified from reads directly mapped to the reference genome while the remaining 9,380 were extracted from de novo assemblies of reads that could not be initially mapped to the reference genome. Evaluating the improved apple reference transcriptome with reads from Golden Delicious and other genotypes used in this and other studies showed that it allowed 62.5 ± 9.3-82.3 ± 2.7 % of reads to be mapped, a marked increase from the low rates of 37.4 ± 7.7-46.6 ± 7.1 % offered by the original reference transcriptome. The improved reference transcriptome therefore represents a step forward towards a complete reference transcriptome in apple.

Cross References
This publication is also available in the following databases:
AGL: USDA National Agricultural LibraryAGL:4824221
PMID: PubMedPMID:24532088
PMID: PubMedPMID:24530873
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