Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets

Publication Overview
TitleGenome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets
AuthorsLi Y, Wei W, Feng J, Luo H, Pi M, Liu Z, Kang C
TypeJournal Article
Journal NameDNA research : an international journal for rapid publication of reports on genes and genomes
Year2017
CitationLi Y, Wei W, Feng J, Luo H, Pi M, Liu Z, Kang C. Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets. DNA research : an international journal for rapid publication of reports on genes and genomes. 2017 Sep 23.

Abstract

The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries. Altogether, 18,641 genes (55.6% out of 33,538 genes) were augmented with information on the 5' and/or 3' UTRs, 13,168 (39.3%) protein-coding genes were modified or newly identified, and 7,370 genes were found to possess alternative isoforms. In addition, 1,938 long non-coding RNAs, 171 miRNAs, and 51,714 small RNA clusters were integrated into the annotation. This new annotation of F. vesca is substantially improved in both accuracy and integrity of gene predictions, beneficial to the gene functional studies in strawberry and to the comparative genomic analysis of other horticultural crops in Rosaceae family.

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Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1756-1663
eISSN1756-1663
Publication Date2017 Sep 23
Journal AbbreviationDNA Res.
DOI10.1093/dnares/dsx038
Elocation10.1093/dnares/dsx038
Copyright© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
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PMID: PubMedPMID:29036429