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Article|01 Mar 2021|OPEN
Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database
Tianjia Liu1, Muzi Li2, Zhongchi Liu2, Yongping Li3 & Xiaoyan Ai1,
1Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences/Fruit and Tea Subcenter of Hubei Innovation Center of Agricultural Science and Technology, Wuhan, China
2Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, USA
3School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong, China

Horticulture Research 8,
Article number: 41 (2021)
doi: 10.1038/hortres.2021.41
Views: 244

Received: 04 Jun 2020
Revised: 16 Dec 2020
Accepted: 22 Dec 2020
Published online: 01 Mar 2021

Abstract

Cultivated strawberry (Fragaria × ananassa) is an important fruit crop species whose fruits are enjoyed by many worldwide. An octoploid of hybrid origin, the complex genome of this species was recently sequenced, serving as a key reference genome for cultivated strawberry and related species of the Rosaceae family. The current annotation of the F. ananassa genome mainly relies on ab initio predictions and, to a lesser extent, transcriptome data. Here, we present the structure and functional reannotation of the F. ananassa genome based on one PacBio full-length RNA library and ninety-two Illumina RNA-Seq libraries. This improved annotation of the F. ananassa genome, v1.0.a2, comprises a total of 108,447 gene models, with 97.85% complete BUSCOs. The models of 19,174 genes were modified, 360 new genes were identified, and 11,044 genes were found to have alternatively spliced isoforms. Additionally, we constructed a strawberry genome database (SGD) for strawberry gene homolog searching and annotation downloading. Finally, the transcriptome of the receptacles and achenes of F. ananassa at four developmental stages were reanalyzed and qualified, and the expression profiles of all the genes in this annotation are also provided. Together, this study provides an updated annotation of the F. ananassa genome, which will facilitate genomic analyses across the Rosaceae family and gene functional studies in cultivated strawberry.