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Updated annotation of the wild strawberry Fragaria vesca V4 genome

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The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry (Fragaria × ananassa, 8x) and the Rosaceae family. The F. vesca genome was initially published in 2011 using… Click to show full abstract

The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry (Fragaria × ananassa, 8x) and the Rosaceae family. The F. vesca genome was initially published in 2011 using older technologies. Recently, a new and greatly improved F. vesca genome, designated V4, was published. However, the number of annotated genes is remarkably reduced in V4 (28,588 genes) compared to the prior annotations (32,831 to 33,673 genes). Additionally, the annotation of V4 (v4.0.a1) implements a new nomenclature for gene IDs (FvH4_XgXXXXX), rather than the previous nomenclature (geneXXXXX). Hence, further improvement of the V4 genome annotation and assigning gene expression levels under the new gene IDs with existing transcriptome data are necessary to facilitate the utility of this high-quality F. vesca genome V4. Here, we built a new and improved annotation, v4.0.a2, for F. vesca genome V4. The new annotation has a total of 34,007 gene models with 98.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCOs). In this v4.0.a2 annotation, gene models of 8,342 existing genes are modified, 9,029 new genes are added, and 10,176 genes possess alternatively spliced isoforms with an average of 1.90 transcripts per locus. Transcription factors/regulators and protein kinases are globally identified. Interestingly, the transcription factor family FAr-red-impaired Response 1 (FAR1) contains 82 genes in v4.0.a2 but only two members in v4.0.a1. Additionally, the expression levels of all genes in the new annotation across a total of 46 different tissues and stages are provided. Finally, miRNAs and their targets are reanalyzed and presented. Altogether, this work provides an updated genome annotation of the F. vesca V4 genome as well as a comprehensive gene expression atlas with the new gene ID nomenclature, which will greatly facilitate gene functional studies in strawberry and other evolutionarily related plant species.Marking up the strawberry genomeAn updated annotation of the wild strawberry genome includes over nine thousand new genes. Since the genome sequence of the wild strawberry was first published in 2011, technological improvements have led to various refinements and updates. Chunying Kang and colleagues at Huazhong Agricultural University in Wuhan, China, found that a large number of genes were either absent or inaccurately described in the annotation of the latest wild strawberry genome. They annotated 5,419 more protein-coding genes, including 139 transcription factor and 92 protein kinase encoding genes, and carried out a comprehensive analysis of the expression patterns of all genes in the new annotation. They also identified microRNAs that contribute to regulate gene expression. These data will aid future comparative and functional studies in widely grown hybrid strawberry species.

Keywords: wild strawberry; genome; annotation; vesca genome; gene

Journal Title: Horticulture Research
Year Published: 2019

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