Updated annotation of the wild strawberry Fragaria vesca V4 genome

Abstract

The diploid strawberry <i>Fragaria vesca</i> serves as an ideal model plant for cultivated strawberry (<i>Fragaria</i> <i>×</i> <i>ananassa</i>, 8<i>x</i>) and the <i>Rosaceae</i> family. The <i>F. vesca</i> genome was initially published in 2011 using older technologies. Recently, a new and greatly improved <i>F. vesca</i> 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 <i>F. vesca</i> genome V4. Here, we built a new and improved annotation, v4.0.a2, for <i>F. vesca</i> 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 <i>FAr-red-impaired Response 1</i> (<i>FAR1</i>) 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 <i>F. vesca</i> 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.