An eFP browser for visualizing strawberry fruit and flower transcriptomes

Abstract

Wild strawberry Fragaria vesca is emerging as an important model system for the cultivated strawberry due to its diploid genome and availability of extensive transcriptome data and a range of molecular genetic tools. Being able to better utilize these tools, especially the transcriptome data, will greatly facilitate research progress in strawberry and other Rosaceae fruit crops. The electronic fluorescent pictograph (eFP) software is a useful and popular tool to display transcriptome data visually, and is widely used in other model organisms including Arabidopsis and mouse. Here we applied eFP to display wild strawberry RNA sequencing (RNA-seq) data from 42 different tissues and stages, including various flower and fruit developmental stages. In addition, we generated eight additional RNA-seq data sets to represent tissues from ripening-stage receptacle fruit from yellow-colored and red-colored wild strawberry varieties. Differential gene expression analysis between these eight data sets provides additional information for understanding fruit-quality traits. Together, this work greatly facilitates the utility of the extensive transcriptome data for investigating strawberry flower and fruit development as well as fruit-quality traits.

Efficient genome editing of wild strawberry genes, vector development and validation

“…Examination of RNA-seq data of diploid strawberry showed that the FveARF8 gene is expressed at a high level in floral organs and fruit, and it is also moderately expressed in seedlings ( Figure S5F; Hawkins et al, 2017). This broad expression pattern of FveARF8 suggests that FveARF8 may repress auxin signalling in many tissues and developmental stages.…”

“…Surprisingly, the young plants derived from T0 mother plant (T0-11) all looked similar to one another ( Figure 4a) despite that some young plants were homozygous for À1a deletion in FveTAA1. Examination of RNA-seq data revealed that FveTAA1 was only expressed at late-stage anther ( Figure S5E; Hawkins et al, 2017;Hollender et al, 2014). Therefore, TAA1 may not play a role in seedling development.…”

“…F. vesca has a small and sequenced genome (2n = 14, 240 Mb genome), relatively short life cycle, ease of growth and, most importantly, facile transformation (Shulaev et al, 2011). While there have been extensive transcriptome data in F. vesca informing the expression pattern of genes during development (Hawkins et al, 2017;Hollender et al, 2014;Kang et al, 2013), the function of most genes is not determined due to a lack of efficient gene knockout method. Establishing an efficient genome editing technology for F. vesca will provide an incredibly useful tool for studying gene function and add another resource to this emerging model.…”

The transcriptional landscape of cultivated strawberry (Fragraia×ananassa) and its diploid ancestor (Fragraia×vesca) during fruit development

“…The most obvious phenomenon during fruit ripening is the synthesis of anthocyanins. Previous transcriptome analysis revealed that flavonoids biosynthesis genes were induced transcription in the receptacle, implicating the importance of these genes 24 . The grey60 color module (Table S6) is correlated with the octoploid receptacle development, and the correlation is getting higher as the receptacle matures (Figure 3c).…”

“…We collected total 80 Illumina-based datasets representing 36 different fruit tissues of diploid and octoploid fruit at different developmental stages, including seven development stages for diploid receptacle (cortex and pith) and other fruit tissues (wall, style, embryo, ovule, ghost) 23,24 . as well as the four development stages (green, white, turning, red) for octoploid achene and receptacle 25 .…”