Rosaceae fruit transcriptome database (ROFT)-a useful genomic resource for comparing fruits of apple, peach, strawberry, and raspberry

Abstract

Rosaceae is a large plant family consisting of many economically important fruit crops including peach, apple, pear, strawberry, raspberry, plum, and others. Investigations into their growth and development will promote both basic understanding and progress toward increasing fruit yield and quality. With the ever-increasing high-throughput sequencing data of Rosaceae, comparative studies are hindered by inconsistency of sample collection with regard to tissue, stage, growth conditions, and by vastly different handling of the data. Therefore, databases that enable easy access and effective utilization of directly comparable transcript data are highly desirable. Here, we describe a database for comparative analysis, ROsaceae Fruit Transcriptome database (ROFT), based on RNA-seq data generated from the same laboratory using similarly dissected and staged fruit tissues of four important Rosaceae fruit crops: apple, peach, strawberry, and red raspberry. Hence, the database is unique in allowing easy and robust comparisons among fruit gene expression across the four species. ROFT enables researchers to query orthologous genes and their expression patterns during different fruit developmental stages in the four species, identify tissue-specific and tissue-/stage-specific genes, visualize and compare ortholog expression in different fruit types, explore consensus co-expression networks, and download different data types. The database provides users access to vast amounts of RNA-seq data across the four economically important fruits, enables investigations of fruit type specification and evolution, and facilitates the selection of genes with critical roles in fruit development for further studies.

Acknowledgements

We would like to thank Mr. Andrew Tong for help in implementing the hyperlinks of the database and members of the Liu lab for helpful comments on the website. This work has been supported by a grant from the National Science Foundation (NSF) (IOS-1444987) to ZL and SMM. ML was supported in part by an National Science Foundation award (DGE-1632976).

Author contributions

ML and ZL conceived the research; ML performed the research, SMM supervised the research and revised the manuscript; ML and ZL wrote the manuscript.

Data availability statement

The SRA accession number of peach and apple early fruit RNA-Seq data is PRJNA661345. The RNA-Seq data of strawberry and red raspberry early fruit development can be found in SRA using accession numbers PRJNA187983 and PRJNA869453, respectively.

Conflict of interests

The authors declare no conflict of interest.

Supplementary information

Supplementary data is available at Horticulture Research online.

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