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.
Fruits represent key evolutionary innovations in angiosperms and exhibit diverse types adapted for seed dissemination. However, the mechanisms that underlie fruit type diversity are not understood. The Rosaceae family comprises many different fruit types, including ‘pome’ and ‘drupe’ fruits, and hence is an excellent family for investigating the genetic basis of fruit type specification. Using comparative transcriptomics, we investigated the molecular events that correlate with pome (apple) and drupe (peach) fleshy fruit development, focusing on the earliest stages of fruit initiation. We identified
- NSF-PAR ID:
- 10445265
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- The Plant Journal
- Volume:
- 109
- Issue:
- 6
- ISSN:
- 0960-7412
- Page Range / eLocation ID:
- p. 1614-1629
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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null (Ed.)Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only important economic drivers in many regions of the world, but also major sources of human nutrition. Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development. With the development of high-throughput sequencing technologies and computational tools, an increasing number of high-quality genomes and transcriptomes of Rosaceae species have become available and will greatly facilitate Rosaceae research and breeding. This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement. The availability of these big data resources will greatly accelerate research progress and enhance the agricultural productivity of Rosaceae.more » « less
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