Abstract
BackgroundSummer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots.ResultsIn total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity.ConclusionsThese findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.
Highlights
Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information
Total transcripts of each tissue varied from 42,429 to 45,239, of which the novel transcripts ranged from 25,093 to 26,870, known genes from 24,355 to 25,197, and novel genes from 1662 to 1829. These numbers are similar to those reported in transcriptome studies with melon [13], with pumpkin [14], and with winter squash, C. pepo Acorn morphotype [15]
In the present study, we developed the first Gene Expression Atlas (CupeGEA) for a C. pepo subsp. pepo summer squash cultivar based on 16 vegetative and fruit tissues during development and ripening
Summary
Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. We present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Summer squash are the tender, young fruits of Cucurbita pepo L. Besides the marked differences in fruit shape, the very numerous cultivars of summer squash display a broad range of diversity in flowering and fruit traits [2]. In order to achieve genotype-phenotype association, combinations of genome-wide data and gene expression profiles for different developmental stages of summer squash development is of utmost importance. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages
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