Xanthopoulou Aliki, Montero-Pau Javier, Picó Belén, Boumpas Panagiotis, Tsaliki Eleni, Paris Harry S, Tsaftaris Athanasios, Kalivas Apostolos, Mellidou Ifigeneia, Ganopoulos Ioannis
Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001, Thermi, Macedonia, Greece.
Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE), Universitat de València, 46022, Valencia, Spain.
BMC Genomics. 2021 May 12;22(1):341. doi: 10.1186/s12864-021-07683-2.
Summer 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.
In 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.
These 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.
西葫芦（南瓜属：葫芦科）是一种广受欢迎的园艺作物，但目前其基因组和转录组信息不足。基因表达图谱对于鉴定植物在不同发育阶段不同组织中表达的基因至关重要。在此，我们展示了首个西葫芦品种的全面基因表达图谱，包括从种子、芽、叶茎、幼叶和成熟叶、雄花和雌花、七个发育阶段的果实以及主根和侧根获得的转录本。
从这16个组织中共注释了27,868个基因和2352个新转录本，所有组织组共有超过18,000个基因。其中，3812个被鉴定为管家基因，其中一半被分配到已知的基因本体论中。花、种子和幼果的特异性基因数量最多，而中期果实的特异性基因数量最少。在不同组织中也存在差异表达的基因，在与其余组织的成对比较中，雄花是差异表达基因最多的组织，而叶茎是差异表达基因最少的组织。果实发育过程中最大的表达变化发生在早期，即从雌花到授粉后两天的果实。对全局基因表达数据集进行的加权相关网络分析将25,413个基因分配到24个共表达组中，其中一些组表现出很强的组织特异性。
这些发现丰富了我们对西葫芦发育和成熟相关转录组事件的理解。这个全面的基因表达图谱不仅有望提供西葫芦所有主要组织中基因表达模式的全局视图，还将成为葫芦科功能基因组学和基因发现的宝贵资源。
