Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.)
Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.)
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DOI：
10.1093/pcp/pcx193
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发表时间：
2018
影响因子：
4.9
通讯作者：
R. Yano;Satoko Nonaka;H. Ezura
中科院分区：
文献类型：
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作者：
R. Yano;Satoko Nonaka;H. Ezura
甜瓜（Cucumis梅洛L.）是世界范围内生产的重要葫芦科作物，表现出广泛的遗传变异，包括跃变型和非跃变型果实类型。在日本，以其甜味和浓郁的香气而闻名的甜瓜品种“伯爵最喜欢的Harukei-3（Harukei-3）”被用于培育高级甜瓜。我们在‘Harukei-3’甜瓜的30个不同组织中进行了RNA测序（RNA-seq）转录组研究。这些包括根，茎，叶，花，再生愈伤组织和子房，除了果肉和果皮样品在果实发育的七个阶段。在至少一个组织中，确定了20，752个基因的表达模式，其中每百万个测序片段的转录物的每个酶的片段（FPKM）>1。主成分分析区分了30个甜瓜组织的基础上的全球基因表达谱，进一步，加权基因相关网络分析分为45个不同的共表达组甜瓜基因。一些共表达组表现出组织特异性基因表达。此外，我们开发并在我们的网站Melonet-DB（http：//melonet-db.agbi.tsukuba.ac.jp/）上发布了名为“基因表达图谱查看器”和“共表达查看器”的网络应用工具，以促进甜瓜功能基因组学研究。通过使用这两种工具，我们分析了番茄果实成熟调节剂的甜瓜同源物，如E8，成熟抑制剂（RIN）和非成熟（NOR）。“共表达观察器”清楚地区分与果实成熟相关的甜瓜RIN/NOR/CNR同源物与在其他组织中表达的同源物。此外，MADS-box、NAM/ATAF/CUC（NAC）和同源异型盒转录因子基因也被鉴定为果实成熟相关基因。我们的工具不仅为甜瓜的研究提供了有用的信息，也为其他肉质水果植物的研究提供了有用的信息。
Melon (Cucumis melo L.) is an important Cucurbitaceae crop produced worldwide, exhibiting wide genetic variations and comprising both climacteric and non-climacteric fruit types. The muskmelon cultivar "'Earl's favorite Harukei-3 (Harukei-3)"' known for its sweetness and rich aroma is used for breeding of high-grade muskmelon in Japan. We conducted RNA sequencing (RNA-seq) transcriptome studies in 30 different tissues of the 'Harukei-3' melon. These included root, stems, leaves, flowers, regenerating callus and ovaries, in addition to the flesh and peel sampled at seven stages of fruit development. The expression patterns of 20,752 genes were determined with fragments per kilobase of transcript per million fragments sequenced (FPKM) >1 in at least one tissue. Principal component analysis distinguished 30 melon tissues based on the global gene expression profile and, further, the weighted gene correlation network analysis classified melon genes into 45 distinct coexpression groups. Some coexpression groups exhibited tissue-specific gene expression. Furthermore, we developed and published web application tools designated "'Gene expression map viewer"' and "'Coexpression viewer"' on our website Melonet-DB (http://melonet-db.agbi.tsukuba.ac.jp/) to promote functional genomics research in melon. By using both tools, we analyzed melon homologs of tomato fruit ripening regulators such as E8, RIPENING-INHIBITOR (RIN) and NON-RIPENING (NOR). The "'Coexpression viewer"' clearly distinguished fruit ripening-associated melon RIN/NOR/CNR homologs from those expressed in other tissues. In addition, several other MADS-box, NAM/ATAF/CUC (NAC) and homeobox transcription factor genes were identified as fruit ripening-associated genes. Our tools provide useful information for research not only on melon but also on other fleshy fruit plants.