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标题：De novo and comparative transcriptome analysis of cultivated and wild spinach
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作者：Chenxi Xu ; Chen Jiao ; Yi Zheng 等
期刊名称：Scientific Reports
电子版ISSN：2045-2322
出版年度：2015
卷号：5
DOI：10.1038/srep17706
出版社：Springer Nature
摘要：Spinach ( Spinacia oleracea L.) is an economically important green leafy vegetable crop. In this study, we performed deep transcriptome sequencing for nine spinach accessions: three from cultivated S. oleracea , three from wild S. turkestanica and three from wild S. tetrandra . A total of approximately 100 million high-quality reads were generated, which were de novo assembled into 72,151 unigenes with a total length of 46.5 Mb. By comparing sequences of these unigenes against different protein databases, nearly 60% of them were annotated and 50% could be assigned with Gene Ontology terms. A total of 387 metabolic pathways were predicted from the assembled spinach unigenes. From the transcriptome sequencing data, we were able to identify a total of ~320,000 high-quality single nucleotide polymorphisms (SNPs). Phylogenetic analyses using SNPs as well as gene expression profiles indicated that S. turkestanica was more closely related to the cultivated S . oleracea than S. tetrandra . A large number of genes involved in responses to biotic and abiotic stresses were found to be differentially expressed between the cultivated and wild spinach. Finally, an interactive online database ( http://www.spinachbase.org ) was developed to allow the research community to efficiently retrieve, query, mine and analyze our transcriptome dataset.