title: De novo and comparative transcriptome analysis of cultivated and wild spinach.
abstract: 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.
authors.affiliation: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
authors.forename: Chenxi
authors.initials: C
authors.lastname: Xu
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.|State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Jiao
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.|National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing 100097, China.
authors.forename: Honghe
authors.initials: H
authors.lastname: Sun
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Wenli
authors.initials: W
authors.lastname: Liu
authors.affiliation: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Cai
authors.affiliation: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Wang
authors.affiliation: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
authors.forename: Shuang
authors.initials: S
authors.lastname: Liu
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Yimin
authors.initials: Y
authors.lastname: Xu
authors.affiliation: USDA, Agricultural Research Station, 1636 E. Alisal Street, Salinas, CA 93905, USA.
authors.forename: Beiquan
authors.initials: B
authors.lastname: Mou
authors.affiliation: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
authors.forename: Shaojun
authors.initials: S
authors.lastname: Dai
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.|USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
authors.forename: Quanhua
authors.initials: Q
authors.lastname: Wang
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D063990:Gene Ontology; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D018724:Spinacia oleracea / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*