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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #316588

Research Project: Genetic Enhancement of Lettuce, Spinach, Melon, and Related Species

Location: Crop Improvement and Protection Research

Title: De novo and comparative transcriptome analysis of cultivated and wild spinach

Author
item Xu, Chenxi - Shanghai Normal University
item Jiao, Chen - Cornell University - New York
item Zheng, Li - Cornell University - New York
item Sun, Honghe - Cornell University - New York
item Liu, Wenli - Boyce Thompson Institute
item Cai, Xiaofeng - Shanghai Normal University
item Wang, Xiaoli - Shanghai Normal University
item Liu, Shuang - Shanghai Normal University
item Xu, Yimin - Cornell University - New York
item Mou, Beiquan
item Dai, Shaojun - Shanghai Normal University
item Fei, Zhangjun - Boyce Thompson Institute
item Wang, Quanhua - Shanghai Normal University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/4/2015
Publication Date: 12/4/2015
Citation: Xu, C., Jiao, C., Zheng, Y., Sun, H., Liu, W., Cai, X., Wang, X., Liu, S., Xu, Y., Mou, B., Dai, S., Fei, Z., Wang, Q. 2015. De novo and comparative transcriptome analysis of cultivated and wild spinach. Scientific Reports. 5:17706. doi: 10.1038/srep17706.

Interpretive Summary: Spinach is an economically important green leafy vegetable crop. However, currently genomic and genetic resources for spinach are very limited. Here we report for the first time the sequencing of gene products in spinach ((Spinacia oleracea), and two wild species S. tetrandra and S. turkestanica. The sequences provide a valuable resource for gene discovery and molecular marker development. Analysis of this sequence dataset provides novel insights into the genetic relationship and genetic diversity of cultivated and wild spinach. Results from this study 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 highly 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 sequences and the associated data.

Technical Abstract: In this study, we performed deep transcriptome sequencing for nine spinach (Spinacia oleracea L., 2n = 2× = 12) accessions, three from cultivated S. oleracea, three from wild S. turkestanica and three from wild S. tetrandra, using the Illumina sequencing technology. 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 against different protein databases using BLASTX, nearly 60% of these unigenes were annotated and around 50% could be assigned with Gene Ontology (GO) terms. A total of 486 biochemical pathways were predicted from the assembled spinach unigenes. From the deep transcriptome sequencing data, we were able to identify a total of ~320,000 high-quality single nucleotide polymorphisms (SNPs) among the nine cultivated and wild spinach accessions. 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 highly 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 sequences and the associated analysis results.