Abstract
Chinese jujube (Ziziphus jujuba Mill.) is an economically important deciduous tree that has high therapeutic value and health benefits. However, a lack of sequence data and molecular markers have constrained genetic and breeding studies for better fruit quality and other traits in Chinese jujube. In this study, two combined cDNA libraries of ‘Dongzao’ fruit representing the early and late stages of fruit development were constructed and sequenced on the 454 GS FLX Titanium platform. In total, 1,124,197 reads were generated and then de novo assembled into 97,479 unigenes. A total of 52,938 unigenes were homologous to genes in the NCBI non-redundant sequence database. A total of 33,123 unigenes were assigned to one or more Gene Ontology terms, and 16,693 unigenes were classified into 319 Kyoto Encyclopedia of Genes and Genomes pathways. The results showed that the Smirnoff-Wheeler pathway was the main pathway for the biosynthesis of ascorbic acid in Chinese jujube. The number of differentially expressed genes between the two stages of fruit development was 1,764, among which 974 and 790 genes were up-regulated and down-regulated, respectively. Furthermore, 9,893 sequences were identified containing SSRs. 93 primer pairs designed from the sequences with a tri-nucleotide repeat showed successful PCR amplification and could be validated in Chinese jujube accessions and Z. mauritiana Lam and Z. acidojujuba as well, of which 71 primer pairs were polymorphic. The obtained transcriptome provides a most comprehensive resource currently available for gene discovery and the development of functional markers in Z. jujuba. The newly developed microsatellite markers could be used in applications such as genetic linkage analysis and association studies, diversity analysis, and marker-assisted selection in Chinese jujube and related species.
Highlights
Ziziphus species of the Rhamnaceae, the buckthorn family, are widespread in both hemispheres [1]
454 sequencing and assembly Two combined cDNA libraries of the ‘Dongzao’ fruit, i.e., S1 representing the early stage and S2 representing the late stage of fruit development based on the fruit growth curve (Figure S1), were constructed using the SMART cDNA Construction Kit (Clontech, USA)
All of the high quality reads were deposited in the National Center for Biotechnology Information (NCBI) and can be accessed in the Short Read Archive (SRA) under the accession number SRR1231563
Summary
Ziziphus species of the Rhamnaceae, the buckthorn family, are widespread in both hemispheres [1]. Chinese jujube (Ziziphus jujuba M.) and Indian jujube (Z. mauritiana Lam.) are two species that have considerable horticultural importance [1]. Chinese jujube ( known as Chinese date) is an important deciduous fruit tree that is grown in temperate and subtropical areas and is one of the most important fruit trees in China, where it has been cultivated and utilized for more than 4,000 years [2]. The jujube fruit is an edible oval drupe, 1.5 to 6.0 centimeters long [1]. Additional health benefits of Chinese jujube fruit have been reported, including anticancer, anti-inflammatory, anti-obesity, immunostimulating, antioxidant, hepatoprotective, and gastrointestinal protective activities and roles in the inhibition of foam cell formation in macrophages [9]. Chinese jujube can be consumed fresh, dehydrated, canned or processed into candy, jam, juice, wine, syrup or vinegar [10]
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