A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library: Annotation and EST-SSR characterization

Jun Liu, Huabo Liu, Liying Ma, Siqi Wang, Jiao Gao, Yingyue Li, Rongling Wu, Xiaoming Pang

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Characterization of gene expression in plants is important to understanding their physiology and breeding programs. This can be approached by generating partial mRNA transcript sequences, known as expressed sequence tags (ESTs). ESTs are useful for gene discovery and to identify molecular markers, such as simple sequence repeats (SSRs). In this study, we constructed a cDNA library using the fruit of Chinese jujube Ziziphus jujuba 'Dongzao', and obtained 1942 high-quality sequences. ESTs were assembled into 965 unigenes, including 239 contigs and 726 singletons. BLAST searches confirmed that 782 (81.0%) unigenes had homology to previously identified plant genes, and the remainder may represent unique clones not previously explored. Sequences with annotations were further clustered with Gene Ontologies (GO). A total of 686 (71.1%) unigenes were functionally classified into one or more categories. Furthermore, we identified 334 simple sequence repeats (SSRs) in the unigenes. Of the 219 primer pairs, 119 amplified successfully in 'Dongzao', among which 66 randomly selected could amplify in sour jujube (Z. acidojujuba C.Y. Cheng et M.J. Liu (Z. spinosa Hu.)) and another four Chinese jujube cultivars. The newly characterized genes and gene-derived markers from our EST library will facilitate genome annotations, novel gene discovery, molecular breeding and comparative genomics in Chinese jujube and related species.

Original languageEnglish (US)
Pages (from-to)99-105
Number of pages7
JournalScientia Horticulturae
Volume165
DOIs
StatePublished - Jan 22 2014

Fingerprint

Ziziphus jujuba
expressed sequence tags
unigenes
microsatellite repeats
fruits
genes
Ziziphus
breeding
cDNA libraries
physiology
clones
genomics
gene expression
genetic markers
genome
cultivars

All Science Journal Classification (ASJC) codes

  • Horticulture

Cite this

Liu, Jun ; Liu, Huabo ; Ma, Liying ; Wang, Siqi ; Gao, Jiao ; Li, Yingyue ; Wu, Rongling ; Pang, Xiaoming. / A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library : Annotation and EST-SSR characterization. In: Scientia Horticulturae. 2014 ; Vol. 165. pp. 99-105.
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A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library : Annotation and EST-SSR characterization. / Liu, Jun; Liu, Huabo; Ma, Liying; Wang, Siqi; Gao, Jiao; Li, Yingyue; Wu, Rongling; Pang, Xiaoming.

In: Scientia Horticulturae, Vol. 165, 22.01.2014, p. 99-105.

Research output: Contribution to journalArticle

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T1 - A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library

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AU - Liu, Jun

AU - Liu, Huabo

AU - Ma, Liying

AU - Wang, Siqi

AU - Gao, Jiao

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AU - Wu, Rongling

AU - Pang, Xiaoming

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