TY - JOUR
T1 - A Chinese jujube (Ziziphus jujuba Mill.) fruit-expressed sequence tag (EST) library
T2 - Annotation and EST-SSR characterization
AU - Liu, Jun
AU - Liu, Huabo
AU - Ma, Liying
AU - Wang, Siqi
AU - Gao, Jiao
AU - Li, Yingyue
AU - Wu, Rongling
AU - Pang, Xiaoming
N1 - Funding Information:
This work was supported by Special Fund for Forestry-Scientific Research in the Public Interest ( 201004017 ), the grants from the Program for New Century Excellent Talents (NCET-10-0223) and the Fundamental Research Funds for the Central Universities ( JD2010-5 , BLYX200924 ).
PY - 2014/1/22
Y1 - 2014/1/22
N2 - 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.
AB - 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.
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U2 - 10.1016/j.scienta.2013.10.033
DO - 10.1016/j.scienta.2013.10.033
M3 - Article
AN - SCOPUS:84888787181
SN - 0304-4238
VL - 165
SP - 99
EP - 105
JO - Scientia Horticulturae
JF - Scientia Horticulturae
ER -