De Novo Assembly and Characterization of the Fruit Transcriptome of Chinese Jujube (Ziziphus jujuba Mill.) Using 454 Pyrosequencing and the Development of Novel Tri-Nucleotide SSR Markers

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.

Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

“…The lower proportion of polymorphisms in dinucleotide repeats indicates that this type of SSR locus is more highly conserved in the genome to ensure species stability. The higher polymorphic rate in trinucleotide repeats was similar to previous study [ 13 ], and that might be attributed to three bases coding for an amino acid, and frameshift mutations could effectively prevent other SSR loci from changing. From the perspective of SSR evolutionary analysis, these changes in the SSR loci could be explained with a stepwise mutation model (SMM); the length of an SSR locus was changed by adding or removing a percentage of the motif, not by adding or removing a single base [ 28 ].…”

“…Using the MISA program to analyze 396.18 Mb (approximately 90.00%) of the estimated jujube genome [ 13 ], 70.83% of the 3,027 scaffold sequences were found to contain SSR loci. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci.…”

De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis

“…The average 1116 bp length of the unigenes was longer than that reported for pumpkin transcriptomes (765 bp) using the Illumina HiSeq™ 2000 sequencing platform [ 17 ]. It was also greater than that of the Chinese jujube (473.4 bp) and Siberian apricot (651.6 bp) transcriptomes, using the 454 GS FLX Titanium genomic sequencer platform [ 19 , 20 ].…”

Composition, antioxidant activities and hepatoprotective effects of the water extract of Ziziphus jujuba cv. Jinsixiaozao

“…7,8 Ziziphus jujuba is one of the most important economic trees in China because of drought and barren soil resistance, high-yield, rich nutrition, signicant benets of economy and ecology. 9,10 Jujube has a high nutritional value and heath care function. The nutrients of jujube including avonoid, polyphenol, polysaccharide, protein, amino acid, fat, nucleotide, triterpenes, saponin, alkaloid, mineral element, vitamin and other bioactive substances, 2,[11][12][13][14][15] contribute to antioxidant, 16,17 antimicrobial, 18 antitumor, 19 hepatoprotective, 2,20 nourish blood, soothe the nerves, boost immunity and so on.…”