Identification and characterization of nucleotide variations in the genome of Ziziphus jujuba (Rhamnaceae) by next generation sequencing.

In this study, single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the genome of Ziziphus jujuba were identified using sequences generated by the Roche 454 GS-FLX sequencer. A total of, 573,141 reads were produced with an average read length of 360 bp. After quality control, 258,754 of the filtered reads were assembled into 23,864 contigs, and 293,458 remained as singletons. Using the contig assemblies as a reference, 17,160 SNPs and 478 InDels were identified. Among the SNPs, transitions occurred three times more frequently than transversions. In transitions, the number of C/T and G/A transitions was similar. Among the transversions, A/T was the most abundant, and C/G was much rarer than any of the other types of transversions, accounting for only about half the numbers of A/C, A/T and G/T transversions. For the InDels, mononucleotide changes amounted to 64.4% of the total number of InDels. In general, the frequency of detected InDels decreased as the length of the InDels increased. This study provides valuable marker resources for future genetic studies of Ziziphus spp.