Bioinformatics Analysis Of EST From CDNA Liabrary Of Ziziphus Jujuba

Ziziphus jujuba Mill hupingzao mainly originated in from China’s TaiGu, Qing xu, Yuci, Taiyuan and other places of Shanxi Province. It has strong vitality and tall body,not just it can grows in the mountains or the ground,but it has the character of prematurity, high yield, stable yield, drought resistance, cold resistance, flood tolerance and salinity tolerance, etc. Therefore, the research of the fruit bearing Shoot of Ziziphus jujuba Mill hupingzao during the early stages of flower bud differentiation is not only crucial for elucidating regulating mechanisms for plant growth, development and genetic expression,also it lays a foundation for the jujube’s variety improvement. Through screening the cDNA library of the fruit bearing Shoot of Ziziphus jujuba Mill hupingzao during the early stages of flower bud differentiation, we obtained867EST sequences.We did gene annotation for these EST,then explored the jujube’s EST-SSR,analysed its characteristics. Also we did bioinformatics analysis of the ribosomal protein and cyclophilin.1. Annotation and analysis of the EST in jujube’s cDNA library: Through screening cDNA library of the fruit bearing Shoot of Ziziphus jujuba Mill hupingzao, we received2633positive clones,1061insert cDNA fragments were got via the enzyme cut assay. Among736EST which got effective sequences results in the867EST above500bp,439EST were annotated, compared with59.65%.In these EST we found a lot of gene about growth, development, material metabolism, energy metabolism, such as histone, ribosomal protein, glucose6-phosphate dehydrogenase, udp glucose dehydrogenase, NADH dehydrogenase, succinate dehydrogenase, pyrophosphatase, serine threonine protein phosphatase and lipid transfer protein, etc. As well as some genes related to the jujube’s cold resistance, drought resistance, strong resistance, such as superoxide dismutase,2-cys peroxiredoxin, peroxidase and ascorbate peroxidase, zeaxanthin epoxidase, shaggy-related protein kinase, cyclophilin, aluminum induced protein, proline rich protein, etc.2. Jujube’s EST-SSR development and its character analysis:through SSR search of the607non-redundant EST,we developed109SSR,17.96%of all EST.607sequences of bases The total length of the607non-redundant EST is460523bp, and equivalent to one EST-SSR on average is4.22Kb EST sequence. In different motifs, dinucleotide repeat type was the most abundant(9.23%), accounting for51.38%of the total SSR, The following were trinucleotide repeats(3.46%) and hexanucleotide repeats(2.47%),accounting for33.03%of all SSR. Among the dinucleotide repeat types, AT/TA motifs had the highest frequency(3.95%).Among the trinucleotide repeat types, AGA/TCT had the the highest frequency (0.66%).The difference of the motifs’frequencies among tetranucleotide repeats, pentanucleotide repEST and hexanucleotide repEST was little. AAAG/CTTT, TATTT, TTATT, CCATGA, TGTTTG had the high proportion relatively.3. Bioinformatics analysis of jujube’s ribosomal protein:based on the bioinformatics analysis of the jujube’s29ribosomal protein which’s molecular weight were6430.49Da-34781.22Da, we found that they were soluble protein. And Alpha helix, Extended strand, Beta turn and Random coil were theirs main secondary structure. Except the5OS ribosomal protein L12which’s pI was weak acid, the rest of them were alkaline. Comparing their potential phosphorylation sites, we found the potential phosphorylation sites of the ribosomal protein in the chloroplast were more than the ribosomal protein in nuclear. Studying the subcellular localization,we found that jujube’s ribosomal proteins distributed in nuclear (65.52%), cytoplasm (17.24%), stroma (6.90%),chloroplast thylakoid membrane (6.90%) and microbody/peroxisome(3.45%). Through the molecular phylogenetic tree, we can see that there were10pairs in the same branches,6pairs having the same subcellular localization and another4pairs with different subcellular localization.4. Bioinformatics analysis of jujube’s cyclophilin:through screening jujube’s cDNA library,we found a complete ORF of jujube’s cyclophilin. The analysis results of the cDNA sequence indicated that the sequence length of525bp encoded a174-amino-acids polypeptide with a predicted isoelectric point of8.37and molecular mass of18.30KDa. Making multiple alignment with Citrus sinensis,Gossypium hirsutum, Hevea brasiliensis, Populus tremuloides, Arabidopsis thalianal, Digitalis lanatal, Pinus halepensis and Elaeis guineensis,we found they were homologous. Through the molecular phylogenetic tree, jujube’s cyclophilin and Citrus’showed similar relationship.Further studies conclusively showed that this cyclophilin belonging to cyclophilin A without transmembrane region and signal peptide was soluble protein. Its had a PPIase catalytic domain and a small quantity of phosphorylation sites. Extended strand and random coil were its main secondary structure. Through comparing tertiary structure with Gossypium hirsutum, we found cyclophilin’s structure is conservative.