| The MADS-box gene family play an important role in nearly all stages of flower development . The rice genome sequencing project provides an opportunity to explore all the MADS-box genes in genome level. According to the known information of MADS-box genes, we analyzed them by searching GeneBank and TIGR rice annotation with key words and by exploring similar sequences using HMMER software. Phylogenetic trees show that there are 64 MADS-box genes encoding different proteins, including 46 cDNA sequences. 23 ABCDE genes are found in total, of which 10 have been studied. Using 3'-RACE and library screening method, we cloned three genes which belong to class A (A5B2) and class E (MW1 and MW2), respectively. These genes are similar to OsMADS14, OsMADS7 and OsMADS7, respectively. A function genes are key to elucidate whether palea and lemma in monocot and sepal in dicot are parallel organs. In situ hybridizations show that OsMADS14 expressed in palea and lemma meristem. With the development of florets, OsMADS14 expressed all around. At the later stage, OsMADS14 was expressed in ovules strongly. The expression pattern of OsMADS14 is similar to that of other FUL-like genes. The strong expression in ovule may indicate its important role in the ovule development. SEPALLATA genes are considered the "flower-specific" factors, which involve in the determine of all four whirl flower organs. In this paper, TrSEP3, a MADS-box gene, was isolated from Taihangia rupestris flower buds using 3'-and 5'-RACE method. The predicted amino acid sequence containing typical M-, I-, K-domain, and C-terminus is close to these of FBP2 and SEP3 proteins. Phylogenetic analysis shows that this gene belongs to SEP subfamily. TrSEP3 first expressed in floral meristem, then in petals and the primordium of two inner floral organs. In mature organs, expression signals were detected only in petals and pistils. This expression pattern was slightly different from other E class genes. CaMV35S::TrSEP3 didn't cause any detectable altered phenotype in Arabidopsis, suggesting that the function of TrSEP3 may be different from that of SEP genes of Arabidopsis. The selection pressure analysis shows that TrSEP3 underwent unaltered negative selection,meaning its function may not as other E class genes. All these results demonstrated that TrSEP3 may not function like other SEP-like genes and it is worth to explore its function furthermore. SAGE(Serial Analysis of Gene Expression) is an effective method to compare different transcription maps, and to find new genes. Tag mapping is to map a short SAGE-tag to its transcript. The mapping efficacy determines the effective explanation of transcription maps and is affected by several factors. Currently, no such detailed research has been done on rice. To compare the difference among rice sequence databases, and to find optimal parameters for rice SAGE, we construct several reference maps using EST sequences and genome sequences, respectively. By extract the virtual SAGE-tags from a full-length cDNA database, we compare the effect of reference map, anchoring enzymes, tag length and the tag-to-gene mapping methods. Also, we calculated the accuracy of tag mapping using EST-constructed reference maps. The results showed that the reference maps derived from EST/cDNA could reliably map most of the virtual SAGE tags to their origin transcript. To fully utilize the genomic sequence, an iterative mapping method can be used. NlaIII, HpyCH4V and AluI are appropriate relatively for mapping tags. 17-bp tag is ideal for rice. By both selecting 17-bp tag and using double-anchoring enzymes, higher mapping efficacy and mapping accuracy can be obtained.
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