Comparative Sequence Analysis Of Orthologous Regions Of Tillering Control Gene (MOC1) In The Oryza Genus

Tillering is the ramifying trait emerging in the period of growth of some grass species e.g. rice, wheat, et al.. Tillering that is close correlate with the creating of ideal plant shape is the main deciding factor of spike numbers and the consequent yield of rice, wheat, et al. The wild rice species distributed in the Torrid Zone and sub-Torrid Zone possess abundant genetic diversity and excellent genes that do not exist in cultivated rice varieties. So, the wild rice species become important gene pools for improving yield, grain quality, stress resistance, and other agronomic traits of cultivated rice varieties. Along with the completion of genome project of Oryza sativa L. ssp. Japonica cv. Nipponbare and Oryza sativa L. ssp. Indica cv. 93-11 and the sequencing cost dropping more and more, to do some work about comparative genomics at DNA sequence level become more and more realizable. So, in order to give some theoretical and technological support for the wild rice resources utilizing effectively, the comparative analysis among MONOCULM1 (MOC1) orthologous regions in Oryza genus has been done by employing the methods of comparative genomics at DNA sequence level and bioinformatics. The results are depicted as follows.The comparative genomics is a strongly method to improving the veracity of gene annotation. One gene annotation error in NCBI was discovered through RT-PCR and subsequently sequencing. 15bp nucleotides in the coding sequence of this gene annotated in NCBI is excessive than the reality of this gene.The majority of orthologous genes and the intron-exon structures of these genes in Oryza genus are much conserved and the gene contents and order is also. Some genome specific genes were found. The orthologous genes existed all over in the BACs sequenced in this research are MOC1 and the gene that probe 42DP1006 is come from on Japonica MOC1 PAC. Other genes on MOC1 PAC except the two mentioned above can be found their orthologous genes from several BACs only. The reason that some orthologous genes cannot be found are mainly the two, short BAC sequences and more repeat appearing in the BACs especially in the BACs created by tetraploid.The exon number per gene on average in each MOC1 homologous BAC is similarity with each other. High gene density is discovered in AA genome type, but one high and one low are found in tetraploid genomes except CCDD genome. One whole cds sequences of new gene generated by de novo have been detected here. by sequence alignment, we find a short conserved DNA sequence comparison within far relative species GG, FF and EE, but the conserved sequence become longer than before gradually within more closely relative species EE and BB and the new gene which has full length cDNA support (AK062635) by 100 percent is originated eventually in AA and BB genomes.The molecular evidence for nonfunctionalization of duplicated gene originated from whole genome duplication and/or gene duplication has been discovered from several species of Oryza. There is one homologous gene of 42DP1006 in all tetraploid Oryza species except CCDD genome has no PCR products in RT-PCR experiments although several times repeated. The homologous gene of 42DP1006 in GG genome, O. granulata, has been duplicated in series and divided by retrotransposon insertion. The upriver homologous cannot be amplified in several times RT-PCR. So, nonfunctionalization of duplicated gene can be presumed.A tetraploid, O. alta, which has an especial gene density and expression comparing with other tetraploid in Oryza genus has been found. Both the subgenome CC and DD of O. alta have high gene density and both the orthologous gene pairs of 42DP1006 can be transcribed to some extend. Further more, the expression of orthologous gene of MOC1 PAC No.6 in O. alta is normal though the third intron of this gene is inserted by about 4kb retrotransposon. The other one of the orthologous gene pairs can be transcribed normally too.The driving force of genome expansion of Oryza genus is the amplification of transposons and retrotransposons. we find the smaller genome size of AA(350Mb~448Mb)and FF(338Mb)possess more MITE (16~21 for AA,30 for FF)and Tc1-IS630-Pogo(18 ~34 for AA,32 for FF), but not for the larger genomes. From the aspect of LTR retrotransposon number, the reverse condition appeared comparison with above, i.e. smaller LTR retrotransposons detected in AA and FF genome than other genome types in Oryza genus. From the aspect of sequence proportion by the accumulated sequence length of transposons and retrotransposons to BAC length, the larger genome size possess high proportion of retrotransposons and less high proportion of transposons. This implies the genome expansion of Oryza genus is the result of amplification of transposons and retrotransposons. and it maybe the law of genome expansion in biology.According to the consensus MOC1 phylogenetic tree constructed by Neighbor-Joining, Maximum Parsimony, and Minimum Evolution, the most close relative genome type with AA genome that contain cultivar rice is BB and then the CC, DD, EE, respectively. The genome type of HHJJ, HHKK, FF and GG have alienated relative with AA genome.