Comparative Analysis Of Orthologous Sequence Between Sorghum Bicolor And BACs Of Saccharum Officinarum, Saccharum Spontaneum

Rounds of Interspecific hybridization and backcross between Saccharum officinarum and Saccharum spontaneum produced modern sugarcane cultivars with complex genome in which 70～80% of the genome from S.officinarum,10～20% was of genome S.spontaneum, and 10% recombinants. Genomic researches in sugarcane better return to ancestral genomes. The construction of bacterial artificial chromosome (BAC) libraries of S.officinarum and S.spontaneum has completed would provide researchers a foundation to decrypt the complex polyploidy sugarcane genome and conveniently serve for sugarcane improvements and gene finding. This study based on two BAC libraries, comparatively analyzed the homologous region between Sorghum and selected BACs to preliminarily reveal the genomic information of two ancestral species and broaden the horizon of sugarcane genomic.First, we searched FT-like genes (Flowering Locus T) in Sorghum gene model database and gained 11 candidate genes for selection probe primes design. The sugarcane FT probes have obtained one FT-BAC in LA-BAC library and 3 in SES library from library screening.454 sequenced all 4 BACs and assembled the reads to Contigs, after primer walking and PCR gap filling, one full length BAC was gained and 3 BACs with 2-6 gaps. Annotated the genes on BACs,4 sugarcane FT-like genes were acquired. Alignment between Sorghum rice and BACs revealed the genes conservation and collinearly among three species and also detected the chromosome rearrangement happened in S.spontaneum evolution. In addition, some regulator gene were found near FT gene region. Completing the sequencing and gap filling on 87 BACs, we enlarged the comparison analysis in homologous region. Some features of sugarcane were found: S. officinarum seems gain expansion comparing to Sorghum monoploid genome; Gypsy LTR retrotransposon was the feature repetitive elements in S.officinarum but no significant feature for S.spontaneum. The survey of LTR retrotransposon with full structure was conducted and gain a fact that in sugarcane genome the TE activity was happened collectively three times and the trace of TE reshape the gene structure and the gain/loss gene were found. Moreover, we gained a FRK gene family in sugarcane and by calculated the Ka/Ks ratio in coding sequence, a FRK appeared to be subjected to the positive-like selection effect. From the paired gene among three species, Ks was calculated between Sorghum and LA, Sorghum and SES and LA to SES to generate a divergence time estimate. We estimated the divergence between Sorghum and sugarcane is 5.4-7.05Mya and between S.officinarum and S.spontaneum is 1.7Mya.This study was on the basis of comparative analysis the orthologous sequences between S.officinarum, S.spontaneum and Sorghum. We obtained the target genes purposely and meanwhile preliminarily reveal the genomic content of two sugarcane species and broaden the understanding of sugarcane genome.