| Rice is the most important food crop and a staple food for more than half the world's population.Following the populaiton lasting increase,the yield of rice will play an important role in safeguarding the security of global food suppies.By the year 2050,to cope with such a challenge,Rice accounts needs to be doubled for the calories consumed.The diversity of the wild rice will be important genetic resources for the cultivated rice breeding and enhancing the crop yield.Comparison genome analysis between O.longistiminata with two cultivate rice(O.sativa and O.glaberrima)is important.To discovery the sequence with highly sysnteny for the O.longistaminata with two cultivated rice,the gene number is similily,gene family and TE have big variaty.Because of O.longistaminata as the older wild ancestry,exploring population genetic and structure among the three African rice species.The results as follow in details:1)Genome assembly.Combined the second and third sequencing technology was used to assemble high quality genome of O.longistaminata,the congtigN50 reach 404 kb,the number of scaffolds reduce to 1059.Wild rice O.longistaminata and two cultivated rice species have collinearity in genes and chromosomes.Further exploring the genomic components,identification and compative analysis the TE,miRNA and lncRNA of O.longistaminata,we discovery the MITE occupied ratio in the genome of wild rice was higher than two cultivated rice species.The identification of novel lncRNAs in O.longistaminata were based on comparing the genome,transcriptome and EST data,totaly about 2212 lncRNA were predicted,666 lncRNA show a tissesic expression.In the meantime,the positon in genome of lncRNA are more distributed in the intronic and exonix region,and it have much more expression in flower tissue than any other tissues.2)Comparative genomics.Comparative analysis orthologous gene family for O.longistaminata seperately with Asian cultivated rice and African cultivated rice.Totally 2562 single copy genes were identificatied in and 13933 orthologous gene were shared in the 8 plant genome.each other special gene clusters were analysis by the GO annotation.These indicted that AA genome rice species are adapt their difffrent geographical and natural enviroment.Phylogenic tree estimated the speciatial time in the 8 speices.It show O.longistaminta divered more than any other cultivated rice.The divergence time between the O.longistaminata and parallel evolution rice are about 2 Mya.The dynamic evolution of gene family size were estimated by CAFE and Paml,the expansion and constraction of gene family in O.longistaminata show that a rapidly change compare with cultivated rice,specially in the PPR and R gene family.Fanally the whole genome PAV indicated small variety and accumulation in the gene structure which leaded to different enviroment adaptationa in the four rice species.3)Based on the 147 lines resequencing data from the three locous African rice species.PCA and NJ-tree constructed were used to analysis the genetic structure.These results showed that the population of O.glaberrima were clusted in tow different sub-group,which belong to the clusters of O.barthii.PCA and NJ-tree Phylogeny results show the population of O.longistaminata distantly separeted from the O.barthii and O.glaberrima.The genetic structure of the three population infers that only a bit of gene introgression between O.longistaminata and O.glaberrima.All these results infers that O.longistaminta is not the directly ancenstry for O.barthii and O.glabarrima,it may be a much older ancenstry in the AA genome rice species. |
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