Phylogeny And Evolution Of The Oryza Allotetraploids With CD Genomes Evidenced With DNA Data

Three allopolyploids with the CCDD genome,distributing in Latin America,include O.alta Swallen,O.grandiglumis(Doell)Prod.,and O.latifolia Desv.The three species belong to O. officinalis complex,and they have a very complicated status in the genus Oryza,due to their overlapping in the distribution,the intricacies of delimitation and phylogenetic relationships, ambiguous of their origins as well as the characteristics of allopolyploidy,which have attracted many scientists to work on these problems for a long time.The main questions are summarized as follows:(1)Delimitation and phylogenetic relationships of the three species has long been a controversial matter,different viewpoint was mentioned by different academicians;(2)There has been a long history of interest in the possible origins of the three American allopolyploids with C and D genomes,on which different hypotheses were proposed;(3)The evolutionary dynamics of duplicated gene derived by polyploidization has long attracted the interest of geneticist.An allopolyploid speciation event entails the merger of two,differentiated genomes in to a common nucleus in only one of the two parent alcytoplasms,which result in genome-wide gene duplication.What are the primary possibilities for the evolutionary fates of duplicated genes from different genomes? What have been taken place to the duplicated genes on genetics in Oryza allotetraploids?The key of these questions need further studying to look for by a series of experiments.In this work,these unsolved questions,as mentioned above,were explored using the sequences of alcohol dehydrogenase(Adh1)gene and G-protein(GPA1)gene:(1)The phylogeny and the possible origins of the three allopolyploidys were discussed by comparing the sequences of the alcohol dehydrogenase(Adh1)gene from genome C and D in Oryza allotetraploids and the sequences from A,B,C,E and F genomes in extant Oryza diploids. The sequence from G genome was treated as the out-group.Phylogenetic analyses were performed using the parsimony and neighbor-join methods in PAUP soft.The result indicated three allotetraploids with CD genome might originate from a single hybridization event;C genome within the tetraploids showed a closer phylogenetic relationship to the C genome of O. officinalis,O.rhizomatis diploids from the Asia;genome D showed a closer affinity to the genome E of O.australiensis from Australia than the other genomes in diploids,which suggested that D and E genome might have a common ancestor.(2)The sequences of GPA1 from C,D genome in allopolyploids,and their close diploid relatives,O.australiensis with E genomes,O.officinalis with C genomes,were analyzed to investigate the patterns of evolution on duplicated genes in Oryza allotetraploids.The result showed the allopolyploid species contained two homoeologous sequences representing descendants of those contributed by the C and D genome donors at the time of polyploid formation;the three wild species appeared to hold very low levels of nucleotide variation compared to other plant species.Average nucleotide variation in GPA1 genes of C genome was higher than that in D genome,especially,in species of O.grandiglumis and O.latifolia,the phenomenon was more prominent.Based on the algorithm of Hudson and Kaplan,the minimum numbers of historical recombination events were not found in these species.Several statistical tests were used to test the hypothesis that GPA1 sequences have been evolving in accordance with expectations under neutral theory.The significant departure from neutrality was only found in O.alta by Fu and Li'D test.The null hypothesis of the isolation model was not rejected in grandiglumis and O.latifolia.The haplotype networks of the 3 species showed O.alta and O. grandiglumis shared more mutual haploidyes.The result further suggested a closer phylogenetic relationship between the two taxa.