Cytonuclear Evolution Of Rubisco Genes In Artificial Rice Hybrids And Polypoloids

Allopolyploidization in plants entails the merger of two divergent nuclear genomesin aspects of both sequence and structuures,whereas only one set(usually the maternal)of parental organellar genomes is maintained in the cytoplasm.The cytonuclear evolutionaryanalysis mainly concerns about how those parental nuclear genomes coordinate with each other in the same nucleus to achieve their eventual compatibility with the cytoplasmic organellar genome.Here,within our study,we chose parental rice subspecies Nip and 93-11(Oryza sativa ssp.japonicaand indica),their reciprocal hybrids(9N and N9),and corresponding artificial allopolyploids at S5 generation as our materials and employed the cytonuclear co-encoded Rubisoco complex and their encoding genes as model systems,to explore the cytonuclear evolution patterns and features in those rice hybrids and allotetraploids.Weinitially identified the composition of rbcL gene and rbcS genes family and characterized their evolutionary processes in divergent parental diploid rice species.The results showed that rbcL gene sequences of those two subspecies are highly conserved with only one synonymous substitution difference.There are five rbcS ortholog groups(rbcS1-rbcS5)identified in this rice lineage.rbcS1 gene orthologs reside in the chromosome 2 of each dipoid species,which has lower sequence similary with theother similar orthologs clustering adjacently in the chromosome 12.The sequence comparison of all those five rbcS ortholog pairs between two parental species revealed their divergent evolution pattern,which is consistent with the classical concerted evolution model of rbcS genes.The cytonuclear coordination in reciprocal hybrids and allotetraploidsat both genomic and transcriptional level were further explored.Within the reciprocal hybrids,there is no genomic coordination involving inter-allelic gene conversions.In addition,at transcriptional level,parental alleles in reciprocal hybrids have anoverallstochastic and inconsistent biased expression pattern.Specifically,in 9N hybrids,paternal rbcS2 and rbcS3 alleles and maternal rbcS4 and rbcS5 alleles were biased expressed in each corresponding rbcS ortholog group;in N9 hybrids,paternal rbcS alleles in all ortholog rbcS ortholog groups were biased expressed.As for the cytonuclear coordination in twelve representative allotetraploid individuals,at genomic level,gene conversions among certain rbcS homoelogsin different directions(maternal-to-paternal and paternal-to-maternal)were detected in four allotetraploid individuals.At transcriptional level,As for the transcriptional coordination between parental homoeologs gene copies in the same gene group,in representative alltetraploid individual 99NN-5,paternal rbcS2,rbcS3,and rbcS5 copies were expressed at higher level than those maternal copies,however,in 99NN-6 individual,all maternal rbcS homoeologs in each homoeolog group were preferentially expressed.Novel biased expression pattern in the same rbcS homoeolog group was also observed among the homoeologs of the same parental origin.Generally,as for the homoeolog with certain maternal-to-paternal conversion,its expression was depressed relative to the paternal homoelog without hosting any gene conversion;as for the homoeolog with certain paternal-to-maternal conversion,no significant expression changes was observed.Therefore,within the reciprocal hybrids and tetraploids utilized in this study,the interactions of component subunits is not the solelydeterminant of cytonuclear coordination.Besides the coordination at genomic and transcriptional levels,there could be other more complexed mechanisms at other layers that are affecting the eventual successful cytonuclear coordination.