Cytonuclear Co-evolution In The Triticum/Aegilops Complex

Hybridization,as one of the important driving forces for plant evolution and speciation,includes allopolyploidization with chromosome doubling,and homoploid hybrid speciation without chromosome doubling.Allopolyploidization is crucial for the speciation and evolution of higher plants.A common feature in the above two hybridization processes is that,the hybrid speciation results from combining two differentiated nuclear genomes,while only having one of the two progenitor genomes in the cytoplasm.Accordingly,the two hybrid processes need to face the same challenge of “Cytonuclear incompatibility”,which includes 1)cytonuclear stoichiometric disruptions caused by combining two diverged nuclear genomes with the maternal inheritance of the cytoplasmic organellar donor;and 2)incompatibility of chimeric protein complexes with diverged subunits from nuclear and cytoplasmic genomes.Thus,how to overcome the challenge mentioned above has been regarding as the focus of the research on cytonuclear co-evolution.Previous studies used RuBisCo enzyme as the research model,to explore the cytonuclear co-evolution at the genomic and transcriptional level,in the allopolyploids Gossypium,Arachis,Brassica,and the respective extant relatives of their diploid parents.However,the following questions still need to be solved:(1)are the above models and mechanisms of cytonuclear co-evolution universal in other allopolyploid species?(2)Are there dynamic changes of the above cytonuclear coevolution patterns during “multiple” allopolyploidization within the same genus?Both questions mentioned above are still not fully understood and urgent scientific problems in the field.Compared with the allopolyploidization,few studies on cytonuclear co-evolution of homoploid hybrid speciation have been reported.(3)Are there any similarities or differences of the cytonuclear co-evolution pattern and mechanisms between homoploid hybrid speciation and allopolyploidization? It is also a key scientific problem in the field.Within this study,we focused on the scientific issues mentioned above,by describing the process,summarizing the results,concluding and discussing the findings.Triticum/Aegilops complex enclosing a series of diploid Triticum/Aegilops and allopolyploid species.Allopolyploid wheats are ideal material system to solve the above questions(1)and(2).In addition,it has been confirmed that the representative species of D-genome lineages,Ae.tauschii and its possible parent ancestors also become an ideal research system to solve the above question(3).In a word,Triticum/Aegilops complex are the ideal system for analyzing the cytonuclear coevolution in allopolyploidization and homoploid hybridization.To investigate the three scientific issues above,we designed the research contents to explore the cytonuclear co-evolution model in the process of homoploid hybridization and allopolyploidization in Triticum/Aegilops complex.The research materials,methods,results and conclusions are summarized as follows:Firstly,we characterized the bi or multiparental ancestors of Ae.tauschii during the homoploid hybridization process.We analyzed the composition of organelle targeted protein coding nuclear genes(CECs)in Ae.tauschii and its ancestral parentage,and compared the sequence changes of CECs nucleotides before and after hybrid speciation,and the nucleotide composition of CECs within Ae.tauschii retained from its ancestors.Detailed results were as follows,we constructed the phylogenetic trees(Neighbor Joining and maximum likelihood tree)of homologous genes within chloroplast genomes using the representive species of A genome lineage(Triticum urartu;Triticum monococcum),representative species of B genome lineage(Ae.speltoides),and representative species of D genome lineage(Ae.tauschii;Ae.longissima;Ae.bicornis;Ae.sharonensis;Ae.searsii)in Triticum/Aegilops complex,together with the outgroup barley.Based on the strict maternal inheritance of both chloroplast and mitochondria backgrounds within Triticum/Aegilops complex,we confirmed a previously inferred derivation that the maternal parent of Ae.tauschii may be the ancestor of A genome lineage after the last hybridization event in the process of homoploid hybridization.Then,in order to explore the subsequent cytonuclear co-evolution pattern,we predicted the CECs genes of related species(including the above mentioned allotetraploid/allohexaploid wheat linages and the diploid species)within Triticum/Aegilops complex and their outgroup barley,and screened the most conserved 150 single-copy homologous of CECs for further analysis.Finally,150 single-copy homologous of CECs within represented species of Triticum/Aegilops complex were subjected to construct phylogenetic tree with“concatenated genes alignment + NJ / MLmethod” and “inferred the phylogenies separately for each gene + Bayesian method”,respectively.It was shown from the two types of phylogenetic trees that,CECs of Ae.tauschii displayed closer phylogenetic relationships with diploid A genomes or polyploid A subgenomes than they did with diploid B-genomes or polyploid B subgenomes,which means CECs of Ae.tauschii clustered with CECs of A genome lineage or A subgenome of polyploid.Moreover,we found that CECs of Ae.tauschii have experienced biased retention of the SNPs from A genome lineage.Then,the SNPs/Indels of the CECs in Ae.tauschii retained from the A-genome lineage were analyzed.We found that,compared with the wholegenome of Ae.tauschii,CECs showed baised retention of the A-genome lineage SNPs/Indels.These results indicated that,accompanied with the ancient homoploid hybrid speciation,CECs in Ae.tauschii have experienced biased retention of the genomic SNPs/Indels from one of its bi-parental genomes,specifically the same genome as that of the maternal organelle donor,under the strict maternal organelles genetic background.Secondly,in order to explore the composition and stability of rbcS gene family during the process of allotetraploidization and hexaploidization,rbcS and rbc L family composition were analyzed in representative Triticum/Aegilops complex species,including diploid species,wild tetraploid wheat,cultivated tetraploid wheat and hexaploid wheat(about 12 species,16 genomes/subgenomes).We also analyzed the cytonuclear co-evolution pattern,the possible dynamic changes and possible causes of specific changes of rbcS gene at genomic level in different polyploids,respectively.Results were as follows:(1)there was only one copy of rbc L gene in each species of the Triticum/Aegilops complex,and it was transmitted by maternal inheritance during allopolyploidization;there were 9 rbcS copies in A-and B-genome/subgenome,but only 8 rbcS copies in D genome/subgenome;(2)rbcS6 homolog of D-genome lineage was completely lost during homoploid hybrid speciation event,and can’t be inherited during the subsequent allohexaploidization process;(3)there was no intergenomic gene conversion detected in wild or domesticated tetraploid wheat;however,intergenomic paternal-to-maternal nonsynonymous gene conversion specifically occurred in the transit peptide region of the rbcS3 D to rbcS3 B homoeologous in allohexaploid wheat(TAA10,AK58,and CS accession);(4)the non-synonymous substitution of rbcS3 existed in 318 re-sequencing and transcriptomic data of hexaploid common wheat,which proved the universality and potential importance of the non-synonymous substitution;(5)by using the molecular function study as a control,we confirmed that the non-synonymous substitution was located in the SASLGS*VSNG domain of transport peptide of SSU3,which was recognized as the domain for small subunit interacting with the chloroplast membrane translocon;(6)by transcriptomic analysis,we found that the non-synonymous substitution of rbcS3 D to rbcS3B-like,which led to the SSU3 D to SSU3A/B-like conversion(a maternal-like SSU3D),facilitated the more abundant interactions between SSU3 D and Toc90 B and Toc90 A counterparts for targeting and transport into chloroplast.In summary,we systematically described the cytonuclear co-evolution patterns in both homoploid hybridization and allopolyploidization process in representative Triticum/Aegilops complex species.Our current study on the homoploid hybridization,not only inferred the maternal parent for Ae.tauschii,but also discovered the cytonuclear co-evolution pattern in homoploid hybrid species Ae.Tauschii,that is the paternal homoeologs of the CECs experienced biased retention of the maternal genomic SNPs/Indels to compatible with the maternal organelles during the ancient homoploid hybrid speciation.We first discovered that there was no cytonuclear response at genomic level of tetraploid wheat in two sequential allopolyploidization processes,and confirmed the effective recognition between SSU3 D and chloroplast translocon TOC90 B,together with the targeting and transporting of SSU3 D into chloroplast in allohexaploid may mediate the cytonuclear response of the corresponding rbcS3 D converted to rbcS3B-like in its transit peptide region.We suggested that our data in Ae.tauschii may facilitate more accurate detection of cytonuclear co-evolution following the process of homoploid hybrid speciation;and the above findings not only represent a novel dimension of cytonuclear evolution mediated by organellar targeting and transportation of nuclear proteins,but also provide new insights for the improvement of wheat breeding.