Spatiotemporal Dynamics Of Gene Expression And Alternative Splicing In Synthetic Allotetraploid Wheat (AADD Genome)

Polyploidy,or whole-genome duplication(WGD),often induces dramatic changes in gene expression due to "transcriptome shock".It still begs three questions worth systematic investigating.(1)How does allopolyploidy(the merging of multiple nuclear genomes in the same nucleus)affect gene expression and alternative splicing within and across multiple tissues and developmental stages during the initial foundation of allopolyploid plants?(2)Is the transcriptome asymmetric response to allopolyploidy-induced transcriptome shock spatio-temporally specific?(3)What are the dynamic variations of the gene expression and alternative splicing patterns of allopolyploid across multipl tissues and developmental stages? Moreover,motivated by “pivotal-differential” genome evolution,an intriguing question was proposed.What outcome would be if the two pivotal A and D genomes were merged by allopolyploidization? Here,a systematic investigation was conducted into the immediate effect of allopolyploidy on gene expression variation and alternative splicing in an artificial allopolyploidy system consisting of a constructed allotetraploid wheat(AADD genome,accession AT2)and its diploid progenitors Triticum urartu(AA)and Aegilops tauschii(DD).The comprehensive RNA sequencing of 81 samples was performed from different genotypes,tissues,and developmental stages,which include: shoots and primary roots at 4 days after germination;second leaves and mature roots from trefoil-stage seedlings and five spike developmental stages.The systematic investigation was conducted into allopolyploidy-induced variations in gene expression and crosstalk in expression regulation between the subgenomes.First,it was found that the intrinsic interspecific differences between the diploid parents played a major role in establishing the expression architecture of the allopolyploid.Nonetheless,allopolyploidy per se also induced dramatic and asymmetric patterns of differential gene expression between the subgenomes,and genes from the D subgenome exhibited a more drastic response.Second,the analysis of homoeolog expression bias(HEB)revealed that the A subgenome exhibited significant expression bias and that de novo-generated HEB was attributed mainly to asymmetrical differential gene expression.The homoeolog-specific expression(HSE)analyses showed that the cis-only regulatory pattern was predominant in AT2,reflecting significant divergence between the parents.The co-expression network analysis revealed that homoeolog expression connectivity(HEC)was significantly correlated with sequence divergence in cis elements between subgenomes.Interestingly,the allopolyploidy-induced re-construction of network modules was also associated with different HSE patterns.Finally,a transcriptome atlas of spike development demonstrated that the phenotypic similarity of AT2 to T.urartu might be attributed to the combination of relatively stable expression of A-subgenome genes and the drastic downregulation of their D-subgenome homoeologs.Alternative splicing(AS)is a crucial mechanism by which plants modulate and fine-tune expression of their genes,and it has profound impact on the protein diversity and gene functional diversity.In this study,a systemic analysis was conducted parallel to the gene expression level.First,by comparing the changes in alternative splicing events(ASEs)after allopolyploidization,it was found that intrinsic interspecific differences between the diploid parents were important in establishing the AS patterns of the allopolyploid.Second,both ASEs and alternative splicing genes(ASGs)in the A and D subgenomes increased,and the protortion of A subgenome was slightly higher than that of D subgenome.Moreover,the A-subgenome homoeologs tended to produce multiple transcripts,while the D-subgenome homoeologs tended to produce a single transcript.Third,ASEs induced by allopolyploidization were asymmetric in A and D subgenomes and showed tissue specificity.Fourth,different from the A subgenomic expression bias,the homoeolog AS event(homoeo-ASE)showed no subgenomic bias.In addition,the homoeolog-specific splicing(HSS)analysis showed that the cis-regulatory pattern played a key role in the newly synthesized tetraploid wheat,and the cis-regulatory effect was more conservative in different tissues and development stages.Finally,the recent study found that A-subgenome homoeolog splicing bias(HSB)might be involved in the establishment of phenotypic similarity in spikelet development between the AT2 and T.urartu.These findings provided a broad,multi-dimensional characterization of allopolyploidy-induced transcriptomic responses and suggested that allopolyploidy could have immediate and complex regulatory effects on the expression and alternative splicing of nuclear genes.