Features Of Homoeologous Exchange And Its Impacts On Gene Expression In A Newly Formed Tetraploid Wheat

Polyploidization or whole-genome duplication(WGD)is a major driving force in genome evolution and speciation throughout the evolutionary history of higher plants.However,the early stage of polyploidy is confronted with many challenges due to genomic shock,among which the most emergent challenge is abnormal chromosome behavior during meiosis,resulting in a wide range of chromosomal variation including aneuploidy and homoeologous exchange(HE),which may affect the fitness of nascent allopolyploid,especially fertility.HE is a recombination phenomenon between homoeologous chromosomes,which affects genome structure and gene expression.HE is widespread and found in natural allopolyploids(such as Brassica,peanut,wheat and banana)and synthetic allopolyploids(such as Brassica and wheat).It is known that HE contributes to phenotypic variations,but the mechanisms that govern its occurrence and its potential impact on genome structure and gene expression are not well understood.Here,we studied HE events in the progeny of a nascent allotetraploid(genome AADD)derived from two diploid progenitors of bread wheat(Triticum aestivum L.,BBAADD)including Triticum urartu(AA)and Aegilops tauschii(DD)using cytological and whole genome sequence analyses to explore the mechanisms of HE occurrence and genomic landscape and its impact on genome-wide gene expression.First,by means of cytogenetics and whole-genome re-sequencing,we compared the karyotypes and genome sequences between a newly synthesized allotetraploid and its diploid parents,and identified 37 pairs of HE junctions from 29 HE events.Due to gamete selection after meiosis,the majority of HE events were non-reciprocal,resulting in a doubling and loss of large chromosomal segments.We found that HEs showed the typical patterns of homologous recombination hotspots being biased towards low-copy,sub-telomeric genic regions of chromosome arms and showing association with the CCN repeat motifs and high GC content.An important difference from homologous recombination(hotspots enriched in both promoter and terminator)is that HE junctions were highly enriched within coding region of genes,giving rise to novel recombinant transcripts which in turn were predicted to give rise to new protein fusion variants.Using RNA-Seq data and locus-specific Sanger sequencing,we confirmed the fusion transcripts and their expression.Meanwhile,we analyzed the highresolution data sets of HE junction in additional allopolyploid species including Brassica,Musa,and Arabidopsis,and we found HE-induced intragenic recombination is a common phenomenon.Second,we investigated HE-induced changes in gene expression by RNA-Seq-based transcriptome profiling.For the genes within HE segments with copy number variations,we found:(1)78%-91% genes showed dosage-dependent expression patterns,namely,expression levels are positively correlated with gene copy numbers;(2)due to dosage effect,approximately 40%-49% homoeologous pairs with biased expression pattern did not compensate for expression of the lost copy after HE,and therefore causing changes of total homoeologous expression level.Meanwhile,HEs also regulate the expression of 10%-21% genes located on non-HE segments through trans-effect:(1)about 42%-49% homoeologous pairs showed convergent response to HE;(2)homoeologous pairs with trans-only regulation tended to show convergent response,while those corresponding with cis-only regulation tended to show subgenome-specific response.Our results suggest that HE in allopolyploid has similar mechanism and genomic characteristics as homologous recombination.However,HE preferentially occurs in coding region,therefore,results in intragenic recombination.This provides a new mechanism for evolutionary novelty by generating new transcript and protein in nascent allopolyploids.Asymmetric substitution of homoeologous chromosome segments also results in extensive gene expression changes,which is manifested as both cis-regulation(for genes located within HE segments)and trans-regulation(genes located in remainder of the genome).Our results provide new insights into our understanding of the mechanisms and impacts of HE in allopolyploid genome evolution,and new clues to polyploid crop improvement.