Expression Alternations And Genomic Variations In The Nascent Generations Of An Allopolyploidy Line By Goldfish And Common Carp

Polyploidization via whole-genome duplication(WGD)involves the integration of more than two complete sets of chromosomes in a cell.Polyploidization occurs most commonly in angiosperms.In plants,with different model systems,genome shock involves whole-genome wide genetic variants including chromosome rearrangement,DNA recombination,base and insert/deletion mutations,and also epigenetic changes.In contrast,polyploidization is relatively rare in animals and it mainly occurs in a handful of speices of insects and vertebrate taxa.Due to lack of suitable system,that why the occurring frequency in animal is much rarer than that in plants raised an open question for decades.Traditional explanations include barriers to sex-determination,physiological and developmental constraints,especially nuclear-cytoplasmic interactions and related factors,and genome shock or dramatic genomic restructuring.By ex situ,the bisexual,goldfish(Carassius auratus,(?),n?100)×common carp(Cyprinus carpio,(?),n=100)hybrids allow for investigations into genomic consequences of allotetraploidization in vertetrates.This allopolyploidy system offers obvious advantages,e.g.,their known parentage separates them from natural polyploids and it is easy to trace the fate of progenitor genes.In order to fully use the system to investigate how the allopolyploidy offspring survive from the more severe genome shock comparing the plants,by analyzing the RNA-seq and resequencing data,the expression alternations and genomic variations were investigated.Firstly,we employed two strategies for transcriptomic data processing,including de novo assembly and reference-based mapping strategies.The results showed that,(1)The expression of tetraploid offspring showed paternal-biased pattern,while the octaploids showed maternal-biased expression;(2)some differentially expressed genes were specifically enriched in mutagenesis site,regulation of cell death and apoptosis in tetraploids;(3)the chimeric genes(the genes in offspring with alternating parental-specific variants)comprised about 10%,most chimeras of maternal/paternal origin do not overlap,and this phenomenon indicates nonreciprocal structural change;the genes with offspring-specific mutations were 1.02%-1.16%in different generations;meanwhile,some of the chimeric and differentially expressed genes relate to mutagenesis,repair,and cancer-related pathways in 2nF1.Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes.Next,for the analyses of resequencing data from parents and six generations(20 samples in total),the genome of goldfish was used as reference genome.The results showed that,(1)variations distributed in untranslated regions(UTR)were significantly more abundant than the ones in coding regions(CDS)and intron;the six individuals of first generation 2nF1 were with the difference of possessing variations;(2)Insertions/Deletions(InDels)distributed in UTR regions were with significantly higher ratios than in intron and CDS;(3)within 13 offspring,chimeric genes comprised about 9.75%-11.21%;six individuals of 2nF1 shared only 2,559 chimeric genes,which indicated the individual difference of variation pattern within this generation;the chimeric genes with mutations were enriched in the regulation of physiological functions and immunoreactivity,and the regulation of programmed cell death and apoptosis.The discoveries yieled by both transcriptomes and resequencing data indicated fast changes including the genomic variations and expression changes,especially in 2nF1.These syndrome effects caused by genome shock might be the reasons of the greatly reduced viability in 2nF2 hybrid offspring,which might be lethiferous in natural polyploids.The results might help explain why polyploid are much rarer in vertebrates than in plants.Although the initial research documented that rapid and extensive genomic changes following tetraploidization,many questions about allopolyploidization remain unanswered.Ultimately,further work remains on exactly how polyploid plants and animals survive from genome shock,which happens more frequently in allopolyploid plants than in animals.Additional functional analyses at the genomic(genetic/epigenetic)level are also await.In the future work,we expect to find out possible key regions in the genomes and key changes in the gene pathways and regulatory elements which are most importantly contributed to the survival and genomic stability for the allopolyploidy.