Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success

Hybridization and polyploidization have made great contributions to speciation,heterosis,and agricultural production within plants,but there is still limited understanding and utilization in animals.Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success.However,the mechanisms have not yet been comprehensively assessed in animals.Here,we produced a high-fidelity reference genome sequence for common carp,a typical allotetraploid fish species cultured worldwide.This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses.Most genes were expressed with subgenome biases,with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development.While subgenome A evolved more rapidly,subgenome B contributed to a greater level of expression during development and under stressful conditions.Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome.Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis.The plasticity of subgenomes and their shifting of dominant expression during early development,and in response to stressful conditions,provide novel insights into the molecular basis of the successful speciation,evolution,and heterosis of the allotetraploid common carp.

Expression patterns and functional divergence of homologous genes accompanied by polyploidization in cotton(Gossypium hirsutum L.)

Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber development was unknown.In this study,through RNA-seq technology,we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton(G.hirsutum)and its diploid progenitors(G.arboreum and G.raimondii)at the fiber early development stage.In tetraploid cotton,genes showed expression level dominance(ELD)bias toward the A genome.This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor(D genome).Gene ontology(GO)enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession,and the ELD-D genes might be involved in transcription regulation and stress inducement.In addition,the number and proportion of completely A-and D-subfunctionalized gene were similar at different fiber development stages.However,for neofunctionalization,the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA.Eventually,we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process,further making the fiber property meet the human demands.Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages,providing new insights into the mechanism of cotton fiber evolution.

Making the Bread： Insights from Newly Synthesized AIIohexaploid Wheat

Bread wheat （or common wheat, Triticum aestivum） is an allohexaploid （AABBDD, 2n = 6x = 42） that arose by hybridization between a cultivated tetraploid wheat T. turgidum （AABB, 2n = 4x = 28） and the wild goatgrass Aegilops tauschfi （DD, 2n = 2x = 14）. Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allo- hexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective pro- genitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat.