Abstract
BackgroundHox transcription factors are master regulators of animal development. Although highly conserved, they can contribute to the formation of novel biological characteristics when modified, such as during the generation of hybrid species, thus potentially serving as species-specific molecular markers. Here, we systematically studied the evolution of genomic sequences of Hox loci in an artificial allotetraploid lineage (4nAT, 4n = 200) derived from a red crucian carp (♀, RCC, 2n = 100) × common carp (♂, CC, 2n = 100) cross and its parents (RCC and CC).ResultsPCR amplification yielded 23 distinct Hox gene fragments from 160 clones in 4nAT, 22 fragments from 90 clones in RCC, and 19 fragments from 90 clones in CC. Sequence alignment of the HoxA3a and HoxC10a genes indicated both the inheritance and loss of paternal genomic DNA in 4nAT. The HoxA5a gene from 4nAT consisted of two subtypes from RCC and two subtypes from CC, indicating that homologous recombination occurred in the 4nAT hybrid genome. Moreover, 4nAT carried genomic pseudogenization in the HoxA10b and HoxC13a loci. Interestingly, a new type of HoxC9a gene was found in 4nAT as a hybrid sequence of CC and RCC by recombination in the intronic region.ConclusionThe results revealed the influence of Hox genes during polyploidization in hybrid fish. The data provided insight into the evolution of vertebrate genomes and might be benefit for artificial breeding programs.
Highlights
Hox transcription factors are master regulators of animal development
Two types of polyploidy have been identified based on genetic origin: autopolyploidy, which originates from the genome duplication of a single species, and allopolyploidy, which occurs via interspecific hybridization and results in haploid chromosomes inherited from different species
Hybrid identification To determine if Allotetraploid hybrids (4nAT) was hybridized from red crucian carp (RCC) and common carp (CC), we examined the genomic composition of RCC, CC, and 4nAT using STRUCTURE
Summary
Hox transcription factors are master regulators of animal development Highly conserved, they can contribute to the formation of novel biological characteristics when modified, such as during the generation of hybrid species, potentially serving as species-specific molecular markers. Two types of polyploidy have been identified based on genetic origin: autopolyploidy, which originates from the genome duplication of a single species, and allopolyploidy, which occurs via interspecific hybridization and results in haploid chromosomes inherited from different species. The F1 and F2 progenies were diploid hybrids (2n = 100), fertile allotetraploid offspring of both sexes were produced from the F3 and later generations (Fig. 1) [11]. Hybrid polyploid fish have wide applications in the Chinese fish industry and they provide an opportunity to study the molecular and genetic mechanisms that underlie the origination of evolutionary novelties including genome evolution and adaptation. Previous studies confirmed the rapid genomic DNA changes in 4nAT [13], and in this study we investigated the genetic elements susceptible to rapid genomic changes
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