Chimeras Linked to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish

Abstract

The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species, and therefore, it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs benefit from the intervention of recombinases. In addition, TRs and TEs can also result in insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.

The chimeric genes in the hybrid lineage of Carassius auratus cuvieri (♀)×Carassius auratus red var. (♂)

“…Furthermore, replication slippage, or the imprecise cutting of an unpaired duplication during large-loop mismatch repair, may represent additional mechanisms for the formation of chimeric genes (Rogers et al, 2009). In addition, double-strand break (DSB) is more likely to occur at tandem repeats locus during the process of DNA replication, thus, a chimera is formed by recombination between different sequences during the process of DSB repair (Ye et al, 2017) However, the causative mechanism(s) involved could not be identified by our present analyses.…”

Localization of 5S rDNA analysis of homologous pairing in tetraploid hybrids of red crucian carp (♀) × common carp (♂)

“…4nAT has two sets of genomes from RCC and two sets of genomes from CC, the stability of which is directly related to the stability of tetraploid germplasm. Previous studies have demonstrated stable heterozygosity by comparing genetic polymorphisms (Li, Liu, Zhang, Lu, & Liu, 2005; Li et al, 2003), mitochondrial genome analysis (Guo, Liu, Yan, & Liu, 2004), BAC library construction (Ye et al, 2017a; Wang et al, 2015), transcriptome and genome sequencing (Liu et al, 2016; Ren et al, 2019), fluorescence in‐situ hybridization (FISH) of somatic chromosomes (Zhang et al, 2015), and so on. However, whether the occurrence of meiotic homologous chromosomes pair between identical chromosomes or between heterologous chromosomes remains unclear, which is directly related to the stability of genetic germplasm in diploid gametes.…”