Rapid genomic DNA changes in allotetraploid fish hybrids

Abstract

Rapid genomic change has been demonstrated in several allopolyploid plant systems; however, few studies focused on animals. We addressed this issue using an allotetraploid lineage (4nAT) of freshwater fish originally derived from the interspecific hybridization of red crucian carp (Carassius auratus red var., ♀, 2n=100) × common carp (Cyprinus carpio L., ♂, 2n=100). We constructed a bacterial artificial chromosome (BAC) library from allotetraploid hybrids in the 20th generation (F20) and sequenced 14 BAC clones representing a total of 592.126 kb, identified 11 functional genes and estimated the guanine–cytosine content (37.10%) and the proportion of repetitive elements (17.46%). The analysis of intron evolution using nine orthologous genes across a number of selected fish species detected a gain of 39 introns and a loss of 30 introns in the 4nAT lineage. A comparative study based on seven functional genes among 4nAT, diploid F1 hybrids (2nF1) (first generation of hybrids) and their original parents revealed that both hybrid types (2nF1 and 4nAT) not only inherited genomic DNA from their parents, but also demonstrated rapid genomic DNA changes (homoeologous recombination, parental DNA fragments loss and formation of novel genes). However, 4nAT presented more genomic variations compared with their parents than 2nF1. Interestingly, novel gene fragments were found for the iqca1 gene in both hybrid types. This study provided a preliminary genomic characterization of allotetraploid F20 hybrids and revealed evolutionary and functional genomic significance of allopolyploid animals.

Genome and Karyotype Reorganization after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum

“…It is known that the vast majority of gene duplicates usually get lost within a few million years, while extant genes in duplicate copies (ohnologs) are usually under strong purifying selection [24]. This leads to significant and dynamic reorganization of the doubled genome, which may eventually reach a re-diploidized state [17,25,26]. Although the long-term processes after WGD, including maintenance, inactivation, and diversification in the function of gene duplicates are comparatively well studied [27], the processes that take place immediately after a WGD are not well studied and understood.…”

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

“…Blood samples (10 ml) from five allotetraploid individuals from the 20 th generation are used to construct a BAC library according to a previously described method (Wang et al 2015). The allotetraploid fish are obtained from the Engineering Research Center of Polyploid Fish Breeding at Hunan Normal University (Changsha, China) and the ploidy of five samples is confirmed by metaphase chromosome assay of kidney cells.…”

Genomic evolution in polyploid vertebrates: Models and progress in research techniques

“…[32,33] . 在异源四倍体鱼类研究中发现, 多 倍体体系初期世代中产生的大量部分同源基因重组、 DNA片段丢失和新基因的形成, 可能导致基因组水平 剧烈的重塑过程 [34] . [8,35] .…”