Hox genes reveal genomic DNA variation in tetraploid hybrids derived from Carassius auratus red var. (female) × Megalobrama amblycephala (male)

BACKGROUND: Allotetraploid F(1) hybrids (4nF(1)) (AABB, 4n = 148) were generated from the distant hybridization of Carassius auratus red var. (RCC) (AA, 2n = 100) (♀) × Megalobrama amblycephala (BSB) (BB, 2n = 48) (♂). It has been reported that Hox gene clusters are highly conserved among plants and vertebrates. In this study, we investigated the genomic organization of Hox gene clusters in the allotetraploid F(1) hybrids and their parents to investigate the polyploidization process. RESULTS: There were three copies of Hox genes in the 4nF(1) hybrids, two copies in RCC and one copy in BSB. In addition, obvious variation and pseudogenization were observed in some Hox genes from 4nF(1.) CONCLUSION: Our results reveal the influence of polyploidization on the organization and evolution of Hox gene clusters in fish and also clarify some aspects of vertebrate genome evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-017-0550-2) contains supplementary material, which is available to authorized users.