| The Hox genes, a large family of transcription factors and organized in clusters in the genome, are characterized by the homeobox which encode a DNA binding motif known as the homeodomain. Hox genes and Hox clusters are strong evidences for the hypothesis that rounds of genome duplications (the one-to-four (-to-eight-to-more in fish) rule) occurred in vertebrates. The information about the impact on Hox genes and clusters following genome duplication, however, is still very limited. A comparative genome analysis between species that undergone a polyploidization event and its original parents is essential to furthering our knowledge in this area. In our previous researches, we gained a bisexual fertile allotetraploid population, and their tetraploidy has been maintained for19generations from F3—F21. The allotetraploid (4nAT) may be the best model population for studying genome duplication and evolution. Hox genes and clusters in allotetraploid compared with its original parents will give some hints of Hox genes and clusters evolution in duplicated genome. The major results in this paper were presented as follows:1. Using two pairs of degenerate primers, approximately108bp DNA fragments or159bp DNA fragments were acquired, we obtained152sequences from allotetraploid,83sequences from common carp, and 88sequences of PCR clones from red crucian carp. The combined data of our PCR products yield22distinct Hox genes fragments in the red crucian carp,19in common carp, and23in allotetraploid.HoxB10a gene and HoxD13a gene do not exist in the two pufferfish species and medaka, but exist in allotetraploid and its original parents and other species (zebrafish and goldfish) of the family Cyprinidae. The loss and retention of Hox genes in clusters may be important clue for the phylogenetic evolution. Meanwhile the DNA fragments isolated in the present study should be very useful for identifying BAC clones containing Hox genes in the BAC library of allotetraploid and its original parents which are under construction now.2. We also detected two isoforms of HoxA3a, HoxA5a and HoxC10a in the genome of common carp and red crucian carp. Our results are consistent with the thought that the ancestor of all species in subfamily Cyprininae had been tetraploid. Four isoforms of HoxA5a sequences, two of them consistent with HoxA5a genes in common carp and the other two consistent with HoxA5a genes in red crucian carp, were isolated in the genome of allotetraploid. We detected three isoforms of HoxA5a and HoxC10a in allotetraploid. All the isoforms of Hox genes in allotetraploid were from its original parents—common carp and red cruclan carp.3. From the phylogenetic analysis, almost all the obtained isoforms of Hox genes in allotetraploid are from common carp and red crucian carp. After the short time of tetraploidization event, most Hox genes haven’t changed much yet, possibly it’s because that Hox genes are vital developmental regulators which have much stress on variation.4. Among152sequences from allotetraploid, one sequence of HoxA10b is with deletion of two nucleotides, while one sequence of HoxC13a has two inserted nucleotide. One sequence of HoxA11a is with a nucleotide deletion in red crucian carp. Using the software Jerryfish to analysis the sequence, the three sequences have turned into a pseudogene. Our research on Hox genes proved that after a tetraploidization event the genome of allotetraploid lose redundant Hox genes through the formation of pseudogenes.5. The full length of HoxC9a in allotetraploid and its original parents were obtained and these sequences were compared and analyzed. Sequence analysis indicated that the HoxC9a gene is including exonl, intron and exon2. The intron junctions are in accordance with the "GT-AG" rule. Two isoforms of HoxC9a gene in allotetraploid (4nAT) were from its original parents. Moreover, a recombinant isoform of HoxC9a gene is found in allotetraploid. Genes exhibite greater diversity after polyploidization. |
PDF Full Text Request