I am trying to identify and elucidate the function of a gene (let say X) in Brassica napus that control flower development in Arabidopsis. Using the sequence of Arabidopsis X, I conducted a phlyogenetic analysis based on protein sequence data. Phylogenetic analysis revealed that there is a single X in Brassica napus genome. After phylogenetic analysis, I isolated the cDNA sequence of X from Brassica napus by RT-PCR and then sequenced 20 randomly selected clone. When the coding sequences of these clones were compared, they revealed two unique sequence which were highly homologous except single nucleotide variation in some position of the coding sequence. When the two unique sequences of Brassica napus X were compared to its progenitor (Brassica rapa and Brassica oleracea X), I found that both of them are highly similar to the sequence of their progenitor X both at nucleotide and amino acid sequence level. The identity between Brassica napus X and Brassica rapa X were 98% (nucleotide level) and 93% (amino acid sequence). The similarity between Brassica napus X and Brassica oleracea X were 100% both at nuclotide and amino acid sequence level. My question is

1. What will be the possible explanation of presence of a single Arabidopsis X in Brassica npaus genome given the fact that Brassica napus is a tetraploid crop?

2. Are the two unique sequences of X found Brassica napus genome represent two different allele or two different genes?

3. I would also welcome any other explanation on this result.