一种来自长柄扁桃、桃和梅的包含AP2结构域基因的生物信息学分析

Bioinformatics Analysis of a Kind of Novel Gene Containing AP2 Domain from Amygdalus pedunculata Pall., Prunus persica(Peach) and Prunus mume(Japanese Apricot)

通过分析长柄扁桃幼苗叶片转录组测序,从中找到一个包含AP2结构域的Unigene,该Unigene包含完整的开放读码框,全长3182bp,编码767个氨基酸,将其命名为ApAP2dc1。以ApAP2dc1的DNA序列作为信息探针,在桃和梅的基因组序列中进行查询比较,发现桃和梅的基因组中均存在ApAP2dc1的直系同源基因,分别命名为PpAP2dc1和PmAP2dc1。在桃和梅的基因组中还各发现一个串联重复的旁系同源基因,分别命名为PpRYdc1和PmRINGdc1。保守结构域分析表明,ApAP2dc1、PpAP2dc1和PmAP2dc1都含有AP2结构域,而PpRYdc1和PmRINGdc1不含AP2结构域;基因结构分析表明,PpAP2dc1和PmAP2dc1、PpRYdc1和PmRINGdc1虽然互为直系同源基因,但其基因结构有明显差异;旁系同源基因的启动子序列也有较大差异。该研究结果表明长柄扁桃、桃和梅基因组上的上述区域在进化上不保守,该区域的基因在结构和表达上正在进行快速趋异进化。

Through the analysis of Unigene obtained by transcriptome sequence of leaves of Amygdalus pedunculata Pall. seedling, we found the Unigene contained a AP2 domain. The Unigene, named Ap AP2dc1,contains a complete open reading frame which is 3 182 bp in length, and encodes 767 amino acids. Using Ap AP2dc1 DNA sequence as querying probe to search against Prunus persica and Prunus mume genome database,the orthologs of Ap AP2dc1 was found, and we named Pp AP2dc1 and Pm AP2dc1 respectively. It is interesting that we also found a tandem repeat of paralog in Prunus persica and Prunus mume respectively, and we named Pp RYdc1 and Pm RINGdc1. Conserved domain analysis showed that Ap AP2dc1, Pp AP2dc1 and Pm AP2dc1 contained AP2 domain, while Pp RYdc1 and Pm RINGdc1 did not contain AP2 domain. Gene structure analysis showed that Pp AP2dc1 and Pm AP2dc1, Pp RYdc1 and Pm RINGdc1 were both orthologous genes, but their genetic structure was significantly different. Promoter sequences of paralogs were quite different. Our study suggested that these regions in the genome of Amygdalus pedunculata Pall., Prunus persica and Prunus mume were not evolutionarily conserved, and the genes in these regions were rapidly diverging at structure and expression levels.