Genomic varieties of apple AFL genes

Abstract

Summary AFL ( A pple F LORICAULA L EAFY) genes were screened from the apple genome. The resultant clones showed the AFL1, AFL2, and AFL1a genes, which included several-kilobase lengths of their 5′ upstream regions. They were highly conserved and consisted of three exons and two introns. The expression analysis with Arabidopsis indicated that the 5′ upstream region of AFL2, about 2.5 kb, linked β-glucuronidase (GUS) showed GUS activity on the young flower buds such as that of the Arabidopsis LFY promoter. The corresponding upstream region from AFL1 had a highly homologous 700 bp region flanking the ATG site. But the upstream region (about 2.4 kb) from the AFL1 genome never showed GUS activity on flower buds. The AFL1 and AFL1a genes were almost identical besides the 790 bp insertion in the first intron of AFL1a. The insertion sequence had an RNA polymerase III motif and a T-rich sequence as well as a 9 bp direct repeat at each end. Some of the insertion sequence's trait indicated that the insertion was a novel Short Interspersed Repetitive Element (SINE) from apple. This insertion occurs at a rate of more than 1,000 copies in an apple genome, and appeared to be conserved in the Malus genus.