PEP1 of Arabis alpina Is Encoded by Two Overlapping Genes That Contribute to Natural Genetic Variation in Perennial Flowering
Figure 3
Analysis of sequence variation in PEP1 cDNA and at the genomic locus of Dor accession demonstrates a complex structure for the PEP1 gene.
(A) PEP1 cDNAs in Dor is a mixture of transcripts that contain a G to A substitution in exon 1 compared to Paj or have a similar sequence to accession Paj but have an insertion of 248 bp in the 5′ UTR. (B) Sequence of the PEP1 genomic locus in the accession Paj shows that the locus is highly duplicated. Exons are indicated with black boxes, UTRs with white boxes and solid lines the inter- and intra-genic regions. Upstream and downstream genes of PEP1 are 35 kb apart. Colored boxes indicate relative positions of the duplicated regions. Overlapping boxes indicate overlapping homologous sequences. Numbers besides duplicated boxes show the length of the duplicated fragment and percentage of homology. Duplicated exon 1 copies are indicated as 1a and 1b. Dotted box shows the PEP1 locus region sequenced in the accession Dor. (C) Sequence of the PEP1 genomic locus in the Dor accession reveals that G to A base substitution is in exon 1a. Grey arrows indicate insertions, black arrows indicate deletions and vertical dotted lines indicate SNPs relative to Paj PEP1 locus. The 248 bp insertion upstream in the 5′ UTR is upstream of exon 1b. Colored boxes indicate relative positions of duplicated regions. (D) Structure of the PEP1 locus and predicted splicing events (E) PEP1 transcripts in the accession Dor detected with two different primers in the 5′ UTR using the same reverse primer in the 3′ UTR. Black and grey arrows indicate the position of two different primers in the 5′ UTR relative to the 248 bp insertion. When primer PEP1_5UTRF1 (black) was used most clones contained the G to A substitution in the exon 1. A few clones that did not contain the G to A base substitution also contained a 248 bp insertion in the 5′ UTR. When primer PEP1_5UTRF2 was used most clones did not contain G to A base substitution.