Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia

Abstract

Background: The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene AP3 was characterized in the dioecious plant species Silene latifolia. It was suggested that this gene had been transferred from an autosome to the Y chromosome.

Results: In the present study we provide evidence for the existence of an X linked copy of the AP3 gene. We further show that the Y copy is probably located in a chromosomal region where recombination restriction occurred during the first steps of sex chromosome evolution. A comparison of X and Y copies did not reveal any clear signs of degenerative processes in exon regions. Instead, both X and Y copies show evidence for relaxed selection compared to the autosomal orthologues in S. vulgaris and S. conica. We further found that promoter sequences differ significantly. Comparison of the genic region of AP3 between the X and Y alleles and the corresponding autosomal copies in the gynodioecious species S. vulgaris revealed a massive accumulation of retrotransposons within one intron of the Y copy of AP3. Analysis of the genomic distribution of these repetitive elements does not indicate that these elements played an important role in the size increase characteristic of the Y chromosome. However, in silico expression analysis shows biased expression of individual domains of the identified retroelements in male plants.

Conclusions: We characterized the structure and evolution of AP3, a sex linked gene with copies on the X and Y chromosomes in the dioecious plant S. latifolia. These copies showed complementary expression patterns and relaxed evolution at protein level compared to autosomal orthologues, which suggests subfunctionalization. One intron of the Y-linked allele was invaded by retrotransposons that display sex-specific expression patterns that are similar to the expression pattern of the corresponding allele, which suggests that these transposable elements may have influenced evolution of expression patterns of the Y copy. These data could help researchers decipher the role of transposable elements in degenerative processes during sex chromosome evolution.

Figure 1

PCR on microdissected chromosomes. POL Retand primers were used as a positive control (present in all chromosomes) and primers for SlAP3A/X K-domain were used for sex chromosomes localization. The template DNA is indicated in the figure (size marker (L) 100 bp, male genomic DNA (♂) female genomic DNA (♀) microdissected X chromosomes (X), microdissected autosomes (A) and negative control (no template). PCR products were subjected to electrophoresis on 1% agarose gel and stained with ethidium bromide.

Figure 2

Alignment of a promoter and coding region of SlAP3X, SlAP3Y and SvAP3 genes. Rectangles represent exon regions of the genes. Corresponding coding sequences are indicated

Figure 3

The structure of SlAP3Y gene. Red rectangles represent coding domains of retrotransposons. Blue rectangles are individual exons of SlAP3Y. Ovals represent long terminal repeats.

Figure 4

RT-PCR analysis. Actin, LTR A, LTR B, integrase, reverse transcriptase (RT) and LINE primers were used. Genomic DNA with actin primers and BAC DNA with element specific primers were used as a positive control. Actin reveals a different sized PCR product when genomic DNA is used as a template than when cDNA is used as a template due to intron excision, and so can be used as an internal control for purity of RNA used for reverse transcription. Template DNA is indicated in the figure (size marker (M) 100 bp ladder), male genomic DNA (♂), female genomic DNA (♀), BAC DNA (30/L22 and 253/J6) S. latifolia male and female cDNA and RNA from leaves (L) and buds (B) and negative control (-, no template). PCR products were subjected to electrophoresis on 1% agarose gel and stained with ethidium bromide.