Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus

Abstract

S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the Asteridae and Rosidae. This conclusion is based on the phylogenetic history of the S-RNase that determines pistil specificity. In Rosaceae, molecular characterizations of Prunus species, and species from the tribe Pyreae (i.e., Malus, Pyrus, Sorbus) revealed different numbers of genes determining S-pollen specificity. In Prunus only one pistil and pollen gene determine GSI, while in Pyreae there is one pistil but multiple pollen genes, implying different specificity recognition mechanisms. It is thus conceivable that within Rosaceae the genes involved in GSI in the two lineages are not orthologous but possibly paralogous. To address this hypothesis we characterised the S-RNase lineage and S-pollen lineage genes present in the genomes of five Rosaceae species from three genera: M. × domestica (apple, self-incompatible (SI); tribe Pyreae), P. persica (peach, self-compatible (SC); Amygdaleae), P. mume (mei, SI; Amygdaleae), Fragaria vesca (strawberry, SC; Potentilleae), and F. nipponica (mori-ichigo, SI; Potentilleae). Phylogenetic analyses revealed that the Malus and Prunus S-RNase and S-pollen genes belong to distinct gene lineages, and that only Prunus S-RNase and SFB-lineage genes are present in Fragaria. Thus, S-RNase based GSI system of Malus evolved independently from the ancestral system of Rosaceae. Using expression patterns based on RNA-seq data, the ancestral S-RNase lineage gene is inferred to be expressed in pistils only, while the ancestral S-pollen lineage gene is inferred to be expressed in tissues other than pollen.

Fig 1. Bayesian phylogenetic tree of Rosaceae T2-RNase lineage, using T-coffee alignment method.

The tree shows the relationship of the M. domestica (M. domestica MDP/MDC), P. persica (P. persica ppa/ppb), P. mume (P. mume scaffold), F. vesca, and F. nipponica T2-RNase lineage genes. The tree was rooted with T2-RNase A. thaliana RNS2 (NM129536). Numbers below the branches represent posterior credibility values above 60. In grey are the reference sequences (S-RNases from Prunus, Pyreae, Solanaceae, and Plantaginaceae, and Fabaceae S-lineage genes). # indicate sequences with more than two introns; (4) the sequences that show in the putative protein sequence amino acid pattern 4, that is absent in all S-lineage genes [4,7]; the + indicate sequences that present stop codons; the {indicate sequences where gaps were introduced to avoid stop codons.

Fig 2. Chromosomal localization of the S-RNase, SFB, SFBB, and SLFL lineage genes.

P. persica (A), M. domestica (B), and F. vesca (C) S-RNase lineage genes are marked in pink, SFB, SFBB, and SLFL lineage genes are marked in blue. Different shapes represent the different S-RNase and F-box SFB-, SFBB-, and SLFL- lineage genes. To represent two or more sequential genes, a bracket at the left of the chromosome is used. Each Prunus chromosome is marked in a different colour: PG1- pink, PG2 light green, PG3 light blue, PG4- purple, PG5- yellow, PG6-green, PG7- orange, and PG8-red. These colours are then used to assign the synteny regions for the M. domestica and F. vesca chromosomes, according to Fig 1in Jung et al., [65]. Regions with unknown synteny but between regions that show synteny with the same chromosome are marked in stripes, and regions with unknown synteny between syntenic regions from different chromosomes are marked in grey. Brackets on the right of each chromosome represent the nine ancestral synteny regions (1 to 9) according to Fig 4 in Illa et al. [72].

Fig 3. Bayesian phylogenetic tree of Rosaceae SFB- and SFBB-like genes, using T-coffee alignment method.

The tree shows the relationship of the M. × domestica (M. domestica MDP/MDC), P. persica (P. persica ppa/ppb), P. mume (P. mume scaffold), F. vesca, and F. nipponica F-box SFBB- and SFB- like genes. In grey are the reference sequences (Prunus SFB, Prunus SLFLs, Pyreae SFBBs, and Petunia SLF genes). The tree was rooted with A. thaliana F-box/kelch-repeat gene (NM111499). Numbers below the branches represent posterior credibility values above 60. The + indicate sequences that present stop codons; the {indicates sequences where gaps were introduced to avoid stop codons. In brackets are indicated the chromosomal location of M. domestica, P. persica and F. vesca genes (S2, S3, and S5 Tables).

Fig 4. M.fusca expression levels (FPKM) for S-RNase, SFB, SFBB, and SLFL lineage genes in 17 tissues.

(A) S- RNase, (B) S- RNase lineages, (C) SFBB, (D) SLFL3-like, (E) SLFL-like, and (F) SFB-like genes.

Fig 5. P. mume expression levels (FPKM) for S-RNase, SFB, SFBB, and SLFL lineage genes in 7 tissues.

(A) S- RNase, (B) S- RNase lineages, (C) SFB, (D) SFB-like, (E) SLFL1-, SLFL2- SLFL3-like, and (F) other F box SLFL-like (F) gene lineages.