DOI: 10.5061/dryad.71rn0
title: Data from: No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes

description: Background: Fabaceae species are important in agronomy and livestock
 nourishment. They have a long breeding history, and most cultivars have
 lost self-incompatibility (SI), a genetic barrier to self-fertilization.
 Nevertheless, to improve legume crop breeding, crosses with wild SI
 relatives of the cultivated varieties are often performed. Therefore, it
 is fundamental to characterize Fabaceae SI system(s). We address the
 hypothesis of Fabaceae gametophytic (G)SI being RNase based, by recruiting
 the same S-RNase lineage gene of Rosaceae, Solanaceae or Plantaginaceae SI
 species. Results: To address if Fabaceae GSI is RNase based we first
 looked for the presence of SSK1 like genes (described only in species
 having RNase based GSI), in the Trifolium pratense, Medicago truncatula,
 Cicer arietinum, Glycine max, and Lupinus angustifolius genomes. Since we
 find these genes in Fabaceae species, we characterize the S-lineage
 T2-RNase genes in these genomes. Except for T. pratense, all species are
 self-compatible (SC). Nevertheless, in T. pratense, but also in M.
 truncatula and C. arietinum we identify S-RNase lineage genes that in
 phylogenetic analyses cluster with Pyrinae S-RNases. In M. truncatula and
 C. arietinum genomes, where large scaffolds are available, these sequences
 are surrounded by F-box genes that in phylogenetic analyses also cluster
 with S-pollen genes. In T. pratense the S-RNase lineage genes show,
 however, expression in tissues not involved in GSI. Moreover, levels of
 diversity are lower than those observed for other S-RNase genes. The M.
 truncatula and C. arietinum S-RNase and S-pollen like genes
 phylogenetically related to Pyrinae S-genes, are also expressed in tissues
 other than those involved in GSI. To address if other T2-RNases could be
 determining Fabaceae GSI, here we obtained a style with stigma
 transcriptome of Cytisus striatus, a species that shows significant
 difference on the percentage of pollen growth in self and
 cross-pollinations. Expression and polymorphism analyses of the C.
 striatus S-RNase like genes revealed that none of these genes, is the
 S-pistil gene. Conclusion: We find no evidence for Fabaceae GSI being
 determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage
 genes. Since none of the C. striatus T2-RNase genes expressed in style
 with stigma is involved in GSI specificity, there is no evidence that
 T2-RNase lineage genes could be determining GSI in this species.
 Therefore, to characterize the Fabaceae S-pistil gene(s), expression
 analyses, levels of diversity, and segregation analyses in controlled
 crosses are needed for those genes showing high expression levels in the
 tissues where GSI occurs.
description: Sequence data sets used
 in Aguiar et al. 2015Sequence data sets used
 in Aguiar et al. 2015: 1- SSK1 like genes in flowering plants: SSK1
 genes(s) have been described only in species having RNase based GSI.
 Therefore, presence/absence of this gene(s) has been reported as a
 diagnosis marker for the presence/absence of RNase based GSI (see
 references in Aguiar et al. 2015). The protein encoded by SSK1 has an
 unique C-terminus, composed of 5 - 9 amino acid residues, following the
 conventional "WAFE" motif. In Rosaceae, this amino acid tail
 shows the conserved sequence “GVDED”. In Solanaceae and Plantaginaceae
 this motif is not so well conserved but a D residue is always found at the
 last position of the motif. When using these features and the NCBI
 flowering plant species database, we retrieved 21 sequences from
 Solanaceae (three), Plantaginaceae (one), Rosaceae (eight), Fabaceae
 (five), Malvaceae (one), Rutaceae (one), Euphorbiaceae (one) and
 Salicaceae (one) species. The two genes from Cytisus striatus were
 obtained from a style with stigma transcriptome. Oryza sativa
 [GenBank:AP003824] and Citrus maxima [GenBank:FJ851401] genes that encode
 proteins not presenting the C-terminus amino acid motif following the
 conventional "WAFE" motif are here included to root the
 phylogenetic tree shown in Figure 1 in Aguiar et al. 2015. 2- Fabaceae
 S-RNase lineage genes: Fabaceae S-RNase lineage genes and Prunus, Pyrinae,
 Solanaceae and Plantaginaceae S-RNases (Figure 2 and Figure 6A in Aguiar
 et al. 2015): Sequences used to determine the phylogenetic relationship of
 M. truncatula, G. max, L. angustifolius, L. corniculatus, L. japonicus, T.
 pratense, P. sativum, C. cajan, C. tetragonoloba, C. arietinum,and C.
 striatus S-RNase lineage genes and the Prunus, Pyrinae, Solanaceae and
 Plantaginaceae S-RNases. 3- CsRNase3: C. striatus CsRNase3 gene and
 Prunus, Pyrinae, Solanaceae and Plantaginaceae S-RNases (Figure 6 in
 Aguiar et al. 2015) 4- F-box genes: F-box SFB -SFBB- and SLFL- like genes
 surrounding the C. arietinum Ca4, M. truncatula Mt3, Mt17, Mt18, and Mt20
 S-RNase like genes, and S-pollen genes from Prunus, Malus, Solanaceae and
 Plantaginaceae, and Prunus S-like genes (genes not involved in GSI
 specificity; see Aguiar et al. 2015 Figure 5). A. thaliana
 F-box/kelch-repeatAguiar et al
 2015.zip