Identification of a Novel SBP1-Containing SCFSFB Complex in Wild Dwarf Almond (Prunus tenella)

Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond (Prunus tenella)

Background: The wild dwarf almond (Prunus tenella) is one of the national key grade II-protected wild plants in China. It is a relic deciduous forest species from the middle Eocene of the ancient Mediterranean Sea and is also known as a "living fossil of plants." It is distributed in Southeast Europe, West Asia, Central Asia, Siberia, and Xinjiang (Tacheng) and other areas of China. The plant grows on arid slopes, steppes, depressions, and valleys at an altitude of 1,200 m. The seeds of wild dwarf almonds are frost resistant and contain oil and bitter lentil glycosides, which possess medicinal value. Additionally, the seeds of wild dwarf almonds can be used as the original material for breeding new varieties of almonds and obtain ornamental flowers and trees. Results: The complete mitochondrial genome of P. tenella was sequenced and assembled using two sequencing platforms, namely, Illumina Novaseq6000 and Oxford Nanopore PromethION. The assembled genome was 452,158-bp long with a typical loop structure. The total number of A, T, C, and G bases in the genome was 122,066 (26.99%), 124,114 (27.45%), 103,285 (22.84%), and 102,693 (22.71%), respectively, with a GC content of 45.55%. A total of 63 unique genes, including 36 protein-coding genes, 24 tRNA genes, and 3 rRNA genes, were identified in the genome. Furthermore, codon usage, sequence duplication, RNA editing, and mitochondrial and chloroplast DNA fragment transfer events in the genome were analyzed. A phylogenetic tree was also constructed using 30 protein-coding genes that are common to the mitochondrial genomes of 24 species, which indicated that the genome of wild lentils is highly conserved with those of apples and pears belonging to Rosaceae. Conclusion: Assembly and annotation of the P. tenella mitochondrial genome provided comprehensive information about the mitochondrial genome of wild dwarf almonds, This study provides information on the mitochondrial genome of Prunus species and serves as a reference for further evolutionary studies on wild dwarf almonds.

Genome-wide identification of members of the Skp1 family in almond (Prunus dulcis), cloning and expression characterization of PsdSSK1

Skp1 (S-phase kinase-associated protein 1) is the core gene of SCF ubiquitin ligase, which mediates protein degradation, thereby regulating biological processes such as cell cycle progression, transcriptional regulation, and signal transduction. A variety of plant Skp1 gene family studies have been reported. However, the almond Skp1 gene family has not yet been studied. In this study, we identified 18 members of the Prunus dulcis PdSkp1 family that were unevenly distributed across six chromosomes of the almond genome. Phylogenetic tree analysis revealed that the PdSkp1 members can be divided into three groups: I, II, and III. PdSkp1 members in each subfamily have relatively conserved motif types and exon/intron numbers. There were three pairs of fragment duplication genes and one pair of tandem repeat genes, and their functions were highly evolutionarily conserved. Transcriptome data showed that PdSkp1 is expressed in almond flower tissues, and that its expression shows significant change during cross-pollination. Fluorescence quantitative results showed that eight PdSkp1 genes had different expression levels in five tissues of almond, i.e., branches, leaves, flower buds, flesh, and cores. In addition, we cloned a PsdSSK1 gene based on PdSkp1. The cloned PsdSSK1 showed the same protein sequence as PdSkp1-12. Results of qPCR and western blot analysis showed high expression of PsdSSK1 in almond pollen. In conclusion, we report the first clone of the key gene SSK1 that controls self-incompatibility in almonds. Our research lays a foundation for future functional research on PdSkp1 members, especially for exploring the mechanism of almond self-incompatibility.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01278-9.

Self-compatibility in peach [Prunus persica (L.) Batsch]: patterns of diversity surrounding the S-locus and analysis of SFB alleles

Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after P. persica and P. dulcis (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.

Molecular and Evolutionary Characterization of Pollen S Determinant (SFB Alleles) in Four Diploid and Hexaploid Plum Species (Prunus spp.)

In more than 60 families of angiosperms, the self- and cross-fertilization is avoided through a complex widespread genetic system called self-incompatibility (SI). One of the major puzzling issues concerning the SI is the evolution of this system in species with complex polyploid genomes. Among plums, one of the first fruits species to attract human interest, polyploid species represent enormous genetic potential, which can be exploited in breeding programs. However, molecular studies in these species are very scarce due to the complexity of their genome. In order to study the SFB gene [the male component of gametophytic self-incompatibility system (GSI)] in plum species, 36 plum accessions belonging to diploid and hexaploid species were used. A total of 19 different alleles were identified; 1 of them was revealed after analyzing sequences. Peptide sequence analysis allowed identifying the five domains features of the SFB gene. Polymorphism analysis showed a subtle difference between domesticated and open pollinated Tunisian accessions and suggested a probable influence of the ploidy level. Divergence analysis between studied sequences showed that a new specificity may appear after 5.3% of divergence at synonymous sites between pairs of sequences in Prunus insititia, 6% in Prunus cerasifera, 8% and 9% in Prunus domestica and Prunus salicina respectively. Furthermore, sites under positive selection, the ones more likely to be responsible for specificity determination, were identified. A positive and significant Pearson correlation was found between the divergence between sequences, divergence time, fixed substitutions (MK test), and PSS number. These results supported the model assuming that functionally distinct proteins have arisen not as a result of chance fixation of neutral variants, but rather as a result of positive Darwinian selection. Further, the role that plays recombination can not be ruled out, since a rate of 0.08 recombination event per polymorphic sites was identified.