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Conserved synteny between the Prunus BACs that contain disease-resistant genes and the genome Medicago. All the intervening genes in the syntenic regions, except those in the 142 kb gap, are also shown. The numbers on the left stand for base pair positions in the Prunus BACs or the Medicago linkage groups. The lengths of the syntenic regions and the total numbers of predicted genes in the regions are given below the bar.
Source publication
Fragmentary conservation of synteny has been reported between map-anchored Prunus sequences and Arabidopsis. With the availability of genome sequence for fellow rosid I members Populus and Medicago, we analyzed the synteny between Prunus and the three model genomes. Eight Prunus BAC sequences and map-anchored Prunus sequences were used in the compa...
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Citations
... The synteny analysis across species provides an in-depth understanding of the evolutionary relationship between different lineages, and it offers an opportunity to study the relationship between genome structure and the function of organisms [74]. We analyzed the synteny between apricot and Arabidopsis, and we identified 31 syntenic gene pairs (Figure 6b, Table S4). ...
The B3 superfamily, which belongs to the plant-specific transcription factors, is widely involved in multiple biological processes. In apricot (Prunus armeniaca), the classification, structure, and function of the B3 superfamily are not yet clear. In this study, a total of 75 B3 genes were identified from the apricot genome. The apricot B3 superfamily can be divided into five subfamilies, i.e., REM, ARF, ABI3, RAV, and HSI, and genes in the same subfamily have similar structures. The distribution of B3 genes on chromosomes presents a clustering phenomenon. Tandem duplication is the main mode of apricot B3 family expansion, and gene duplication mainly occurs in the REM and ARF subfamilies. Many B3 genes originated from a common ancestor of Arabidopsis and apricot before lineage divergence, and ancestor genes expanded fewer times in apricot than in Arabidopsis. Gene ontology analysis showed that apricot B3 genes were closely related to vernalization, flower development, and shoot system development. PaABI3-1 and PaABI3-2 might play a positive regulation role in the transcription of PaOleosin, which encodes a lipid body protein. This study lays a foundation for the further study of the B3 superfamily function in apricot, especially the specific functions of the ABI3 subfamily in apricot kernel oil storage.
... More recently, this technique has been applied to plum (Fiol et al. 2022). These reference studies in other Prunus should be of great interest to develop CRISPR technology in almond for the efficient exploitation of the genome knowledge taking in account the great synteny between different Prunus species at genome (Jung et al. 2009) and transcriptome level (Martínez-Gómez et al. 2011). ...
... Such low level of homology in the ROI within P. salicina could be attributable to the interspecific origin of the species together with a putative mis-assembly of the region in the 'Zhongli No. 6' genome, in which two LG3-MYB10 regions were assembled 2 Mb apart instead of the single one expected for Prunus. The low identity between the Prunus ROI contrasts with the high synteny described at the whole genome level within the Prunus genus [42] and confirms the high complexity of this region in Prunus in general and in Japanese plums in particular. ...
Background
Genome complexity is largely linked to diversification and crop innovation. Examples of regions with duplicated genes with relevant roles in agricultural traits are found in many crops. In both duplicated and non-duplicated genes, much of the variability in agronomic traits is caused by large as well as small and middle scale structural variants (SVs), which highlights the relevance of the identification and characterization of complex variability between genomes for plant breeding.
Results
Here we improve and demonstrate the use of CRISPR-Cas9 enrichment combined with long-read sequencing technology to resolve the MYB10 region in the linkage group 3 (LG3) of Japanese plum ( Prunus salicina ). This region, which has a length from 90 to 271 kb according to the P. salicina genomes available, is associated with fruit color variability in Prunus species. We demonstrate the high complexity of this region, with homology levels between Japanese plum varieties comparable to those between Prunus species. We cleaved MYB10 genes in five plum varieties using the Cas9 enzyme guided by a pool of crRNAs. The barcoded fragments were then pooled and sequenced in a single MinION Oxford Nanopore Technologies (ONT) run, yielding 194 Mb of sequence. The enrichment was confirmed by aligning the long reads to the plum reference genomes, with a mean read on-target value of 4.5% and a depth per sample of 11.9x. From the alignment, 3261 SNPs and 287 SVs were called and phased. A de novo assembly was constructed for each variety, which also allowed detection, at the haplotype level, of the variability in this region.
Conclusions
CRISPR-Cas9 enrichment is a versatile and powerful tool for long-read targeted sequencing even on highly duplicated and/or polymorphic genomic regions, being especially useful when a reference genome is not available. Potential uses of this methodology as well as its limitations are further discussed.
... The few markers added on the LG8 of both the parental maps resulted in the improvement of the coverage in regions where fruit acidity QTLs are located. The positions of the new markers on LG8 were in agreement with those observed in the peach genome thus confirming the synteny between the peach and apricot genomes, already described in the literature (Dondini et al., 2007;Jung et al., 2009). To date, this analysis is strongly facilitated by the release of the apricot genome (Groppi et al., 2021). ...
Apricot breeding programs could be strongly improved by the availability of molecular markers linked to the main fruit quality traits. Fruit acidity is one of the key factors in consumer acceptance, but despite its importance, the molecular bases of this trait are still poorly understood. In order to increase the genetic knowledge on the fruit acidity, an F1 apricot population (‘Lito’ × ‘BO81604311’) has been phenotyped for titratable acidity and juice pH for the three following years. In addition, the contents of the main organic acids of the juice (malate, citrate, and quinate) were also evaluated. A Gaussian distribution was observed for most of the traits in this progeny, confirming their quantitative inheritance. An available simple sequence repeat (SSR)-based molecular map, implemented with new markers in specific genomic regions, was used to perform a quantitative trait loci (QTL) analysis. The molecular map was also anchored to the recently published apricot genome sequence of ‘Stella.’ Several major QTLs linked to fruit acidity-related traits have been identified both in the ‘Lito’ (no. 21) and ‘BO81604311’ (no. 13), distributed in five linkage groups (LG 4, 5, 6, 7, and 8). Some of these QTLs show good stability between years and their linked markers were used to identify candidate genes in specific QTLs genomic regions.
... Prunus species are important members of the Rosaceae family and include various ornamental and economically important fruit trees such as P. yedoensis, P. persica, and P. dulcis [46][47][48][49][50][51]. Although the different species show a variety of karyotypes in nature [52], Prunus genomes are usually very similar in size and basic synteny [53,54]. The chromosome numbers of the genus Prunus are x = 8, and Prunus species evolved from a common ancestor with x = 9 [55,56]. ...
... The chromosome numbers of the genus Prunus are x = 8, and Prunus species evolved from a common ancestor with x = 9 [55,56]. The karyotypes of Prunus plants remain highly conserved, implying close relationships among these species [54,55]. However, no genome-wide analysis has been performed to investigate the evolutionary patterns of VQ and WRKY genes and their interactions in closely related Prunus species. ...
Genes encoding VQ motif-containing (VQ) transcriptional regulators and WRKY transcription factors can participate separately or jointly in plant growth, development, and abiotic and biotic stress responses. In this study, 222 VQ and 645 WRKY genes were identified in six Prunus species. Based on phylogenetic tree topologies, the VQ and WRKY genes were classified into 13 and 32 clades, respectively. Therefore, at least 13 VQ gene copies and 32 WRKY gene copies were present in the genome of the common ancestor of the six Prunus species. Similar small Ks value peaks for the VQ and WRKY genes suggest that the two gene families underwent recent duplications in the six studied species. The majority of the Ka/Ks ratios were less than 1, implying that most of the VQ and WRKY genes had undergone purifying selection. Pi values were significantly higher in the VQ genes than in the WRKY genes, and the VQ genes therefore exhibited greater nucleotide diversity in the six species. Forty-one of the Prunus VQ genes were predicted to interact with 44 of the WRKY genes, and the expression levels of some predicted VQ-WRKY interacting pairs were significantly correlated. Differential expression patterns of the VQ and WRKY genes suggested that some might be involved in regulating aphid resistance in P. persica and fruit development in P. avium.
... armeniaca), and plum (P. domestica) have high genomic synteny (Dirlewanger et al., 2004;Jung et al., 2009). Based on extensive genomic data, the current study proposes to characterize shared molecular mechanisms during the endodormancy to ecodormancy transition in floral bud tissues across two related Prunus species, peach and apricot. ...
Dormancy is a physiological state that plants enter for winter hardiness. Environmental-induced dormancy onset and release in temperate perennials coordinate growth cessation and resumption, but how the entire process, especially chilling-dependent dormancy release and flowering, is regulated remains largely unclear. We utilized the transcriptome profiles of floral buds from fall to spring in apricot (Prunus armeniaca) genotypes with contrasting bloom dates and peach (Prunus persica) genotypes with contrasting chilling requirements (CR) to explore the genetic regulation of bud dormancy. We identified distinct gene expression programming patterns in endodormancy and ecodormancy that reproducibly occur between different genotypes and species. During the transition from endo- to eco-dormancy, 1,367 and 2,102 genes changed in expression in apricot and peach, respectively. Over 600 differentially expressed genes were shared in peach and apricot, including three DORMANCY ASSOCIATED MADS-box (DAM) genes (DAM4, DAM5, and DAM6). Of the shared genes, 99 are located within peach CR quantitative trait loci, suggesting these genes as candidates for dormancy regulation. Co-expression and functional analyses revealed that distinctive metabolic processes distinguish dormancy stages, with genes expressed during endodormancy involved in chromatin remodeling and reproduction, while the genes induced at ecodormancy were mainly related to pollen development and cell wall biosynthesis. Gene expression analyses between two Prunus species highlighted the conserved transcriptional control of physiological activities in endodormancy and ecodormancy and revealed genes that may be involved in the transition between the two stages.
... Although closely related plant species show extensive genome colinearity [55,56,[82][83][84][85], plant species that are more diverged do not show large amounts of synteny conservation. However, microsynteny of small genomic regions (of several genes) can be found between distant plant lineages, with examples found even between rice and Arabidopsis (diverged 200 MYA) [53,57]. ...
Background
Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system.
Results
The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae.
Conclusions
We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.
Electronic supplementary material
The online version of this article (10.1186/s12870-018-1574-0) contains supplementary material, which is available to authorized users.
... Relatedness and collinearity among the genomes of Prunus species such as almond, peach, and Japanese apricot (Dirlewanger et al., 2004;Jung et al., 2009) were exploited to characterize putative sequences and the chromosomal locations of candidate CYP genes involved in amygdalin biosynthesis in almond. Specifically, sequences of PmCYP79D16 and PmCYP71AN24, functionally shown to be involved in prunasin and amygdalin biosynthesis in Japanese apricot (Yamaguchi et al., 2014), were used for BLASTN searches against the draft almond genome sequence (Koepke et al., 2013). ...
Almond (Prunus dulcis) is the principal Prunus species in which the consumed and thus commercially important part of the fruit is the kernel. As a result of continued selection, the vast majority of almonds have a non-bitter sweet kernel. However, in the field there are trees carrying bitter kernels, which are toxic to humans and, consequently, need to be removed. The toxicity of bitter almonds is caused by accumulation of the cyanogenic diglucoside amygdalin, which releases toxic hydrogen cyanide upon hydrolysis. In this study, we identified and characterized the enzymes involved in the amygdalin biosynthetic pathway: PdCYP79D16 and PdCYP71AN24 as the cytochrome P450 (CYP) enzymes catalyzing phenylalanine to mandelonitrile conversion, PdUGT94AF3 as an additional monoglucosyl transferase (UGT) catalyzing prunasin formation, and PdUGT94AF1 and PdUGT94AF2 as the two enzymes catalyzing amygdalin formation from prunasin. Here, this was accomplished by constructing a sequence database containing UGTs known, or prospected to catalyse a β(1→6)-O glycosylation reaction, and a BLAST search of the draft version of the almond genome versus these sequences. Functional characterization of candidate genes was achieved by transient expression in Nicotiana benthamiana. Reverse transcription quantitative PCR demonstrated that the expression of PdCYP79D16 and PdCYP71AN24 was not detectable or only reached minute levels in the sweet almond genotype during fruit development, while it was high and consistent in the bitter genotype. Therefore, the basis for the sweet kernel phenotype is a lack of expression of the genes encoding the two cytochrome P450s catalyzing the first steps in amygdalin biosynthesis.
... Past studies only targeted hydrogen cyanamide-induced expression changes of specific genes, leaving a knowledge gap on the broad spectrum of gene expression changes and on putative effects of hydrogen cyanamide on phytohormone levels. Considering the high synteny within the Prunus genus (Jung et al., 2009), results obtained in sweet cherry are likely to be transferable to other fruit tree species. ...
Release of bud dormancy in perennial woody plants is a temperature-dependent process and thus flowering in these species is heavily affected by climate change. The lack of cold winters in temperate growing regions often results in reduced flowering and low fruit yields. This is likely to decrease the availability of fruits and nuts of the Prunus spp. in the near future. In order to maintain high yields, it is crucial to gain detailed knowledge on the molecular mechanisms controlling the release of bud dormancy. Here, we studied these mechanisms using sweet cherry (Prunus avium L.), a crop where the agrochemical hydrogen cyanamide (HC) is routinely used to compensate for the lack of cold winter temperatures and to induce flower opening. In this work, dormant flower buds were sprayed with hydrogen cyanamide followed by deep RNA sequencing, identifying three main expression patterns in response to HC. These transcript level results were validated by quantitative real time polymerase chain reaction and supported further by phytohormone profiling (ABA, SA, IAA, CK, ethylene, JA). Using these approaches, we identified the most up-regulated pathways: the cytokinin pathway, as well as the jasmonate and the hydrogen cyanide pathway. Our results strongly suggest an inductive effect of these metabolites in bud dormancy release and provide a stepping stone for the characterization of key genes in bud dormancy release.
... In this case, they are located in homologous regions. Comparative mapping of genomes of diploid species showed their high collinearity [9,17]. This property of the genome of Amygdaloideae makes it possible to compare the degree of genetic affinity between the species. ...
A study of the collection of sour cherry, sweet cherry, common plum, diploid and tetraploid types of plums, and apricots grown in Belarus carried out using 20 SSR markers showed that they are characterized by high genetic diversity. Among 106 genotypes, 524 polymorphic alleles were identified. The average number of alleles was 15.4 in common plum samples, 11.3 in diploid and tetraploid plum, 9.3 in sour cherry, 6.0 in apricot, and 4.9 in sweet cherry. The greatest genetic diversity is characteristic of common plum cultivars (PD = 0.811). The genetic diversity decreases as follows: diploid plum (PD = 0.741), sour cherry (PD = 0.721), apricot (PD = 0.673), and sweet cherry (PD = 0.655). Cluster analysis shows that the degree of intraspecific divergence in sour cherry and sweet cherry cultivars is less than that of common plum, diploid plum, and apricot plum. Although apricots and plums belong to the subgenus Prunophora, according to the results of SSR analysis, apricot cultivars form a cluster that is more distant from both Cerasus and Prunophora. A set of seven SSR markers (EMPA001, EMPA005, EMPA018, EMPA026 and BPPCT025, BPPCT026, BPPCT039) was selected for DNA identification of cultivars of sour cherry, sweet cherry, common plum, diploid plum, and apricot, as well as species and interspecies hybrids.
