Rosaceae Species Research Articles

Highly Contiguous Genome Resource of Colletotrichum fructicola Generated Using Long-Read Sequencing

Colletotrichum fructicola is a plant-pathogenic fungus with a broad host range. It causes significant losses to important crops, including apple, pear, strawberry, and other Rosaceae and non-Rosaceae species. To date, two short read-based C. fructicola genomes are publicly available, but both are fragmented. In this study, we re-sequenced the genome of C. fructicola using nanopore long-read technology and refined the assembly with Hi-C map data. The resulting high-quality assembly is an important resource for further comparative and experimental studies with C. fructicola.

Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae

Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The family also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), and achenetum (strawberry). Phylogenetic analysis and ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy fruit types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, and close relatives; referred to as Maleae here) may have contributed to the evolution of pome fruit. MADS-box genes, known to regulate floral organ identity, are emerging as important regulators of fruit development. The differential competence of floral organs to respond to fertilization signals may explain the different abilities of floral organs to form fleshy fruit. Future comparative genomics and functional studies in closely related Rosaceae species with distinct fruit types will test hypotheses and provide insights into mechanisms of fleshy fruit diversity. These efforts will be facilitated by the wealth of genome data and resources in Rosaceae.

Identification of early fruit development reference genes in plum.

An RNAseq study of early fruit development and stone development in plum, Prunus domestica, was mined to identify sets of genes that could be used to normalize expression studies in early fruit development. The expression values of genes previously identified from Prunus as reference genes were first extracted and found to vary considerably in endocarp tissue relative to whole fruit tissue. Nine other genes were chosen that varied less than 2-fold amongst the 20 RNAseq libraries of early fruit development and endocarp tissues. These gene were tested on a series of developmental plum fruit samples to determine if any could be used as a reference gene in the analyses of fruit-based tissues in plum. The three most stable genes as determined using RefFinder were IPGD (imidazole glycerol-phosphate dehydratase), HAM1 (histone acetyltransferase) and SNX1 (sorting nexin 1). These were further tested to analyze genes expressed differentially in endocarp tissue between normal and minimal endocarp cultivars. To determine the universality of those nine genes as fruit development reference genes, three other data sets of RNAseq from peach and apple were analyzed to determine the reference gene expression. Multiple genes exhibited tissue specific patterns of expression while one gene, the SNX1, emerged as possessing a universal pattern between the Rosaceae species, at all developmental stages, and tissue types tested. The results suggest that the use of existing RNAseq data to identify standard genes can provide stable reference genes for a specific tissues or experimental conditions under exploration.

Expression and evolutionary analysis of soluble inorganic pyrophosphatase gene family in pear and four other Rosaceae species

In plants, soluble inorganic pyrophosphatase (PPA) play an indispensable role in inorganic pyrophosphate hydrolysis. However, the expression and the evolutionary history of PPA gene family remain unclear in pear and Rosaceae species. In this study, thirty-nine PPA genes were identified from five Rosaceae species including pear (Pyrus bretschneideri), apple (Malus domestica), peach (Prunus persica), strawberry (Fragaria vesca) and Japanese apricot/mei (Prunus mume). Based on the structural characteristics of the genes and phylogenetic analysis, members of PPA gene family were classified into two main subfamilies (A and B). Whole-genome duplication (WGD) and dispersed gene duplication were the main force, which drove the expansion of PPA gene family in pear and other Rosaceae species. Purifying selection played a dominant role in the evolution of PPA genes. Subcellular localization analysis demonstrated that pear PPA genes located in the cytosol, chloroplasts or near the nuclear envelope. PPA genes showed multiple expression patterns in different pear tissues. Several members of PPA gene family presented particularly higher expression level in only one of the six tissues, such as PbrPPA2, PbrPPA5 and PbrPPA8. Expression analysis showed that five PPA genes were involved in the growth of pear pollen tube, meanwhile four PPA genes could respond to excess of PPi in pear pollen tube. Overall, we established a comprehensive landscape in the functional characterization and evolution of PPA gene family in pear and Rosaceae species, and provided gene expression data for exploring the functional roles of PPA genes in the growth of pear pollen tube.

Chromosome-level genome assembly and annotation of the loquat (Eriobotrya japonica) genome.

BackgroundThe loquat (Eriobotrya japonica) is a species of flowering plant in the family Rosaceae that is widely cultivated in Asian, European, and African countries. It blossoms in the winter and ripens in the early summer. The genome of loquat has to date not been published, which limits the study of molecular biology in this cultivated species. Here, we used the third-generation sequencing technology of Nanopore and Hi-C technology to sequence the genome of Eriobotrya.FindingsWe generated 100.10 Gb of long reads using Oxford Nanopore sequencing technologies. Three types of Illumina high-throughput sequencing data, including genome short reads (47.42 Gb), transcriptome short reads (11.06 Gb), and Hi-C short reads (67.25 Gb), were also generated to help construct the loquat genome. All data were assembled into a 760.1-Mb genome assembly. The contigs were mapped to chromosomes by using Hi-C technology based on the contacts between contigs, and then a genome was assembled exhibiting 17 chromosomes and a scaffold N50 length of 39.7 Mb. A total of 45,743 protein-coding genes were annotated in the Eriobotrya genome, and we investigated the phylogenetic relationships between the Eriobotrya and 6 other Rosaceae species. Eriobotrya shows a close relationship with Malus and Pyrus, with the divergence time of Eriobotrya and Malus being 6.76 million years ago. Furthermore, chromosome rearrangement was found in Eriobotrya and Malus.ConclusionsWe constructed the first high-quality chromosome-level Eriobotrya genome using Illumina, Nanopore, and Hi-C technologies. This work provides a valuable reference genome for molecular studies of the loquat and provides new insight into chromosome evolution in this species.

The complete chloroplast genome of Potentilla chinensis

Potentilla chinensis is traditional Chinese medicine source species. The cp genome of P. chinensis showed a typical quadripartite cycle with 157,117 bp, including a pair of inverted repeat regions (IRa and IRb, 26,194 bp each), a large single-copy region (LSC, 85,989 bp), and a small single-copy region (SSC, 18,740 bp). 129 unique genes were assembled in the cp genome, including 84 protein genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 17 cp genome of related species of Rosaceae showed that the P. chinensis was closely related to Potentilla stolonifera and Potentilla freyniana. This study provides important information for identification and application of P. chinensis.

Microbiological, antioxidant and lipoxygenase-1 inhibitory activities of fruit extracts of chosen Rosaceae family species.

Extracts from the Rosaceae family fruits are rich in natural, biologically active polyphenols, but their antibacterial properties are still poorly understood. Therefore, we focused our research on their activity against uropathogenic Escherichia coli strains. This research also concerned the proof of their ability to reduce oxidative stress and modulate the activity of lipoxygenase-1 (LOX-1). It is well-known that plants represent a source of bioactive compounds whose antioxidant activity may be useful in protecting against oxidative damage in cells, which have been linked to the pathogenesis of many oxidative diseases. The study determined the biological activity of methanol (ME) and water (WE) extracts rich in polyphenols from the hawthorn (Crataegus monogyna Jacq.), dog rose (Rosa canina L.), quince (Cydonia oblonga Mill.), and Japanese quince (Chaenomeles speciosa (Sweet) Nakai). The antioxidant capacity was evaluated using 1,1diphenyl-2-picrylhydrazyl (DPPH▪) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS+▪) radical scavenging methods. The inhibition of liposome membrane oxidation was studied using the thiobarbituric acid reactive substances assay. Lipoxygenase-1 inhibitory activity was measured using the spectrophotometric method. Bacterial growth was determined by evaluating the number of colony forming units per milliliter (CFU/mL). Hydrophobicity was established with salt aggregation hydrophobicity test (SAT). Swimming and swarming motilities were evaluated using soft-agar plates. Production of curli fimbriae was estimated on CFA agar. The P fimbriae were detected using the hemagglutination of erythrocytes. Adhesion of bacteria to human uroepithelial cells was assessed. The amount of biofilm was determined spectrophotometrically. We showed that most of these extracts are effective antioxidants and free radical scavengers, possess reasonable potential anti-inflammatory activity, reduce the adhesion of E. coli to uroepithelial cells, and reduce the ability of these bacteria to form biofilm. The extracts examined, showing very promising biological properties, seem to be able to join the list of substances that can be used as dietary supplements aimed at preventing, for example, urinary tract infections, or as support of drug treatment in many diseases.

Comparative analysis of the P-type ATPase gene family in seven Rosaceae species and an expression analysis in pear (Pyrus bretschneideri Rehd.)

P-type ATPases are integral membrane transporters that play important roles in transmembrane transport in plants. However, a comprehensive analysis of the P-type ATPase gene family has not been conducted in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. Here, we identified 419 P-type ATPase genes from seven Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, Prunus mume, Pyrus communis and Pyrus betulifolia). Structural and phylogenetic analyses revealed that P-type ATPase genes can be divided into five subfamilies. Different subfamilies have different conserved motifs and cis-acting elements, which may lead to functional divergence within one gene family. Dispersed duplication and whole-genome duplication may play critical roles in the expansion of the P-type ATPase family. Purifying selection was the primary force driving the evolution of P-type ATPase family genes. Based on the dynamic transcriptome analysis and transient transformation of Chinese white pear fruit, Pbr029767.1 in the P3A subfamily were found to be associated with malate accumulation during pear fruit development. Using a co-expression network, we identified several transcription factors that may have regulatory relationships with the P-type ATPase gene family. Overall, this study lays a solid foundation for understanding the evolution and functions of P-type ATPase genes in Chinese white pear and six other Rosaceae species.

The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae).

The rapid alkalinization factor (RALF) gene family is essential for the plant growth and development. However, there is little known about these genes among Rosaceae species. Here, we identify 124 RALF-like genes from seven Rosaceae species, and 39 genes from Arabidopsis, totally 163 genes, divided into four clades according to the phylogenetic analysis, which includes 45 mature RALF genes from Rosaceae species. The YISY motif and RRXL cleavage site are typical features of true RALF genes, but some variants were detected in our study, such as YISP, YIST, NISY, YINY, YIGY, YVGY, FIGY, YIAY, and RRVM. Motif1 is widely distributed among all the clades. According to screening of cis-regulatory elements, GO annotation, expression sequence tags (EST), RNA-seq, and RT-qPCR, we reported that 24 RALF genes coding mature proteins related to tissue development, fungal infection, and hormone response. Purifying selection may play an important role in the evolutionary process of RALF-like genes among Rosaceae species according to the result from ka/ks. The tandem duplication event just occurs in four gene pairs (Fv-RALF9 and Fv-RALF10, Md-RALF7 and Md-RALF8, Pm-RALF2 and Pm-RALF8, and Pp-RALF11 and Pp-RALF14) from four Rosaceae species. Our research provides a wide overview of RALF-like genes in seven Rosaceae species involved in identification, classification, structure, expression, and evolution analysis.

The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

Sorbus setschwanensis Koehne is a pinnate‐leaved Sorbus s.str. species endemic to China with narrow distribution and intriguing phylogeny that needs wider attention. In this paper, the complete chloroplast (cp) genome of S. setschwanensis is reported, and its phylogenetic position is analyzed. The complete cp genome of S. setschwanensis is 160 064 bp in size with 36.50% GC content. It has a typical quadripartite structure including a pair of inverted repeat regions (IRs) of 26 378 bp that separates a large single copy (LSC) region of 86 013 bp and a small single copy (SSC) region of 19 295 bp. The cp genome encodes 108 genes, comprising 76 protein‐coding genes, 28 tRNA genes and 4 rRNA genes. Additionally, 52 simple sequence repeats (SSRs) and 43 dispersed repeats were identified. Comparison of the whole cp genome with those of other Sorbus species showed an overall high degree of sequence similarity, but there are six highly variable regions (trnR‐atpA, petN‐psbM, ndhC‐trnV, trnE‐trnT, trnT‐trnL and rpl32‐trnL) located in intergenic spacers that may be useful as molecular markers in future population genetic and phylogenetic studies in the genus. Phylogenetic analyses based on 108 coding genes from 25 species in Rosaceae revealed that S. setschwanensis is nested within Sorbus sect. Sorbus together with other pinnately leaved species, but does not form a sister lineage to S. rufopilosa belonging to the same series Multijugae. Thus, the systematic position of S. setschwanensis and relationships with other species in the genus needs to be further studied.

Genome-wide comparative analysis of the BAHD superfamily in seven Rosaceae species and expression analysis in pear (Pyrus bretschneideri)

BackgroundThe BAHD acyltransferase superfamily exhibits various biological roles in plants, including regulating fruit quality, catalytic synthesizing of terpene, phenolics and esters, and improving stress resistance. However, the copy numbers, expression characteristics and associations with fruit aroma formation of the BAHD genes remain unclear.ResultsIn total, 717 BAHD genes were obtained from the genomes of seven Rosaceae, (Pyrus bretschneideri, Malus domestica, Prunus avium, Prunus persica, Fragaria vesca, Pyrus communis and Rubus occidentalis). Based on the detailed phylogenetic analysis and classifications in model plants, we divided the BAHD family genes into seven groups, I-a, I-b, II-a, II-b, III-a, IV and V. An inter-species synteny analysis revealed the ancient origin of BAHD superfamily with 78 syntenic gene pairs were detected among the seven Rosaceae species. Different types of gene duplication events jointly drive the expansion of BAHD superfamily, and purifying selection dominates the evolution of BAHD genes supported by the small Ka/Ks ratios. Based on the correlation analysis between the ester content and expression levels of BAHD genes at different developmental stages, four candidate genes were selected for verification as assessed by qRT-PCR. The result implied that Pbr020016.1, Pbr019034.1, Pbr014028.1 and Pbr029551.1 are important candidate genes involved in aroma formation during pear fruit development.ConclusionWe have thoroughly identified the BAHD superfamily genes and performed a comprehensive comparative analysis of their phylogenetic relationships, expansion patterns, and expression characteristics in seven Rosaceae species, and we also obtained four candidate genes involved in aroma synthesis in pear fruit. These results provide a theoretical basis for future studies of the specific biological functions of BAHD superfamily members and the improvement of pear fruit quality.

Proteome analysis provides new insight into major proteins involved in gibberellin-induced fruit setting in triploid loquat (Eriobotrya japonica).

Parthenocarpy can be induced by gibberellin (GA) treatment in plants. The fruits of the loquat exhibit many seeds. GA treatment can induce the development of seedless fruit and increase fruit quality during production. However, the molecular mechanism of fruit setting under GA treatment is still unclear. Our aim was to explore GA-induced parthenocarpy in triploid loquat by proteome analysis to identify the differentially expressed proteins. A proteome analysis was performed using TMT protein labeling and LC-MS/MS in triploid loquat. A total of 7290 protein groups were identified in the two stages of fruit setting. The quantitative results showed that 923 differentially expressed proteins (DEPs) were isolated, which were enriched in five pathways: ribosome, citrate cycle (TCA cycle), pentose phosphate, carbon metabolism, and carbon fixation. Twenty-four DEPs were annotated as putative key regulatory proteins involved in fruit setting, which were related to the auxin response, gibberellin metabolism, ethylene synthesis, and cell division. In addition, thirty-five DEPs were involved in the formation of the cell wall, which might be downstream proteins involved in cell proliferation during fruit setting. Our report reveals new insight into the protein dynamics of loquat fruit setting induced by GA treatment via the analysis of proteome profiles and provides a reference for other Rosaceae species.

Whole chloroplast genome sequence of a subtropical tree Eriobotrya bengalensis (Rosaceae)

Eriobotrya bengalensis (Roxb.) is a subtropical plant under the family Rosaceae with high economic and medicinal value. The whole chloroplast genome of E. bengalensis was sequenced to better understand its phylogenetic position relative to other Rosaceae species. The total length of the E. bengalensis chloroplast genome was 159,270 bp, which was composed of a large single-copy (LSC) region of 87,362 bp, a small single-copy (SSC) region of 19,184 bp, and a pair of inverted repeats (IRs) with a length of 26,362 bp separated by LSC and SSC. The total G + C content of the whole chloroplast genome was 36.7%. Phylogenetic analysis of maximum likelihood (TVM + F+R2) was completed using 15 complete chloroplast genomes of Rosaceae species. The results of phylogenetic analysis show that sisterhood exists in E. bengalensis with nine other species of Eriobotrya.

The complete chloroplast genome sequence of Prunus sibirica

In this study, the chloroplast genome sequence of Prunus sibirica was obtained from the whole genome sequencing data of Prunus sibirica. Its length is 158,248 bp, which consists of 86,331 bp large single-copy region (LSC), 26,408 bp two reverse repeat regions (IR) and 19,101 bp small single-copy region (SSC). GC content of the whole chloroplast genome is 36.71%. Those of LSC region, SSC region, and IR region were 35, 30, and 43%, respectively. There are 131 unique genes in the chloroplast genome, including 90 protein-coding genes, 33 tRNA genes, and 8 rRNA genes. A maximum-likelihood phylogenetic tree was generated from the chloroplast genomes of 10 species of Rosaceae and 11 peripheral plants. The results showed that Prunus sibirica belongs to Rosaceae and is sister to Prunus salicina.

Sequencing and characterization of the complete chloroplast genome of Sorbaria arborea (Rosaceae)

Sorbaria arborea is a species which is endemic to China. We utilized next-generation Illumina sequencing technology to sequence and assemble its chloroplast genome. The 160,137 bp genome contained four main sections, including a pair of inverted repeat regions which were 26,332 bp in length, and a small single-copy region was 19,418 bp, as well as a large single-copy region, which was 88,055 bp. The genome had a GC content of 36.1% and contained 113 unique genes, including 4 rRNAs, 30 tRNAs, and 79 protein-coding genes. The phylogenetic relationship of 25 Rosaceae species was constructed based on their chloroplast genome sequences, which supported a close relationship between S. arborea and Amygdaloideae. This newly sequenced plastid genome provides useful information for assessing the genetic diversity and phylogenetic position of S. arborea.

Investigation of Tocopherol Biosynthesis in Blackberry Seeds (Rubus spp.)

Tocopherol (vitamin E) is widely recognized as a cellular antioxidant and can prevent oxidative damage during seed quiescence and dormancy in all angiosperms. Tocopherols biosynthesis was highly accumulated in blackberry seeds, but limited study was done on expression of critical genes involved in this biosynthesis pathway. In the present study, each RuHPT and RuTMT cDNA sequence was isolated from boysenberry (Rubus idaeus × fruticosus × loganobaccus Darrow) and their expression patterns and regulation of tocopherols contents were investigated during different seed development stages from 14 to 42 days. RuHPT contained an open reading frame (ORF) of 1224 bp that encoded 407 amino acid residues, and for RuTMT, an ORF of 1056 bp encoding 351 amino acid residues. Phylogenetic analysis indicated that RuHPT and RuTMT were closely related to other Rosaceae species, Rosa chinensis and Fragaria vesca, respectively. The transcript level of both RuHPT and RuTMT gradually increased and reached a maximum level in the seeds of late ripening stages, 35 days after flowering (DAF) and 42 DAF. Assay of total tocopherol, α-tocopherol, γ‑tocopherol and δ-tocopherol contents by HPLC all revealed a similar changing trend concomitantly with the rising expression of RuHPT, and reached the peak on Day 35. The α-tocopherol level showed itself a trend of descending after ascending and reached its peak on Day 28. Therefore, RuHPT and RuTMT may both play a role in tocopherols biosynthesis in the seeds of ripening fruits. These results provide a novel foundation for investigating the functions of key enzyme genes on tocopherols biosynthesis in blackberry plants.

Spatial distribution pattern and interspecific correlation analysis of main species of Rosaceae in a deciduous broad-leaved forest in Yaoluoping

Spatial distribution pattern and interspecific correlation analysis of main species of Rosaceae in a deciduous broad-leaved forest in Yaoluoping

Fatty acid profile and in vitro biological properties of two Rosacea species (Pyrus glabra and Pyrus syriaca), grown as wild in Iran.

The high demands for the consumption of edible oils have caused scientists to struggle in assessing wild plants as a new source of seed oils. Therefore, in this study, the oil yield, fatty acid and tocopherol compositions, antioxidant and antibacterial activities of the oils obtained from Iran's two endemic plants (Pyrus glabra and Pyrus syriaca) were investigated. The obtained oil yields from the P. glabra and P. syriaca seeds were 33 ± 0.51 and 26 ± 0.28 w/w%, respectively. Oleic acid (C18:1) with the amount of 49.51 ± 1.05% was the major fatty acid in the P. glabra oil, while the main fatty acids in the P. syriaca seed oil belonged to linoleic acid (C18:2) and oleic acid (C18:1) with the amounts of 46.99 ± 0.37 and 41.43 ± 0.23%, respectively. The analysis of tocopherols was done by HPLC, and the results indicated that the P. glabra and P. syriaca seed oils were rich in α‐tocopherol (69.80 ± 1.91 and 45.50 ± 1.86 mg/100 g oil, respectively), constituting 86.24 and 89.01% of total detected tocopherols, respectively. The study on the reducing capacity of the oils indicated that the P. glabra oil had more reducing capacity than the P. syriaca oil. Moreover, the antioxidant activity of the P. glabra seed oil (43.4 ± 0.7 µg/ml) was higher than the P. syriaca seed oil (46.3 ± 1.2 µg/ml). Also, the investigation of the antibacterial activities indicated that the P. glabra and P. syriaca oils have an inhibitory effect on the studied bacteria. The results indicate that the oils of these plants can be appropriate sources of plant oils which can act as natural antibacterial agents.

Phylogenetic relationships and characterization of the complete mitochondrial genome of Eriobotrya japonica in southeast of China

Eriobotrya japonica is an evergreen fruit tree originating in southeastern China. Its fruit is juicy with a pleasant taste and considerable medical value. However, there is no complete mitochondrial (cmt) genome resource for this species. This is the first report of the cmt genome of Eriobotrya japonica from southeastern China. The whole cmt genome was 434,980 bp in size with 37.80% GC content. The cmt genome of Eriobotrya japonica contains 41 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. A phylogenetic maximum-likelihood (ML) tree was constructed based on 22 mitochondrial genomes from plant species. Eriobotrya japonica grouped closely with other Rosaceae species, which provides strong support for the traditional classification.

Effect of temperature on pollen germination for several Rosaceae species: influence of freezing conservation time on germination patterns.

Between February 2018 and April 2018, flowers were collected from eight Rosaceae species. Flowers were kept in a freezer at −20 °C for three freezing times (Treatment 1, two months; Treatment 2, four months; Treatment 3, six months). After extracting pollen, in vitro germination was induced in a culture medium and incubated at six different temperatures for 72 h. The percentage of pollen germination, average pollen tube length and maximum pollen tube length were measured. Pollen germination was maximum for all species between 15 °C and 30 °C. Cydonia oblonga, Malus sylvestris, Prunus avium, Prunus domestica, Prunus dulcis, Prunus persica and Pyrus communis obtained 30–52% pollen germination between 15 °C and 20 °C. Prunus cerasifera had 40% pollen germination at 30 °C. All species studied reached the maximum pollen tube length between 10 °C and 25 °C. Germination did not change significantly for any of the species with freezing time, but we found significant differences in the three parameters measured between treatments. The highest germination percentages were obtained in Treatment 2 (four months frozen at −20 °C), while the maximum pollen tube length was reached in Treatment 1 (two months frozen at −20 °C). According to our results, freezing time affected the germination-temperature patterns. This could indicate that studies on the effect of temperature on pollen germination should always be carried out with fresh pollen to obtain more conclusive data.