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

BACKGROUND: The 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. FINDINGS: We 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. CONCLUSIONS: We 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.

Volatile metabolite profiling reveals the changes in the volatile compounds of new spontaneously generated loquat cultivars.

In recent years, the advantageous traits of three new loquat cultivars have drawn the attention of breeders and growers. All three have spontaneously arisen from the 'Algerie' cultivar: the new 'Xirlero' cultivar is a bud mutant of 'Algerie', while 'Amadeo' and 'Raúl' arose as chance seedlings. Following a non-targeted approach based on HS-SPME-GC-MS, the volatile compounds profile of the fruits from the new cultivars were obtained and compared to the original 'Algerie' cultivar. Carboxylic acids clearly dominated the volatile profile of all the loquat cultivars, but esters, aldehydes, ketones and alcohols were also predominant compounds. Interestingly when the bud mutant event did not lead to marked changes in the volatile compounds complement, pronounced changes in the volatile composition of chance seedling-generated cultivars 'Amadeo' and 'Raúl' were observed. 'Amadeo' fruits showed lower levels of 2-methyl butanoic acid and much higher levels of methylhexanoate, methylbutanoate and 2-hydroxy-5-methylacetophenone. The 'Raúl' cultivar also had a distinctive volatile profile characterised by high levels of C6-aldehydes, (E)-2-hexanal, 2-hexenal, (Z)-3-hexenal and hexanal, and several carotenoid-derived volatiles; e.g. 2-pentene-1,4-dione 1-(1,2,2-trimethylcyclopentyl), (S)-dihydroactinidiolide, isodurene, cis-geranyl acetone, ß-damascenone, ß-ionone, α-ionone and 3,4-dehydro-ß-ionone. These changes in volatiles were associated with a more intense flavour in cultivars 'Amadeo' and 'Raúl', according to the sensory evaluation of the flavour intensity carried out by a semi-trained panel. A metabolomic correlation network analysis provided insights as to how volatiles were regulated, and revealed that the compounds modified in 'Amadeo' were uncoupled from the rest of the volatilome, while the volatiles modified in 'Raul' changed according to specific groups. To conclude, this work provides a holistic view of how the loquat volatilome was affected, and this information was integrated with the physical-chemical-sensory attributes to understand the changes that occur in the new cultivars.

Pomological Traits, Sensory Profile and Nutraceutical Properties of Nine Cultivars of Loquat (Eriobotrya japonica Lindl.) Fruits Grown in Mediterranean Area.

In this paper the diversity of fruit quality within nine loquat cultivars, including five international affirmed cultivars (Algerie, Golden Nugget, Peluche, Bueno, El Buenet) and four local cultivars (Sanfilippara, Nespolone di Trabia, BRT20 and Claudia), were investigated in order to discriminate the variation in pomological characteristics, sensory profile, and antioxidant properties. Finally, to evaluate potential bioactivity, antiproliferative activity of hydrophilic extracts from loquat fruits was assessed, at dietary relevant concentrations, against three human epithelial cell lines. Even though the international cultivars confirmed an appropriate level of commercial qualities in association to high levels in antioxidant compounds, the local cultivars revealed the best performances in a wide range of chemical-physical and sensory characteristics. Concerning bioactivity, our results indicate that hydrophilic extracts from all tested cultivars showed concentration-dependent antiproliferative activity with a significant variability of effects between different cell lines and between different cultivars. HeLa cells, the most sensitive and hydrophilic extracts from Peluche, showed the highest inhibitory effect followed by Nespolone di Trabia and Claudia. The results of this trial provide useful information on the pomological traits and the not yet known specific nutritional and functional properties of loquat fruits. Our data, besides helping to promote specific local cultivars, could serve to establish a database that will permit to improve the utilization of specific genetic resources in breeding programs.

EjMYB8 Transcriptionally Regulates Flesh Lignification in Loquat Fruit.

Transcriptional regulatory mechanisms underlying lignin metabolism have been widely studied in model plants and woody trees, but seldom in fruits such as loquat, which undergo lignification. Here, twelve EjMYB genes, designed as EjMYB3-14, were isolated based on RNA-seq. Gene expression indicated that EjMYB8 and EjMYB9 were significantly induced in fruit with higher lignin content resulting from storage at low temperature (0°C), while two treatments (low temperature conditioning, LTC; heat treatment, HT) both alleviated fruit lignification and inhibited EjMYB8 and EjMYB9 expression. Dual-luciferase assays indicated that EjMYB8, but not EjMYB9, could trans-activate promoters of lignin-related genes EjPAL1, Ej4CL1 and Ej4CL5. Yeast one-hybrid assay indicated that EjMYB8 physically bind to Ej4CL1 promoter. Furthermore, the putative functions of EjMYB8 were verified using transient over-expression in both N. tabacum and loquat leaves, which increased lignin content. Moreover, combination of EjMYB8 and previously isolated EjMYB1 generated strong trans-activation effects on the Ej4CL1 promoter, indicating that EjMYB8 is a novel regulator of loquat fruit lignification.

New Sesquiterpene Glycosides from the Leaves of Eriobotrya japonica.

One new sesquiterpene glycoside, named nerolidol-3-O-α-L-rhamnopyranosyl-(1 --> 6)-ß-D-glucopyranoside (1), along with one novel natural product nerolidol-3-O-α-L-rhamnopyranosyl-(1 --> 2)-[α-L-rhamnopyranosyl-(1 --> 6)]-ß-D-glucopyranoside (2) and two known sesquiterpene glycosides (3-4), were isolated from the leaves of Eriobotrya japonica (Thunb.) Lindl.. Their structures were elucidated on the basis of 1D, 2D NMR and HR-MS data. The chemotaxonomic significance of this type of constituents was discussed.

Phytochemical content, antioxidants and cell wall metabolism of two loquat (Eriobotrya japonica) cultivars under different storage regimes.

Changes in quality, phytochemical content and cell wall metabolism of two loquat cultivars (Eriobotrya japonica cvs. 'Morphitiki', 'Karantoki') under different storage regimes were studied. The fruit were harvested at commercial maturity stage and analyzed after 1, 3, 5, 7, and 11 days maintenance at room temperature (RT, ∼ 20°C) or after cold storage (14 days at 4°C) and additional ripening at RT for 1, 3 and 5 days, respectively. Compositional analysis revealed substantial cultivar differences; the 'Morphitiki' fruit was more acidic and showed higher contents of total phenolics, flavonoids and hydroxycinnamic acid-derivatives as well as greater antioxidant potency. Although firmness did not change markedly during storage, the cell wall exhibited extensive remodeling. Greater changes were observed in the pectin backbones than in polyuronide side chains and cross-linking glycans. Polygalacturonase (PG) showed better association with cell wall solubilization at RT than the enzymes involved in arabinan or galactan disassembly. During postharvest ripening after harvest, 'Karantoki' showed more extensive pectin solubilization than 'Morphitiki'. Interestingly, cold storage inhibited the cell wall disassembly in 'Karantoki' but not in 'Morphitiki', suggesting that the cultivars may differ in their susceptibility to chilling-related wall disorders. Low temperature-induced alterations in wall disassembly may impact juice and phytochemical release upon consumption.

[Study on fingerprint spectrum of loquat leaf by HPLC].

OBJECTIVE: To establish the fingerprint spectrum of Loquat Leaf of Fujian authentic medicinal herbs by HPCE. METHODS: The HPLC fingerprints of Loquat Leaf were obtained from instrument HP1100. The HPLC separation was performed on a Eclipse XDB-C18 (4.6 mm x 150 mm, 5 microm) analytical column diluted with methanol-l% glacial acetic acid (90:10) at the flow rate of 1.0 ml/min. The temperature of column was room temperature. The UV detection wavelength was 215 nm. RESULTS: Detected 12 batches samples of different species Lopuat Leaf Fingerprint by the method of HPLC. Eight peaks in the chromatogram were common. All the similarity were above 0.9, the fingerprints integer feature were coincident essentially. CONCLUSION: The method is convenient, quick and exact, and its reproducibility is good. It will be a scientific reference for qualitation identification and quality evaluation of Loquat Leaf.

Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers.

Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus x domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (-0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus x domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family.