Metabolomic analyses of plasma and liver of mice fed with immature Citrus tumida peel.

In this study, we investigated the effects of dietary supplementation of Citrus tumida hort. ex Tanaka on food intake, body and fat tissue weights, and metabolic profiles of plasma and liver in mice. Supplementation with 5% (w/w) of peels of immature C. tumida (PIC) for 4 weeks significantly suppressed body weight gain and decreased adipose tissue weight in epididymal, perirenal, and subcutaneous fats. Metabolome analyses showed that 2-hydroxyvaleric acid levels were reduced in the blood plasma of mice fed with PIC. PIC supplementation significantly elevated dipeptide (Thr-Asp, Ser-Glu, and Ala-Ala), glucuronic acid, and S-methylglutathione levels, and significantly reduced betaine aldehyde levels in the liver. In conclusion, PIC supplementation affects the metabolism of fatty acids, pectin, glutathione, and choline, showing potential beneficial effects for metabolic syndrome and obesity. PIC may be developed as a functional food and used in the treatment of these diseases.

Comparative transcriptome analysis of translucent flesh disorder in mangosteen (Garcinia mangostana L.) fruits in response to different water regimes.

Translucent flash disorder (TFD) is one of the important physiological disorders in mangosteen (Garcinia mangostana L.). TFD has symptoms such as flesh arils that become firm and appear transparent similar to watercore in apple or pear. Information on the changes of gene expression in TFD-affected tissues remain limited, and investigations into the effects of different water regimes still need to be undertaken. Through an RNA sequencing approach using the Ion Proton, 183,274 contigs with length ranging from 173-13,035 bp were constructed by de novo assembly. Functional annotation was analyzed using various public databases such as non-redundant protein NCBI, SwissProt, and Gene Ontology, and KEGG pathway. Our studies compared different water regimes to incidence and differentially expressed genes of TFD-like physiological disorders. From the differentially expressed gene (DEG) between normal air and TFD-affected aril, we identified DEG-related TFD events, which 6228 DEGs in the control condition and 3327 DEGs in under water stress treatment condition remained, and confirmed these with RT-qPCR, including sucrose synthase (SUSY), endoglucanase (GUN), xyloglucan endotransglucosylase/hydrolase (XTH), and polygalacturonase (PG) showed statistically significant. In addition, transcription factors also indicated changes in MYB, NAC and WRKY between tissues and different water regimes.

Dietary intake of the citrus flavonoid hesperidin affects stress-resilience and brain kynurenine levels in a subchronic and mild social defeat stress model in mice.

Depressive disorders are partly caused by chronic inflammation through the kynurenine (KYN) pathway. Preventive intervention using anti-inflammatory reagents may be beneficial for alleviating the risk of depression. In this study, we focused on the Japanese local citrus plant, Citrus tumida hort. ex Tanaka (C. tumida; CT), which contains flavonoids such as hesperidin that have anti-inflammatory actions. The dietary intake of 5% immature peels of CT fruits slightly increased stress resilience in a subchronic and mild social defeat (sCSDS) model in mice. Moreover, the dietary intake of 0.1% hesperidin significantly increased stress resilience and suppressed KYN levels in the hippocampus and prefrontal cortex in these mice. In addition, KYN levels in the hippocampus and prefrontal cortex were significantly correlated with the susceptibility to stress. In conclusion, these results suggest that dietary hesperidin increases stress resilience by suppressing the augmentation of KYN signaling under sCSDS.

Dietary Intake of Immature Citrus tumida Hort. ex Tanaka Peels Suppressed Body Weight Gain and Fat Accumulation in a Mouse Model of Acute Obesity.

Citrus fruits have several potential benefits for maintaining our health. In this study, we investigated the anti-obesity effects of immature Citrus tumida hort. ex Tanaka (C. tumida) peels using an acute obesity mice model. C57BL/6J male mice were divided into 2 groups; HFD-LL subjected to a high fat diet (HFD) and constant light exposure (LL), and HFDC-LL subjected to a HFD containing immature peel powder of C. tumida (5% w/w) and LL. Dietary ingestion of immature C. tumida peels significantly suppressed body weight gain following decreased epidydimal, perirenal, and subcutaneous fat weights. Blood levels of triglyceride and total cholesterol in the HFDC-LL were significantly lower than those in the HFD-LL group; however, there was no significant difference in food or calorie intake between the 2 groups. These results suggested that immature C. tumida peels have a beneficial effect on the prevention of obesity and metabolic syndrome via its biochemical activities of lipid metabolism.

Datasets for genome assembly of six underutilized Indonesian fruits.

Indonesia has a high genetic diversity of tropical fruits. However, studies on genomics are still very limited. In this data article, six underutilized Indonesian fruits were analyzed for the estimated genome size and partial data of genome assembly including Artocarpus nangkadak (Artocarpus heterophyllus x Artocarpus integer), Salacca sumatrana, Flacourtia inermis, Lansium domesticum, Pometia pinnata, and Syzygium samarangense. These genome data may be used to construct molecular markers for plant systematics and breeding program of these species. Our genome data were sequenced paired-end libraries using BGISeq-500 and generated approximately 5 Gb of bases per species. The raw sequences have been deposited in the DNA Data Bank of Japan (DDBJ) under the DDBJ BioProject umbrella with accession number PRJDB7265 and to the DDBJ Read Archive for each species following Artocarpus nangkadak (DRA007398), Salacca sumatrana (DRA007394), Flacourtia inermis (DRA007395), Lansium domesticum (DRA007393), Pometia pinnata (DRA007396), Syzygium samarangense (DRA007397).

Dataset from de novo transcriptome assembly of Nephelium lappaceum aril.

Nephelium lappaceum (Rambutan), is one of tropical fruit in which - cultivated widely in Indonesia and has good taste and aroma. However, the transcriptomic study of rambutan has limited. In this study, we performed transcriptome assembly using paired-end Illumina technology. The assembled transcriptome was constructed using Trinity and after filtering and removal sequences redundancy produced 36,303 contigs. The contig ranged 201-11,770 bp and N50 has 1327 bp. The contig was annotated with several databases such as SwissProt, TrEMBL, and nr/nt of NCBI databases. The raw reads are deposited in the DDBJ with DRA accession number, DRA007359: https://www.ncbi.nlm.nih.gov/sra/?term=DRA007359. The assembled contigs of transcriptome are deposited in the DDBJ TSA repository with accession number IADQ01000001-IADQ01036303: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/tsa/IADQ.gz and also can be accessed at http://rujakbase.id.

Dataset of the first de novo transcriptome assembly of the arillode of Baccaurea motleyana.

Baccaurea motleyana Müll. Arg. (rambai) is one of the underutilized fruit natives to Indonesia, Thailand, and Malaya Peninsula and it is mostly cultivated in Java island (Lim, 2012) [1]. The edible part of fruits is white and reddish arillodes in which having sweet to acid-sweet tastes. However, nucleotide as well as transcriptome information of this species is still scarce, no information has been deposited in GenBank. In this data article, we performed for the first time of de novo assembly of transcriptome using paired-end Illumina technology. The assembled contigs were constructed using Trinity and after filtering and clustering, produced 37,077 contigs. The contig ranged 201-4972 bp and N50 has 696 bp. The contig was annotated with several database such as SwissProt, TrEMBL, nr and nt NCBI databases. The raw reads were deposited in DDBJ with DRA numbers, DRA007358. The assembled contigs of transcriptome are deposited in the DDBJ TSA with accession number, IADP01000001-IADP01037077 and also can be accessed at http://rujakbase.id.

De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.

Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai).

Using an F1 population from a cross between Japanese pear (Pyrus pyrifolia Nakai) cultivars 'Akiakari' and 'Taihaku', we performed quantitative trait locus (QTL) analysis of seven fruit traits (harvest time, fruit skin color, flesh firmness, fruit weight, acid content, total soluble solids content, and preharvest fruit drop). The constructed simple sequence repeat-based genetic linkage map of 'Akiakari' consisted of 208 loci and spanned 799 cM; that of 'Taihaku' consisted of 275 loci and spanned 1039 cM. Out of significant QTLs, two QTLs for harvest time, one for fruit skin color, and one for flesh firmness were stably detected in two successive years. The QTLs for harvest time were located at the bottom of linkage group (LG) Tai3 (nearest marker: BGA35) and at the top of LG Tai15 (nearest markers: PPACS2 and MEST050), in good accordance with results of genome-wide association study. The PPACS2 gene, a member of the ACC synthase gene family, may control harvest time, preharvest fruit drop, and fruit storage potential. One major QTL associated with fruit skin color was identified at the top of LG 8. QTLs identified in this study would be useful for marker-assisted selection in Japanese pear breeding programs.

Agrobacterium-mediated transformation of Javanica rice cv. Rojolele.

The Agrobacterium-mediated transformation system was extended to a famous Javanica rice variety, Rojolele, that is cultivated in Indonesia now. Efficient callus induction from immature and mature seeds of Rojolele did not succeed by any previous method for any rice cultivar. In this study, the callus from mature seeds of Rojolele exhibited a compact and nodular appearance on C medium after the carbon source and medium pH was modified. Scutellum-derived calli from mature seeds were co-cultivated with Agrobacterium tumefaciens strains EHA101 or LBA4404 that carried plasmid pAFT14, which contained the genes for beta-glucuronidase (gus) and hygromycin resistance (hpt). Finally, the transformation efficiency of Rojolele variety using A. tumefaciens strain EHA101 (pAFT14) was improved to about 23%, similar to that of the Japonica rice variety Nipponbare. The seed fertility of transgenic Rojolele was more than 90%. The copy number of the transgene varied from one to three copies in the T(0) transgenic lines. Both the gus and the hpt genes were inherited and expressed in the progeny.