Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach.

ABSTRACT: Satsuma (Citrus unshiu Marc.) is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma ("Miyagawa Wase") was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds. Pseudomolecules of Satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of Clementine, pummelo, and sweet orange. Gene prediction by modeling with MAKER-P proposed 29,024 genes and 37,970 mRNA; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. BUSCO scores for the assembled scaffold and predicted transcripts, and another analysis by BAC end sequence mapping indicated the assembled genome consistency was close to those of the haploid Clementine, pummel, and sweet orange genomes. The number of repeat elements and long terminal repeat retrotransposon were comparable to those of the seven citrus genomes; this suggested no significant failure in the assembly at the repeat region. A resequencing application using the assembled sequence confirmed that both kunenbo-A and Satsuma are offsprings of Kishu, and Satsuma is a back-crossed offspring of Kishu. These results illustrated the performance of the hybrid assembly approach and its ability to construct an accurate heterozygous diploid genome.

SUBMITTER: Shimizu T

PROVIDER: S-EPMC5723288 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Parental diagnosis of satsuma mandarin (Citrus unshiu Marc.) revealed by nuclear and cytoplasmic markers.

Project description:Satsuma mandarins (Citrus unshiu Marc.) are the predominant cultivated citrus variety in Japan. Clarification of its origin would prove valuable for citrus taxonomy and mandarin breeding programs; however, current information is limited. We applied genome-wide genotyping using a 384 citrus single nucleotide polymorphism (SNP) array and MARCO computer software to investigate the satsuma mandarin parentage. Genotyping data from 206 validated SNPs were obtained to evaluate 67 citrus varieties and lines. A total of five parent-offspring relationships were newly found by MARCO based on the 206 SNP genotypes, indicating that 'Kishuu mikan' type mandarins (Citrus kinokuni hort. ex Tanaka accession 'Kishuu mikan' and 'Nanfengmiju') and 'Kunenbo' type mandarins (Citrus nobilis Lour. var. kunip Tanaka accession 'Kunenbo' and 'Bendiguangju') are possible parents of the satsuma mandarin. Moreover, cleaved amplified polymorphic sequences analysis showed that the genotypes of four regions in chloroplast DNA of 'Kishuu mikan' type mandarins were identical to that of the satsuma mandarin. Considering the historical background, satsuma mandarins may therefore derive from an occasional cross between a 'Kishuu mikan' type mandarin seed parent (derivative or synonym of 'Nanfengmiju') and a 'Kunenbo' type mandarin pollen parent (derivative or synonym of 'Bendiguangju').

| S-EPMC5282755 | biostudies-literature

Effect of temperature treatment on fruit quality and immunoregulation of Satsuma (Citrus unshiu Marc.) during storage.

Project description:Satsuma (Citrus unshiu Marc.) is rich in high levels of nutrients and popular for its unique flavor, but the consumption of satsuma is limited by some adverse reactions in human body. Previous studies have mainly focused on the effects of storage temperature on the postharvest quality of satsumas, and little attention has paid to the effect of postharvest satsumas on human body immunoregulation. The purpose of this study was to explore the differences in fruit quality, and the effect of satsuma fruits stored at different temperatures on human health. Satsumas stored at low temperature (5.8°C, LT) and room temperature (23 ± 2°C, RT) for 60 days were sampled every 10 days to measure the fruit quality. Sixty volunteers were recruited for the oral stimulation experiment of satsumas, and then the effect of satsumas on human health was examined through the immunoregulation of RAW 264.7 macrophages. The results showed that compared with RT treatment, LT treatment could delay the degradation of satsuma fruit quality. Both the results of the volunteer experiment and cell experiment indicated that postharvest temperature treatments could reduce the adverse effects of satsuma fruits on human body. These findings indicated that 10-day storage at room temperature plus subsequent storage at low temperature was the optimal treatment to maintain fruit quality and functional components of postharvest satsumas. This study provides useful information on satsuma consumption and research work from the perspective of immunoregulation evaluation.

| S-EPMC7590330 | biostudies-literature

Physiological and Ultrastructural Alterations Linked to Intrinsic Mastication Inferiority of Segment Membranes in Satsuma Mandarin (Citrus unshiu Marc.) Fruits.

Project description:Chewing texture is important for fresh citrus fruits, and the mastication trait of a segment directly determines chewing texture. Roughing disorder impairs the quality of Satsuma mandarin fruits, and it is typically correlated with intrinsic mastication inferiority (IMI). This study explored the role of segment membranes (SMs) in IMI. Similar to IMI in roughing-disordered fruits, segment shear force significantly enhanced relative to controls (CK); cell layers and cell wall thickness increased also in inferior masticating SMs. The 'Miyamoto Wase' cultivar exhibited larger segment shear force and more SM cell layers than 'Juxiangzao'. In SMs, vessel cells could be divided into outside layers where segments adjoin and inside layers where juice sacs grow from. The inside vessel cell layers in the inferior masticating SMs were denser. Vessels with a length of 200 to 300 μm and a diameter of 5 to 15 μm predominated in SMs. The average vessel diameter enlarged by 13% to 16.5% in inferior masticating SMs, depending on cultivars. Furthermore, there was a decrease in vessels with a diameter <5 μm and an increase in vessels >10 μm in the inferior masticating SMs. Between phenotypes, protopectin increased significantly throughout development of inferior masticating SMs, while water-soluble pectin increased during the later stages of development. In one inferior masticating SM sample, protopectin and water-soluble pectin levels were higher in the inner-ring area than those in the outer-ring area. Correspondingly, expression of CuPME21 which is involved in pectin hydrolysis was consistently upregulated in the inferior masticating SMs throughout fruit development. The findings in this work provide novel insights into citrus SM structure and its IMI.

| S-EPMC8747345 | biostudies-literature

Transcriptome and Metabolome Analyses Provide Insights into the Occurrence of Peel Roughing Disorder on Satsuma Mandarin (Citrus unshiu Marc.) Fruit.

Project description:Roughing disorder (RD) is a significant quality barrier in citrus fruit, prevalent on easy-peeling mandarins. As RD is not yet well-understood, this study aimed to examine the changes and synergic molecular processes involved in peel RD. Peel with RD was induced by severely defruiting Satsuma mandarin trees. Morphology observations, RNA-sequencing, and targeted and untargeted metabolic analyses were conducted. The results showed that the primary metabolites of sugars, organic acids and amino acids are dramatically changed in RD peel. The RD peel was always characterized by higher magnesium content during development. Comparative transcriptome profiling was performed for CK and RD peels at 30, 80, and 170 days after full bloom (DAFB) which represented fruit at cell division stage, cell enlargement stage and fruit maturity stage, respectively. Physiological and molecular biological evidence suggested that the month after full bloom is a crucial stage for RD initiation. A total of 4,855 differentially expressed genes (DEGs) in RD peel, relative to CK peel were detected at cell division stage, about 2 to 4-fold more than other stages had. Among the differentially expressed transcription factors, the bHLH family were affected most by RD, and six bHLH transcription factors functionally involved in GA metabolism were assessed to associate with RD occurrence. Gene set enrichment analysis suggested that RD significantly altered starch and GA metabolism in peel. Higher starch content and hydrolysed chain status were found in RD peel at cell division stage. RD occurrence on the peel was influenced significantly by GA, especially abundant GA before July. These changes may mean a significant alteration in sink strength of RD peel. The findings of this study provide insights into the emergence, development and molecular mechanisms of RD.

| S-EPMC5682035 | biostudies-literature

Molecular characterization of Satsuma mandarin (Citrus unshiu Marc.) VASCULAR PLANT ONE-ZINC FINGER2 (CuVOZ2) interacting with CuFT1 and CuFT3.

Project description:Shortening the juvenility is a burning issue in breeding fruit trees such as Satsuma mandarin (Citrus unshiu Marc.). Decreasing the breeding period requires a comprehensive understanding of the flowering process in woody plants. Throughout the Arabidopsis flowering system, FLOWERING LOCUS T (FT) interacts with other transcription factors (TFs) and functions as a transmissible floral inducer. In a previous study, a VASCULAR PLANT ONE-ZINC FINGER1 (VOZ1)-like TF from the Satsuma mandarin, CuVOZ1, showed protein-protein interaction with two citrus FTs in a yeast two-hybrid (Y2H) system and precocious flowering in Arabidopsis. In this study, another VOZ, CuVOZ2, was isolated from the Satsuma mandarin 'Aoshima' and protein-protein interaction was confirmed between CuVOZ2 and CuFTs. No apical meristem (NAM) and zinc coordination motifs were identified within the N-terminal of CuVOZ2. Docking simulation predicted that interactions between CuVOZ2 and CuFTs might occur in domain B of CuVOZ2, which contains a zinc finger motif. According to docking predictions, the distances between the amino acid residues involved ranged from 1.09 to 4.37 Å, indicating weak Van der Waals forces in the interaction. Cys216, Cys221, Cys235, and His239 in CuVOZ2 were suggested to bond with a Zn2+ in the Zn coordination motif. Ectopic expression of 35SΩ:CuVOZ2 in Arabidopsis affected the flowering time, length of inflorescence and internode, and number of siliques, suggesting that CuVOZ2 might regulate both vegetative and reproductive development, act as a trigger for early flowering, and be involved in the elongation of inflorescence possibly in a slightly different way than CuVOZ1.

| S-EPMC10777139 | biostudies-literature

Green satsuma mandarin orange (Citrus unshiu) extract reduces adiposity and induces uncoupling protein expression in skeletal muscle of obese mice.

Project description:Increased fat mass, which is induced by the storage of excess nutrients, is considered a causal factor for various metabolic disorders, including insulin resistance, type 2 diabetes, hyperlipidemia, hyperglycemia, hypertension, atherosclerosis, and non-alcoholic fatty liver disease. Therefore, it is necessary to prevent hyperadiposity to sustain a healthy life. Recently, uncoupling proteins (UCPs) were suggested to be molecular targets for curing obesity and its complications. In this study, green satsuma mandarin orange (Citrus unshiu) extract (GME) increased UCP3 expression in cultured myocytes. In a diet-induced obese animal model, administration of GME reduced fat mass and average fat cell size. Similar to in vitro experiments, GME restored expression of UCP3 in skeletal muscle. Moreover, GME also induced UCP2 expression in skeletal muscle. In conclusion, GME is suggested to be a novel functional dietary supplement for adiposity control through induction of UCPs.

| S-EPMC6484071 | biostudies-literature

Identification of Late Ripening Citrus Mutant, Ara-unshiu (Citrus unshiu), and Its Selectable Marker.

Project description:'Miyagawa-wase' mandarin (Citrus unshiu Marc. cv. Miyagawa-wase early) is one of the most widely cultivated citrus varieties on Jeju Island in Korea. Mutation breeding is a useful tool for the induction of genetic diversity for the rapid creation of new plant variants. We previously reported the use of gamma irradiation for the development of new citrus varieties. Here, we report a new mutant, Ara-unshiu, with a unique late fruit ripening phenotype. We investigated the fruit morphological characteristics including weight, vertical/transverse diameter, peel thickness, hardness, and color difference, as well as sugar and acid contents of the Ara-unshiu compared to wild-type controls. We then used whole genome re-sequencing and functional annotation by gene ontology to identify and characterize single nucleotide polymorphism (SNP) and insertion/deletion (InDel) variants in the Ara-unshiu, finding a greater abundance of annotated genes containing InDels compared to SNPs. Finally, we used allele-specific PCR to identify molecular markers among the homozygous SNPs detected from the Ara-unshiu genome sequencing. We report a primer set that effectively distinguishes the Ara-unshiu from the wild-type control and other citrus varieties. Our findings provide insights into the mechanisms controlling the timing of fruit ripening and tools for the molecular breeding of citrus varieties.

| S-EPMC10574479 | biostudies-literature

Chloroplast genome draft assembly of Falcataria moluccana using hybrid sequencing technology.

Project description:ObjectivesFalcataria moluccana, known locally as Sengon, is a fast-growing legume tree that is commonly planted in community forests of Java Island, Indonesia. However, the plantations face attacks of Boktor stem borer (Xystrocera festiva) and gall-rust disease (Uromycladium falcatariae) as major threats to its productivity. To control those pest and disease, it is necessary to grow resistant sengon clones, which are developed through tree improvement program, of which needs genetic and genomic information. This dataset was created to construct draft of sengon chloroplast genome and to study the evolution of sengon based on matK and rbcL barcode genes.Data descriptionGenomic DNA was extracted from leaf samples of one individual healthy tree in a private plantation. The DNA was sequenced using Illumina Novaseq 6000 (Novogen AIT, Singapore) for short-reads data, and MinION of Nanopore following manufacture's protocols SQK-LSK110 for long-reads data. The 66,3 Gb short-reads and 12 Gb long-reads data were hybrid assembled and used to construct a 128.867 bp of F. moluccana chloroplast genome with a quadripartite structure, containing a pair of inverted repeats, a large single-copy and a small single-copy region. Phylogenetic tree constructed using matK and rbcL showed monophyletic origin of F. moluccana and other legume trees.

| S-EPMC9996948 | biostudies-literature