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Transforming growth factor β (TGFβ) is present in blood of patients who do not respond to anti-programmed cell death (ligand) 1 [PD-(L)1] treatment, and through synergy with vascular endothelial growth factor (VEGF), it helps to create an environment that promotes tumor immune evasion and immune tolerance. Therefore, simultaneous inhibition of TGFβ/VEGF is more effective than targeting TGFβ alone. In this study, the dual inhibitory mechanism of TU2218 was identified through in vitro analysis mimicking the tumor microenvironment, and its antitumor effects were analyzed using mouse syngeneic tumor models. TU2218 directly restored the activity of damaged cytotoxic T lymphocytes (CTLs) and natural killer cells inhibited by TGFβ and suppressed the activity and viability of regulatory T cells. The inactivation of endothelial cells induced by VEGF stimulation was completely ameliorated by TU2218, an effect not observed with vactosertib, which inhibits only TGFβ signaling. The combination of TU2218 and anti-PD1 therapy had a significantly greater antitumor effect than either drug alone in the poorly immunogenic B16F10 syngeneic tumor model. The mechanism of tumor reduction was confirmed by flow cytometry, which showed upregulated VCAM-1 expression in vascular cells and increased influx of CD8 + CTLs into the tumor. As another strategy, combination of anti-CTLA4 therapy and TU2218 resulted in high complete regression (CR) rates in CT26 and WEHI-164 tumor models. In particular, immunological memory generated by the combination of anti-CTLA4 and TU2218 in the CT26 model prevented the development of tumors after additional tumor cell transplantation, suggesting that the TU2218-based combination has therapeutic potential in immunotherapy. [ABSTRACT FROM AUTHOR]

Agastache rugosa, also known as Korean mint, is a perennial plant from the Lamiaceae family that is traditionally used for various ailments and contains antioxidant and antibacterial phenolic compounds. Molecular breeding of A. rugosa can enhance secondary metabolite production and improve agricultural traits, but progress in this field has been delayed due to the lack of chromosome-scale genome information. Herein, we constructed a chromosome-level reference genome using Nanopore sequencing and Hi-C technology, resulting in a final genome assembly with a scaffold N50 of 52.15 Mbp and a total size of 410.67 Mbp. Nine pseudochromosomes accounted for 89.1% of the predicted genome. The BUSCO analysis indicated a high level of completeness in the assembly. Repeat annotation revealed 561,061 repeat elements, accounting for 61.65% of the genome, with Copia and Gypsy long terminal repeats being the most abundant. A total of 26,430 protein-coding genes were predicted, with an average length of 1,184 bp. The availability of this chromosome-scale genome will advance our understanding of A. rugosa's genetic makeup and its potential applications in various industries. [ABSTRACT FROM AUTHOR]

Purpose: Iodine is a vital trace element for systemic metabolic control as well as thyroid hormone synthesis. Though iodine has significant antioxidant and anti-inflammatory effects, reports on its effects on metabolic disorders are limited and inconsistent. Methods: Impact of urinary iodine concentrations (UICs) on fasting blood glucose (FBG) levels and blood pressure (BP) in the general Korean population was evaluated adjusting for covariates including thyrotropin level and presence of thyroid diseases. Results: The median UIC was 302.3 μg/L in all participants and was significantly lower in those with dysglycemia (303.6 μg/L in normal participants, 285.1 μg/L in participants with FBG levels of 100–125 mg/dL, and 261.8 μg/L in participants with FBG levels ≥ 126 mg/dL; p = 0.002). Similarly, the UIC was lower in participants with higher BP (311.6 μg/L in normal participants, 288.7 μg/L in prehypertensive participants, and 265.8 μg/L in hypertensive participants; p < 0.001). The multiple linear regression model showed a negative correlation between the UIC and FBG levels (p = 0.002), and the UIC and systolic BP (p < 0.001). One standard deviation increase in the UIC showed odds ratios of 0.84 (95% confidence interval [CI] = 0.73–0.98) for elevated FBG levels (≥ 100 mg/dL) and 0.94 (95% CI = 0.88–0.99) for elevated SBP (≥ 120 mm Hg) after full adjustment. Conclusion: Higher UICs were associated with lower FBG and BP levels, independent of thyroid function and other confounding factors in Korea, an iodine-replete country. [ABSTRACT FROM AUTHOR]

Background: Although type 2 diabetes (T2D) remission after gastric cancer surgery has been reported, little is known about the predictors of postoperative T2D remission. Methods: This study used data from a nationwide cohort provided by the National Health Insurance Service in Korea. We developed a diabetes prediction (DP) score, which predicted postoperative T2D remissions using a logistic regression model based on preoperative variables. We applied machine-learning algorithms [random forest, XGboost, and least absolute shrinkage and selection operator (LASSO) regression] and compared their predictive performances with those of the DP score. Results: The DP score comprised five parameters: baseline body mass index (< 25 or ≥ 25 kg/m2), surgical procedures (subtotal or total gastrectomy), age (< 65 or ≥ 65 years), fasting plasma glucose levels (≤ 130 or > 130 mg/dL), and antidiabetic medications (combination therapy including sulfonylureas, combination therapy not including sulfonylureas, single sulfonylurea, or single non-sulfonylurea]). The DP score showed a clinically useful predictive performance for T2D remission at 3 years after surgery [training cohort: area under the receiver operating characteristics (AUROC) 0.73, 95% confidence interval (CI), 0.71–0.75; validation cohort: AUROC 0.72, 95% CI 0.69–0.75], which was comparable to that of the machine-learning models (random forest: AUROC 0.71, 95% CI 0.68–0.74; XGboost: AUROC 0.70, 95% CI 0.67–0.73; LASSO regression: AUROC 0.75, 95% CI 0.73–0.78 in the validation cohort). It also predicted the T2D remission at 6 and 9 years after surgery. Conclusions: The DP score is a useful scoring system for predicting T2D remission after gastric cancer surgery. [ABSTRACT FROM AUTHOR]

Atopic dermatitis (AD) has been increasing worldwide over the past few decades. AD has been reported to be associated with an increased risk of osteoporosis and fractures in adult AD patients. The aim of this study was to investigate the bone mineral density (BMD) to evaluate osteoporosis risk in young adults with AD by sex. This was a case–control cohort study using a national dataset from the Korea National Health and Nutrition Examination Survey 2007–2009. We included young adult AD patients (men aged 19 ≤ and < 50 years, premenopausal women aged 19 ≤ and < 50 years) and 1:5 propensity score weighting controls by age, sex, body mass index (BMI), vitamin D level, and alcohol/smoking status. BMD was measured by double energy X-ray absorptiometry at the lumbar spine, femur neck, and total femur. The prevalence of low BMD, defined by a Z-score ≤ − 2.0, was compared between AD and without AD. We analyzed 311 (weighted n = 817,014) AD patients and 8,972 (weighted n = 20,880,643) controls. BMD at the lumbar spine was significantly lower in the male AD group than in the male control group (mean ± SE, 0.954 ± 0.016 vs. 0.989 ± 0.002, P = 0.03). The prevalence of low BMD (Z-score) did not significantly differ between AD and non-AD subjects in both men (3.8% vs. 2.7%, P = 0.56) and women (6.4% vs. 3.3%, P = 0.40). Among AD patients, early age at diagnosis of AD, longer duration of AD, lower BMI, rural residence (for men), less education, low vitamin D level, late menarche, and more pregnancies (for women) were associated with low BMD. In conclusion, low BMD did not occur more frequently in young adults with AD than in non-AD controls. However, early-onset/longer AD duration and lower BMI were associated with low BMD among young adult patients with AD. [ABSTRACT FROM AUTHOR]

Possible links between periodontitis and various cardiometabolic and autoimmune diseases have been advocated on the basis of chronic inflammation or oxidative stress. However, the association between periodontitis and thyroid dysfunction is under-researched. Participants without previous thyroid disease or ongoing thyroid-related medication were included from a nationwide population-level survey. Participants were categorized into tertiles of thyroid stimulating hormone (TSH) levels (first tertile < 1.76 mIU/L; second tertile 1.76–2.83 mIU/L; third tertile > 2.83 mIU/L), and periodontal condition was assessed using the Community Periodontal Index. Of the total of 5468 participants, 1423 had periodontitis (26%). A significant difference in the weighted prevalence of periodontitis according to TSH tertiles was observed, with the highest prevalence in the first tertile (26.5%) and the lowest prevalence in the third tertile (20.9%, p = 0.003). Subjects in the first TSH tertile had higher odds for periodontitis than those in the third tertile (OR 1.36, 95% CI 1.10–1.68; p for trend = 0.005) after adjusting for covariates. This association was consistent across subgroups and within sensitivity analyses among subjects without specific factors affecting thyroid function or diseases reported to be related to periodontitis. The present study demonstrated that low TSH levels were associated with significantly higher odds for periodontitis. [ABSTRACT FROM AUTHOR]

The triglyceride-glucose (TyG) index is a simple surrogate marker of insulin resistance. We evaluated the association of the TyG index with low muscle mass using a nationwide population-based representative data. This is a cross-sectional study that included 9477 participants aged ≥ 40 years from the Korea National Health and Nutrition Examination Survey between 2008 and 2011. The TyG index was calculated as ln[triglyceride (mg/dL) × fasting plasma glucose (mg/dL)/2]. Dual-energy X-ray absorptiometry was used to measure appendicular lean mass (ALM). Low muscle mass was defined an ALM/weight of 2 standard deviations (SD) below of young participants. The overall prevalence of low muscle mass was 4.7%. The prevalence of low muscle mass increased linearly with the quartiles of the TyG index, 2.5%, 4.2%, 5.6%, and 6.7% in Q1–Q4, respectively. The TyG index was negatively associated with ALM/weight both in men (r = − 0.302) and women (r = − 0.230). The odds ratio (OR) for low muscle mass was 2.08 in the highest quartile compared to the lowest quartile. High TyG index was associated with an increased risk of low muscle mass (OR for 1SD increase: 1.13). Increased TyG index was associated with the risk of low muscle mass independent of confounding factors. [ABSTRACT FROM AUTHOR]

The aim of this study is to investigate whether GGT variability is able to predict the risk of end-stage renal disease (ESRD). The study subjects were Koreans who conducted health exams supported by the Korean National Health Insurance Corporation during 2009–2012 (baseline). After excluding individuals aged < 40 years, heavy alcoholics, or those with histories of chronic liver disease or ESRD, we followed 6,058,995 individuals. We calculated the average successive variability (ASV) of GGT values during the 5 years before the baseline as a parameter of variability. Using Cox proportional analyses, we evaluated the risk of ESRD according to GGT ASV quartiles, defined as the initiation of renal replacement therapy or kidney transplantation, or December 31, 2016. During 38,663,279.3 person-years of follow-up, 12,057 cases of ESRD were identified. Compared with GGT ASV quartile 1, the risk of ESRD was higher in ASV quartiles 3–4 and increased serially, even after adjustment for several metabolic parameters, baseline renal function, presence of comorbidities, low income, and baseline GGT and hemoglobin level. The fully adjusted hazard ratios (95% confidence intervals) of GGT ASV quartiles 3 and 4 were 1.06 (1.01–1.12) and 1.12 (1.06–1.18), respectively. In conclusion, GGT variability is a putative risk factor for ESRD in Koreans. [ABSTRACT FROM AUTHOR]

In analyses of the entire study population and in the German and Korean subgroups, irisin and IL-15 serum concentrations were not significantly different between T2D patients with or without evidence for diabetic retinopathy (data not shown). In conclusion, our data suggest that neither irisin nor IL-15 serum concentrations reflect cardiometabolic risk factors or T2D complications in two independent cohorts from Korea and Germany. [Extracted from the article]

Two-dimensional molybdenum diselenide (MoSe2) has application potential in optical and optoelectronic devices. In this study, we fabricated field-effect transistors based on two-dimensional MoSe2 flakes and investigated the effect of flake thickness on the optoelectronic properties of the devices. An increase in MoSe2 flake thickness caused an enhancement in the optoelectronic performance of the device under 532 nm laser illumination. The thickest MoSe2 flake-based device showed the highest photoresponsivity of approximately 753 A W−1, and the external quantum efficiency and specific detectivity of the device were 175.891%, and 2.8 × 1011 cm Hz1/2 W−1, respectively. The prepared two-dimensional MoSe2 flakes exhibited promising properties for nano-optoelectronic device applications. [ABSTRACT FROM AUTHOR]

This study investigates the synergistic effects of graphene oxide (GO) on the woven carbon fiber (CF)-reinforced epoxy composites. The GO nanofiller was incorporated into the epoxy resin with variations in the content, and the CF/epoxy composites were manufactured using a vacuum-assisted resin transfer molding process and then cured at 70 and 120 °C. An analysis of the mechanical properties of the GO (0.2 wt.%)/CF/epoxy composites showed an improvement in the tensile strength, Young’s modulus, toughness, flexural strength and flexural modulus by ~ 34, 20, 83, 55 and 31%, respectively, when compared to the CF/epoxy composite. The dynamic mechanical analysis of the composites exhibited an enhancement of ~ 56, 114 and 22% in the storage modulus, loss modulus and damping capacity (tanδ), respectively, at its glass transition temperature. The fiber-matrix interaction was studied using a Cole-Cole plot analysis. [ABSTRACT FROM AUTHOR]

Matrix effects observed during the multiresidue analysis of seven organochlorine pesticides in six different agricultural products with GC-ECD were assessed. The presence of matrix coextractives, a major cause of observed matrix effects, directly and/or indirectly influenced the chromatographic responses of some pesticides. Two types of external calibrations, solvent calibration (SC) and matrixmatched calibration (MC), were used to assess matrix effects. Greater matrix effects were observed at the lower concentrations of each pesticide. The extent of matrix effects varied unpredictably with matrix type. Among the analyzed pesticides, iprodione, cyhalothrin, and cypermethrin exhibited greater matrix effects (>150%) for almost all matrices. The pesticide recovery rates obtained with MC were not statistically different from a 100% recovery rate in most samples, which indicates that MC may diminish the overestimates occurred due to matrix effects in GC analysis. [ABSTRACT FROM AUTHOR]

Aloe species, which have been used as medicinal plants, belong to the Asphodelaceae family consisting of 530 species. In this study, genetic diversity and phylogenetic relationships among 40 Aloe species including a putative interspecies hybrid were analyzed using PCR band profiles from eight chloroplast intergenic space markers and nucleotide sequence diversity in the psbK- psbI intergenic region. A phylogenetic tree based on psbK- psbI sequences supported the revised classification of the genus Aloe as polyphyletic with several species be re-allocated into three genera Kumara, Aloidendron, and Aloiampelos. Further, the origin of the putative interspecies Aloe hybrid was characterized through molecular cytogenetics. Fluorescence and genomic in situ hybridization illustrated that the hybrid has a bimodal karyotype with a chromosome complement of 2 n = 14, of which complementary halves were derived from two parental species, A. vera and A. arborescens. These findings revealed that the hybrid species was allodiploid. The phylogenetic analysis showed that A. arborescens was the maternal genome donor of the hybrid, as both have identical chloroplast genome sequences. We thus conclude that the allodiploid hybrid should be called A. arborescens × A.vera. [ABSTRACT FROM AUTHOR]

Perilla ( Perilla frutescens), an herbal plant belonging to the Lamiaceae family, has long been cultivated in Asia. Perilla is notable as an aroma-rich leaf vegetable and as the oilseed crop richest in omega-3 fatty acids. However, molecular analysis of this herbal plant is lacking due to insufficient genetic resources. Here, we constructed a normalized cDNA library from whole young perilla plants and analyzed expressed sequence tags (ESTs). A total of 4,582 uniESTs were generated from analysis of 5,435 ESTs. Among these, 307 uniESTs (6.7%) were identified as unique in perilla and 3,625 uniESTs were assigned at least one GO term through similarity searches in public databases. The most frequent GO terms were related to abiotic and biotic stress responses. In addition, we identified 141 uniESTs involved in lipid metabolism, of which four genes encoded fatty acid desaturases. We found one new candidate omega-3 fatty acid desaturase gene, in addition to the four that were previously reported. This analysis of uniESTs from perilla provides a valuable genetic resource to elucidate the molecular underpinnings of lipid metabolism and for molecular breeding of perilla species. [ABSTRACT FROM AUTHOR]

Gene and genome duplication events have long been accepted as driving forces in the evolution of angiosperms. Panax ginseng C. A. Meyer and Panax quinquefolius L., which inhabit eastern Asia and eastern North America, respectively, are famous medicinal herbs and are similar in growth condition, morphological and genetic characteristics. However, no molecular data regarding their evolution has been available. In this study, expressed sequence tags (ESTs) were generated from a cDNA library of P. ginseng and comparative analyses were conducted to reveal genome-level duplication and speciation of P. ginseng and P. quinquefolius by in-depth comparison of paralog and orthlog ESTs. Sequencing and assembly of 5,760 clones from the cDNA library resulted in 4,552 uniESTs of P. ginseng and these were subjected to initial annotation steps. Comparative analysis was conducted with the uniESTs and transcriptome data of P. quinquefolius retrieved from the public database. Paralog pairing and analysis of the distribution of synonymous substitutions per synonymous site (Ks) showed two coincident peaks in both Panax species, implying two rounds of genome duplication in their common ancestor. Comparison of orthologs revealed one Ks peak that is younger than the two peaks identified from the analysis of paralogs. However, absolute dating of genome duplication and speciation events is needed to address caveats related to their long generation times, speculated to be more than 8-10 years in the wild. This is the first report regarding the evolutionary relationship of Panax species at the genome-wide level, and will provide a foundation to unravel the genome structure of the enigmatic genus Panax and the family Araliaceae. [ABSTRACT FROM AUTHOR]

Ginseng is an important medicinal plant, but almost no genomic information is known for it. For the primary step to understand the Panax genome, we inspected the chloroplast genome sequence diversity and used that to infer the evolution of Panax species using them. We inspected a total of 101 intergenic spacers (IGS) covering 44,563 bp (96.8 % of the total IGS) from four Panax species. Diversity was inspected by three steps: gel electrophoresis, high resolution melting (HRM) analysis, and further confirmation by sequencing. Even though low levels of InDel polymorphism were detected by gel electrophoresis, high levels of reproducible polymorphisms were identified by HRM analysis. Sequencing of the HRM-polymorphic spaces and pair-wise multiple sequence alignments revealed up to 247 sequence variations between species. We have identified 62 IGS showing polymorphism between species. Among them, the trnE- trnT, trnT- psbD, ndhF- rpl32, and rpl14- rpl16 spaces are more informative for studying the diversity of Panax relatives. Phylogenetic analysis and molecular evolution studies revealed that P. notoginseng is most diverged from the other Panax species, with a nucleotide substitution rate of 0.0039. P. quinquefolius shows a close relationship with P. ginseng and P. japonicus, with a nucleotide substitution rate of 0.0009. Meanwhile, no sequence variation was detected between P. ginseng and P. japonicus. Calculation of molecular clocks revealed that P. notoginseng diverged more than 1.30 million years ago from the other Panax species and then, P. quinquefolius diverged from P. ginseng by migration in the American continent more than 0.29 million years ago. [ABSTRACT FROM AUTHOR]

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21987-7 [ABSTRACT FROM AUTHOR]

Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants. Anthraquinones are aromatic polyketides and have been used for treating various diseases, but the biosynthetic pathway is unclear. Here, the authors assemble the genome of an anthraquinone-producing medicinal plant Senna tora and show the evidences that CHS-like genes may be involved in anthraquinone biosynthesis. [ABSTRACT FROM AUTHOR]

We examined whether long-term gamma-glutamyl transferase (GGT) variability can predict cardiovascular disease (CVD) and mortality in individuals with diabetes. We included 698,937 Koreans diabetes patients older than 40 years without histories of CVD, chronic liver disease, or heavy alcoholics who received health exams supported by the Korean government more than once in 2009–2012 (baseline). We used Cox proportional analyses to estimate the risk of stroke, myocardial infarction (MI), and all-cause mortality until December 31, 2016, according to the quartiles of the average successive variability (ASV) of GGT measured during the five years before the baseline. A total 26,119, 15,103, and 39,982 cases of stroke, MI, and death, respectively, were found. GGT ASV quartile 4 had a significantly higher risk of stroke and all-cause mortality than quartile 1, with adjustment for risk factors, such as baseline glucose and GGT level, and comorbidities. Hazard ratios (95% confidence intervals) for GGT ASV quartile 4 were 1.06 (1.03–1.10) and 1.23 (1.20–1.27) for stroke and mortality, respectively. This significant association was shown consistently across the baseline GGT quartiles. GGT variability was related to the risk of stroke and all-cause mortality. The effect was most pronounced in all-cause mortality, irrespective of baseline GGT level. [ABSTRACT FROM AUTHOR]

This study was conducted to investigate the effects of sodium-glucose cotransporter 2 (SGLT2) inhibitors on individual renal outcomes in patients with type 2 diabetes. We searched MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials from inception to September 2017 to identify randomized controlled trials comparing SGLT2 inhibitors with placebo or antidiabetic drugs and reporting any renal outcomes in patients with type 2 diabetes. Additionally, we identified 4 articles which were published after the predefined period to include relevant data. A meta-analysis was performed to calculate weighted mean differences (WMDs) and relative risks (RRs) with 95% confidence intervals (CIs) for each renal outcome. We included 48 studies involving 58,165 patients in the analysis. SGLT2 inhibitors significantly lowered urine albumin-to-creatinine ratio (UACR) (WMD, −14.64 mg/g; 95% CI, −25.15 to −4.12; P = 0.006) compared with controls. The UACR-lowering effects of SGLT2 inhibitors were greater with a higher baseline UACR. Overall changes in estimated glomerular filtration rate (eGFR) were comparable between two groups (WMD, 0.19 mL/min/1.73 m2; 95% CI, −0.44 to 0.82; P = 0.552). However, SGLT2 inhibitors significantly slowed eGFR decline in patients with a higher baseline eGFR and a longer duration of treatment. Compared with controls, SGLT2 inhibitors significantly reduced the risk of microalbuminuria (RR, 0.69; 95% CI, 0.49 to 0.97; P = 0.032), macroalbuminuria (RR, 0.49; 95% CI, 0.33 to 0.73; P < 0.001), and worsening nephropathy (RR, 0.73; 95% CI, 0.58 to 0.93; P = 0.012). In addition, the risk of end-stage renal disease was significantly lower in SGLT2 inhibitors than in controls (RR, 0.70; 95% CI, 0.57 to 0.87; P = 0.001). In conclusion, SGLT2 inhibitors had beneficial renal effects by lowering the risk of albuminuria development or progression and reducing the risk of end-stage renal disease compared with placebo or other antidiabetic drugs. [ABSTRACT FROM AUTHOR]

We propose a new anthropometric index, weight-adjusted-waist index (WWI), to assess adiposity by standardizing waist circumference (WC) for weight. WWI, calculated as WC (cm) divided by the square root of weight (kg) (cm/√kg), was measured from 465,629 subjects in the Korean nationwide cohort (2008-2013). Cox regression analysis was used to compare WWI with BMI, WC, waist-to-height ratio (WHtR), and a body shape index (ABSI) for cardiometabolic morbidity and mortality risk in diagnostic and prognostic prediction models. For incident hypertension, type 2 diabetes and cardiovascular disease (CVD), BMI had the strongest predictive power, followed by WWI and WC. However, WWI showed the best predictive performance for CVD mortality. Also, a linear positive association between adiposity indices and cardiovascular and all-cause mortality was only shown in WWI and ABSI, not BMI, WC and WHtR which showed inverse J-shaped patterns. In the test of joint effects of each index, WWI combined with BMI was the strongest in both diagnostic and prognostic models. WWI is a unique adiposity index that shows linear positive association with both cardiometabolic morbidity and mortality. It also predicts incident cardiometabolic disease, cardiovascular and all-cause mortality risk with excellence in predictive power, especially when combined with BMI. [ABSTRACT FROM AUTHOR]

Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis. [ABSTRACT FROM AUTHOR]