De-novo RNA Sequencing and Metabolite Profiling to Identify Genes Involved in Anthocyanin Biosynthesis in Korean Black Raspberry (Rubus coreanus Miquel)

Summary Disentangling the evolutionary histories of polyploids, especially those with high ploidies, can reveal fundamental processes in speciation. Despite occurring frequently during evolution, the origins of many extant polyploid plant species remain largely unknown.By integrating linkage mapping, polyploid phylogeny and sex‐determining region (SDR) in a unified framework, we statistically evaluated evolutionary hypotheses concerning the origin of a recently recognized decaploid strawberry (Fragaria cascadensis).The maximum‐likelihood phylogenies and topology tests across homeologous groups consistently rejected the seemingly parsimonious hypothesis of ‘contemporary sympatric speciation’ via hybridization between octoploid and diploid congeners. Instead, most chromosomes supported ‘ancient hybrid speciation’ between a maternal octoploid progenitor ancestral to extant octoploid strawberries and a paternal, extinct Fragaria iinumae‐like diploid progenitor, probably in Beringia during the Pleistocene. The absence of a shared SDR between the decaploid and other Fragaria is also consistent with an older origin rather than a recent hybrid origin in situ.Our study reveals a long evolutionary history of the decaploid despite its recent discovery, and highlights the pitfalls of inferring polyploid origins from niche/range alone or combined with morphology. It can serve as an exemplary starting step towards building much‐needed model systems of established polyploids that have been, and remain to be, recognized.

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“…We built the ML tree for each of chromosomes I-VII rooted with Rubus coreanus Miq. (Hyun et al, 2014).…”

Section: Phylogenetic Inference Of Subgenome Originsmentioning

confidence: 99%

Present‐day sympatry belies the evolutionary origin of a high‐order polyploid

et al. 2017

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“…Black raspberry is one of the most economically important crops and has become a popular food because it is a rich source of vitamins and polyphenolic compounds with high antioxidant capacities [18]. Black raspberry is a common name for three Rubus species: Rubus coreanus , native to Eastern Asia; Rubus occidentalis , native to Midwestern and Eastern North America; and Rubus leucodermis , native to the Pacific Northwest [19].…”

Section: Introductionmentioning

confidence: 99%

Integration of Traditional and Metabolomics Biomarkers Identifies Prognostic Metabolites for Predicting Responsiveness to Nutritional Intervention against Oxidative Stress and Inflammation

et al. 2017

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Various statistical approaches can be applied to integrate traditional and omics biomarkers, allowing the discovery of prognostic markers to classify subjects into poor and good prognosis groups in terms of responses to nutritional interventions. Here, we performed a prototype study to identify metabolites that predict responses to an intervention against oxidative stress and inflammation, using a data set from a randomized controlled trial evaluating Korean black raspberry (KBR) in sedentary overweight/obese subjects. First, a linear mixed-effects model analysis with multiple testing correction showed that four-week consumption of KBR significantly changed oxidized glutathione (GSSG, q = 0.027) level, the ratio of reduced glutathione (GSH) to GSSG (q = 0.039) in erythrocytes, malondialdehyde (MDA, q = 0.006) and interleukin-6 (q = 0.006) levels in plasma, and seventeen NMR metabolites in urine compared with those in the placebo group. A subsequent generalized linear mixed model analysis showed linear correlations between baseline urinary glycine and N-phenylacetylglycine (PAG) and changes in the GSH:GSSG ratio (p = 0.008 and 0.004) as well as between baseline urinary adenine and changes in MDA (p = 0.018). Then, receiver operating characteristic analysis revealed that a two-metabolite set (glycine and PAG) had the strongest prognostic relevance for future interventions against oxidative stress (the area under the curve (AUC) = 0.778). Leave-one-out cross-validation confirmed the accuracy of prediction (AUC = 0.683). The current findings suggest that a higher level of this two-metabolite set at baseline is useful for predicting responders to dietary interventions in subjects with oxidative stress and inflammation, contributing to the emergence of personalized nutrition.

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“…To analyze biochemical changes during fruit ripening process at molecular level, the transcriptome of KB fruits was sequenced, assembled, and annotated (Hyun et al, 2014b). Such a stage-specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process.…”

Section: Genomics and Transcriptomicsmentioning

confidence: 99%