title: De-novo RNA sequencing and metabolite profiling to identify genes involved in anthocyanin biosynthesis in Korean black raspberry (Rubus coreanus Miquel).
abstract: The Korean black raspberry (Rubus coreanus Miquel, KB) on ripening is usually consumed as fresh fruit, whereas the unripe KB has been widely used as a source of traditional herbal medicine. Such a stage specific utilization of KB has been assumed due to the changing metabolite profile during fruit ripening process, but so far molecular and biochemical changes during its fruit maturation are poorly understood. To analyze biochemical changes during fruit ripening process at molecular level, firstly, we have sequenced, assembled, and annotated the transcriptome of KB fruits. Over 4.86 Gb of normalized cDNA prepared from fruits was sequenced using Illumina HiSeq™ 2000, and assembled into 43,723 unigenes. Secondly, we have reported that alterations in anthocyanins and proanthocyanidins are the major factors facilitating variations in these stages of fruits. In addition, up-regulation of F3'H1, DFR4 and LDOX1 resulted in the accumulation of cyanidin derivatives during the ripening process of KB, indicating the positive relationship between the expression of anthocyanin biosynthetic genes and the anthocyanin accumulation. Furthermore, the ability of RcMCHI2 (R. coreanus Miquel chalcone flavanone isomerase 2) gene to complement Arabidopsis transparent testa 5 mutant supported the feasibility of our transcriptome library to provide the gene resources for improving plant nutrition and pigmentation. Taken together, these datasets obtained from transcriptome library and metabolic profiling would be helpful to define the gene-metabolite relationships in this non-model plant.
authors: Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
authors: Tae Kyung
authors: TK
authors: Hyun
authors: Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea.
authors: Sarah
authors: S
authors: Lee
authors: Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
authors: Yeonggil
authors: Y
authors: Rim
authors: Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
authors: Ritesh
authors: R
authors: Kumar
authors: Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
authors: Xiao
authors: X
authors: Han
authors: Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
authors: Sang Yeol
authors: SY
authors: Lee
authors: Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea.
authors: Choong Hwan
authors: CH
authors: Lee
authors: Division of Applied Life Science (BK21plus), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
authors: Jae-Yean
authors: JY
authors: Kim
mesh_terms: D000872:Anthocyanins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D018076:DNA, Complementary / Q000235:genetics; D005638:Fruit / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D044945:Proanthocyanidins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics*; D027824:Rosaceae / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D000872:Anthocyanins; D018076:DNA, Complementary; D044945:Proanthocyanidins; D018749:RNA, Plant