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Background Nitraria sibirica  Pall. is an economic plant with two kinds of fruit color, widely spreads in the Qinghai Tibet Plateau. The chemical analysis and pharmacological evaluation had been carried out for several tens of years, the mechanism behind the fruit color differentiation is still unclear. Results In this manuscript, the chemical analysis of the extractions showed that the chemical composition of fruit color was anthocyanin, and two kind of  Nitraria sibirica  Pall. were caused by the content differentiation with the same anthocyanin kinds. Cyanidin-3-[2”-(6′”-coumaroyl)-glucosyl]-glucoside (C3G) was the major anthocyanin. Transcriptome analysis and the qRT-PCR revealed that the structural genes relative to anthocyanin biosynthesis except  CHS ,  F3’5’H  and  ANS  were up-regulated in the peels of BF (Black fruit) compared with the peels of RF (Red fruit), which indicated that transcript factor should be the reason for the expression difference of the structure genes. In the unigenes of the transcript factor MYB and bHLH, relative to anthocyanin, only  NsMYB1  ( Cluster 8422.10600 ), was high-expression and up-expression in the peels of BF.  NsMYB1  encoded the same length protein with four amino acid differences in the RF and BF, and both contained the intact DNA, HTH-MYB and SANT domains.  NsMYB1  was close to the  AtMYB114 ,  AtMYB113  and  AtPAP1 , regulating anthocyanin biosynthesis, in phylogenetic relationship. Both  NsMYB1r  and  NsMYB1b  could promote the transcript of the structural genes, and induced the anthocyanin accumulation in all tissues of transgenic tobacco. The insertion of ‘TATA’ in the promoter of  NsMYB1r  gave one more promoter region, and was the reason for higher transcripts in black fruit possibly. Conclusions Cyanidin-3-[2′’-(6′”-coumaroy l )-glucosyl]-glucoside was the major anthocyanin in black fruit of  Nitraria sibirica  Pall..  NsMYB1  was a functional R2R3-MYB transcription factor, regulated the anthocyanin biosynthesis, and led to the fruit color differentiation in  Nitraria sibirica  Pall.

bmc plant biology

Functional R2R3-MYB transcription factor NsMYB1, regulating anthocyanin biosynthesis, was relative to the fruit color differentiation in Nitraria sibirica Pall.