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Transcriptome Analysis Identifies the Key Genes Responsible for High Anthocyanin Content in the Fruits of Lycium ruthenicum Murray


Affiliations
1 Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China
2 College of Biologic and Geographic Sciences, Qinghai Normal University, Xining 810008, China
3 State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, China
 

Lycium ruthenicum Murray (black wolfberry) is an important economic plant producing black fruit with high anthocyanin content. The transcriptome of its fruits was compared with that of Lycium barbarum L. (wolfberry), which produces orange-red fruits, with its pigmentation depending largely on carotenoids, with the aim of identifying the key genes responsible for anthocyanin accumulation through RNA sequencing. A total of 32.05 and 28.52 Gb clean reads was obtained after filtering in L. barbarum and L. ruthenicum respectively. Altogether 192,869 unigenes were assembled with an average length of 1064 bp. These unigenes were predicted to encode 152,209 specific proteins with the help of protein databases. Compared with L. barbarum, 733,070 genes were upregulated while 25,779 genes appeared downregulated in the fruits of L. ruthenicum. The genes of the anthocyanin biosynthesis pathway exhibited more differences between the two species than did those of any other biosynthetic pathway. All structural genes in connection with anthocyanin biosynthesis had higher expression level in L. ruthenicum than in L. barbarum, except F3′H and 3GT. The downregulation of F′H and 3GT in L. ruthenicum would be responsible for the absence of cyanidin and glycosylation in this species. The MYB and bHLH genes regulating anthocyanin biosynthesis also displayed higher transcript levels in L. ruthenicum than in L. barbarum, especially the MYB transcription factor gene, which should be the reason for the activation of the anthocyanin biosynthesis structural genes. More work should be carried out to isolate the MYB and bHLH transcription factor genes, and to confirm their functions in producing the pigments found in the black fruits of L. ruthenicum.

Keywords

Anthocyanin Biosynthesis, Key Genes, Transcriptome Analysis, Wolfberry.
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  • Zheng, J. et al., Anthocyanins composition and antioxidant activity of wild Lycium ruthenicum Murr. from Qinghai-Tibet Plateau. Food Chem., 2011, 126(3), 859-865.

  • Zhang, H., Xia, L.-I. and Wang, J., The structure characteristic of the plant community in the lower reaches of Tarim River. Ecol. Environ., 2007, 4, 1219-1224.

  • Bowen-Forbes, C.-S., Zhang, Y.-J. and Nair, M.-G., Anthocyanin content, antioxidant, anti-inflammatory and anticancer properties of blackberry and raspberry fruits. J. Food Compos. Anal., 2010, 23(6), 554-560.

  • Wang, L.-S. and Stoner, G.-D., Anthocyanins and their role in cancer prevention. Cancer Lett., 2008, 269(2), 281-290.

  • Mazza, G., Bioactivity, absorption and metabolism of anthocyanins. In Proceedings of the First International Symposium on Human Health Effects of Fruits and Vegetables, 2007, pp. 117- 125.

  • Feng, W., En-Peng, H.-E. and Chen, X.-Q., Study on the effect of Lycium ruthenicum Murray fruit polysaccharide on the athletic ability of mice and the dose-effect. Arid Zone Res., 2010, 26(4), 586-590.

  • Wang, J.-H., Chen, X.-Q. and Zhang, W.-J., Study on hypoglycemic function of polysaccharides from Lycium ruthenicum Murr. fruit and its mechanism. Food Sci., 2009, 30, 244-248.

  • Zhang, Y., Butelli, E. and Martin, C., Engineering anthocyanin biosynthesis in plants. Curr. Opin. Plant Biol., 2014, 19, 81-90.

  • Saito, K. et al., The flavonoid biosynthetic pathway in Arabidopsis: structural and genetic diversity. Plant Physiol. Biochem., 2013, 72, 21-34.

  • Nishihara, M. and Nakatsuka, T., Genetic engineering of novel flower colors in floricultural plants: recent advances via transgenic approaches. Methods Mol. Biol., 2010, 589, 325-334.

  • Xu, W., Dubos, C. and Lepiniec, L., Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci., 2015, 20(3), 176-185.

  • Zeng, S. et al., Comparative analysis of anthocyanin biosynthesis during fruit development in two Lycium species. Physiol. Plant., 2014, 150(4), 505-516.

  • Liu, D. et al., Transcriptome analysis of purple pericarps in common wheat (Triticum aestivum L.). PLoS ONE, 2016, 11(5), e0155428.

  • Zhang, N. et al., Transcriptome characterization and sequencing based identification of drought-responsive genes in potato. Mol. Biol. Rep., 2014, 41(1), 505-517.

  • Dorn, K.-M., Fankhauser, J.-D., Wyse, D.-L. and Marks, M.-D., De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock. Plant J., 2013, 75(6), 1028-1038.

  • Firon, N. et al., Transcriptional profiling of sweet potato (Ipomoea batatas) ischolar_mains indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage ischolar_main formation. BMC Genomics, 2013, 14(1), 460.

  • Grabherr, M.-G. et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnol., 2011, 29(7), 644-652.

  • Iseli, C., Jongeneel, C.-V. and Bucher, P., ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In ISMB, 1999, pp. 138-148.

  • Conesa, A., Götz, S., Garcíagómez, J.-M., Terol, J., Talón, M. and Robles, M., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005, 21(18), 3674-3676.

  • Ye, J. et al., WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. (Web Server issue), 2006, 34, W293.

  • Mortazavi, A., Williams, B.-A., Mccue, K., Schaeffer, L. and Wold, B., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 2008, 5(7), 621.

  • Audic, S. and Claverie, J.-M., The significance of digital gene expression profiles. Genome Res., 1997, 7(10), 986-995.

  • Benjamini, Y. and Yekutieli, D., The control of the false discovery rate in multiple testing under dependency. Ann. Stat., 2001, 29(4), 1165-1188.

  • Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. and Hattori, M., The KEGG resource for deciphering the genome. Nucleic Acids Res. (Database issue), 2004, 32, 277-280.

  • Katsir, L., Chung, H.-S., Koo, A. J.-K. and Howe, G.-A., Jasmonate signaling: a conserved mechanism of hormone sensing. Curr. Opin. Plant Biol., 2008, 11(4), 428-435.

  • Johnson, C., Boden, E. and Arias, J., Salicylic acid and NPR1 induce the recruitment of trans-activating TGA factors to a defense gene promoter in Arabidopsis. Plant Cell, 2003, 15(8), 1846-1858.

  • Kim, T. W. and Guan, S.-Y., Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors. Nature Cell Biol., 2009, 11(10), 1254-1260.

  • Kim, T. W. and Wang, Z.-Y., Brassinosteroid signal transduction from receptor kinases to transcription factors. Annu. Rev. Plant Biol., 2010, 61, 681-704.

  • Chapman, E.-J. and Estelle, M., Mechanism of auxin-regulated gene expression in plants. Annu. Rev. Genet., 2009, 43, 265-285.

  • Mason, M. G. et al., Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. Plant Cell, 2005, 17(11), 3007-3018.

  • Chen, Y.-F., Etheridge, N. and Schaller, G.-E., Ethylene signal transduction. Ann. Bot., 2005, 95(6), 901-915.

  • Qiu, Z., Wang, X., Gao, J., Guo, Y., Huang, Z. and Du, Y., The tomato Hoffman’s anthocyaninless gene encodes a bHLH transcription factor involved in anthocyanin biosynthesis that is developmentally regulated and induced by low temperatures. PLoS ONE, 2016, 11(3), e0151067.

  • Tuan, P. A. et al., The crucial role of PpMYB10.1 in anthocyanin accumulation in peach and relationships between its allelic type and skin color phenotype. BMC Plant Biol., 2015, 15(1).

  • Takos, A.-M., Jaffé, F.-W., Jacob, S.-R., Bogs, J., Robinson, S.-P. and Walker, A.-R., Light-induced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol., 2006, 142(3), 1216-1232.


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  • Transcriptome Analysis Identifies the Key Genes Responsible for High Anthocyanin Content in the Fruits of Lycium ruthenicum Murray

Abstract Views: 196  |  PDF Views: 86

Authors

Xuebin Zhu
Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China
Jianmin Li
College of Biologic and Geographic Sciences, Qinghai Normal University, Xining 810008, China
Yuan Zong
Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China
Xuemei Sun
State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 800010, China
Shiming Li
Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China
Dong Cao
Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China
Bo Zhang
Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China
Wenjie Chen
Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China
Baolong Liu
Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining 810008, China

Abstract


Lycium ruthenicum Murray (black wolfberry) is an important economic plant producing black fruit with high anthocyanin content. The transcriptome of its fruits was compared with that of Lycium barbarum L. (wolfberry), which produces orange-red fruits, with its pigmentation depending largely on carotenoids, with the aim of identifying the key genes responsible for anthocyanin accumulation through RNA sequencing. A total of 32.05 and 28.52 Gb clean reads was obtained after filtering in L. barbarum and L. ruthenicum respectively. Altogether 192,869 unigenes were assembled with an average length of 1064 bp. These unigenes were predicted to encode 152,209 specific proteins with the help of protein databases. Compared with L. barbarum, 733,070 genes were upregulated while 25,779 genes appeared downregulated in the fruits of L. ruthenicum. The genes of the anthocyanin biosynthesis pathway exhibited more differences between the two species than did those of any other biosynthetic pathway. All structural genes in connection with anthocyanin biosynthesis had higher expression level in L. ruthenicum than in L. barbarum, except F3′H and 3GT. The downregulation of F′H and 3GT in L. ruthenicum would be responsible for the absence of cyanidin and glycosylation in this species. The MYB and bHLH genes regulating anthocyanin biosynthesis also displayed higher transcript levels in L. ruthenicum than in L. barbarum, especially the MYB transcription factor gene, which should be the reason for the activation of the anthocyanin biosynthesis structural genes. More work should be carried out to isolate the MYB and bHLH transcription factor genes, and to confirm their functions in producing the pigments found in the black fruits of L. ruthenicum.

Keywords


Anthocyanin Biosynthesis, Key Genes, Transcriptome Analysis, Wolfberry.

References





DOI: https://doi.org/10.18520/cs%2Fv116%2Fi2%2F256-263