De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

Yong Peng, Huiqin Ma, Shangwu Chen

Abstract


 Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

DOI: 10.2298/ABS160123125P

Received: January 23, 2016; Revised: March 16, 2016; Accepted: April 4, 2016; Published online: November 11, 2016

How to cite this article: Peng Y, Ma H, Chen S. De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening. Arch Biol Sci. 2017;69(1):181-90.


Keywords


de novo characterization; digital gene expression profiles; fruit development; Lycium ruthenicum; transcriptome

Full Text:

PDF

References


Chen H, Pu L, Cao J, Ren X. Current Research State and Exploitation of Lycium ruthenicum Murr. Heilongjiang Agr Sci. 2008;5:155-7.

Gan QM LG, Li PY, Zhuoma DZ, Chen YR, Zuo ZC. Study on the development and utilization of Tibetan medicine Lycium ruthenicum Murr. Qinghai Sci Tech. 1997;4(1):17-9.

Zheng J, Ding C, Wang L, Li G, Shi J, Li H, Wang HL, Suo YR. Anthocyanins composition and antioxidant activity of wild Lycium ruthenicum Murr. from Qinghai-Tibet Plateau. Food Chem. 2011;126(3):859-65.

Li J, Qu W, Zhang S, Lv H. Study on antioxidant activity of pigment of Lycium ruthenicum. China J Chinese Mater Med. 2006;31(14):1179-83.

Kosar M, Altintas A, Kirimer N, Baser KHC. Determination of the free radical scavenging activity of Lycium extracts. Chem Nat Compd. 2003;39(6):531-5.

Altintas A, Kosar M, Kirimer N, Baser K, Demirci B. Composition of the essential oils of Lycium barbarum and L. ruthenicum fruits. Chem Nat Compd. 2006;42(1):24-5.

Wang JH, Chen XQ, Zhang WJ. Study on hypoglycemic function of polysaccharides from Lycium ruthenicum Murr. fruit and its mechanism. Food Sci. 2009;30(5):244-8.

Peng Q, Liu H, Shi S, Li M. Lycium ruthenicum polysaccharide attenuates inflammation through inhibiting TLR4/NF-κ B signaling pathway. Int J Bio Macromol. 2014;67:330-5.

Li J, Yuan H, Zeng X-C, Han B, Shi D-H. Toxicological assessment of pigment of Lycium ruthenicum Murr. Food Sci. 2007;28(7):470-5.

Liu Z, Shu Q, Wang L, Yu M, Hu Y, Zhang H, Tao Y, Shao Y. Genetic diversity of the endangered and medically important Lycium ruthenicum Murr. revealed by sequence-related amplified polymorphism (SRAP) markers. Biochem Syst Ecol. 2012;45:86-97.

Chen H, Zhong Y. Microsatellite markers for Lycium ruthenicum (Solananeae). Mol Biol Rep. 2014;41(9):5545-8.

Wang S-Z, Pan L, Hu K, Chen C-Y, Ding Y. Development and characterization of polymorphic microsatellite markers in Momordica charantia (Cucurbitaceae). Am J Bot. 2010;97(8):e75-e78.

Vilanova S, Manzur JP, Prohens J. Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins. Mol Breeding. 2012;30(2):647-60.

Liu W, Lu XY, He GY, Gao X, Li MX, Wu JH, Li ZJ, Wu JH, Wang JC, Luo C. Cytosolic protection against ultraviolet induced DNA damage by blueberry anthocyanins and anthocyanidins in hepatocarcinoma HepG2 cells. Biotechnol Lett. 2013;35(4):491-8.

Jin H, Liu Y, Yang F, Wang J, Fu D, Zhang X, Peng XJ, Liang XM. Characterization of anthocyanins in wild Lycium ruthenicum Murray by HPLC-DAD/QTOF-MS/MS. Anal Method. 2015;7:4947-56.

Liu J, Osbourn A, Ma P. MYB transcription factors as regulators of phenylpropanoid metabolism in plants. Mol Plant. 2015;8(5):689-708.

Reid KE, Olsson N, Schlosser J, Peng F, Lund ST. An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Boil. 2006;6(1):27.

Liang C, Liu X, Yiu SM, Lim BL. De novo assembly and characterization of Camelina sativa transcriptome by paired-end sequencing. BMC Genomics. 2013;14(1):146.

Wang H, Jiang J, Chen S, Qi X, Peng H, Li P, Song A, Guan Z, Fang W, Liao Y, Chen F. Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery. PloS One. 2013;8(4):e62293.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644-52.

Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674-6.

Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li ST, Li RQ, Bolund L, Wang J. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006;34(suppl 2):W293-W297.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36(Suppl. 1):D480-D484.

Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999:138-48.

Li R, Yu C, Li Y, Lam T-W, Yiu S-M, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25(15):1966-7.

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Method. 2008;5(7):621-8.

Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat. 2001;29(4):1165-88

De Jong W, Eannetta N, De Jong D, Bodis M. Candidate gene analysis of anthocyanin pigmentation loci in the Solanaceae. Theor Appl Genet. 2004;108(3):423-32.

Zeng S, Wu M, Zou C, Liu X, Shen X, Hayward A, Liu C, Wang Y. Comparative analysis of anthocyanin biosynthesis during fruit development in two Lycium species. Physiol Plantarum. 2014;150(4):505-16.

Kiferle C, Fantini E, Bassolino L, Povero G, Spelt C, Buti S, Giuliano G, Quattrocchio F, Koes R, Perata P, Gonzali S. Tomato R2R3-MYB Proteins SlANT1 and SlAN2: Same Protein Activity, Different Roles. PloS One. 2015;10(8):e0136365.

Czemmel S, Heppel SC, Bogs J. R2R3 MYB transcription factors: key regulators of the flavonoid biosynthetic pathway in grapevine. Protoplasma. 2012;249(Suppl 2):S109-S118.

Ince A, Onus A, Elmasulu S, Bilgen M, Karaca M. In silico data mining for development of Capsicum microsatellites. Acta Hortic. 2004;729:123-7.

Portis E, Nagy I, Sasvári Z, Stágel A, Barchi L, Lanteri S. The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping. Plant Sci. 2007;172(3):640-8.

Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet. 2004;109(4):800-5.

Thiel T, Michalek W, Varshney R, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 2003;106(3):411-22.

Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi M, Nagata N, Isobe S, Tabata S. Development of Capsicum EST-SSR markers for species identification and in silico mapping onto the tomato genome sequence. Mol Breeding. 2013;31(1):101-10.

Shirasawa K, Asamizu E, Fukuoka H, Ohyama A, Sato S, Nakamura Y, Tabata S, Sasamoto S, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Isobe S. An interspecific linkage map of SSR and intronic polymorphism markers in tomato. Theor Appl Genet. 2010;121(4):731-9.

Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Suzuki S, Hasegawa M, Kiyoshima H, Isobe S. Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Mol Breeding. 2012;30(1):125-38.

Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M, Kishida Y, Kohara M, Takahashi C, Tsuruoka H, Wada T, Sakai T, Isobe S. An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res. 2011;18(4):221-32.

Kayesh E, Shangguan L, Korir NK, Sun X, Bilkish N, Zhang Y, Han J, Song CN, Cheng ZM, Fang JG. Fruit skin color and the role of anthocyanin. Acta Physiol Plant. 2013;35(10):2879-90.

Zhao J, Li H, Xi W, An W, Niu L, Cao Y, Han J, Song CN, Cheng ZM, Fang JG. Changes in sugars and organic acids in wolfberry (Lycium barbarum L.) fruit during development and maturation. Food Chem. 2015;173:718-24.


Refbacks

  • There are currently no refbacks.


Copyright (c) 2017 ARCHIVES OF BIOLOGICAL SCIENCES

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.