Transcriptome analysis by illumina high-throughout paired-end sequencing reveals the complexity of differential gene expression during in vitro plantlet growth and flowering in Amaranthus tricolor L

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Liu, Shengcai ^a   Kuang, Huaqin ^a   Lai, Zhongxiong ^a  

^a FUJIAN AGRICULTURE AND FORESTRY UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; UBIQUITIN; BIOLOGICAL MARKER; MESSENGER RNA; PLANT RNA;

AMARANTHUS TRICOLOR; ARABIDOPSIS; ARTICLE; CATALYSIS; CELL ORGANELLE; CIRCADIAN RHYTHM; DOWN REGULATION; FLOWERING; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; IN VITRO STUDY; NONHUMAN; OPEN READING FRAME; OXIDATIVE PHOSPHORYLATION; PERIODICITY; PIGMENTATION; PLANT DEVELOPMENT; PLANT GROWTH; PLANTLET; PROTEIN DEGRADATION; PYROSEQUENCING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA PROCESSING; SEEDLING; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SUCROSE METABOLISM; UBIQUITINATION; UPREGULATION; AMARANTHUS; DNA MICROARRAY; FLOWER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; PLANT GENE; REAL TIME POLYMERASE CHAIN REACTION;

AMARANTHUS; BIOLOGICAL MARKERS; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENES, PLANT; IN VITRO TECHNIQUES; METABOLIC NETWORKS AND PATHWAYS; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; RNA, PLANT; SEEDLING;

EID: 84903553208     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100919     Document Type: Article

References (81)

1. Mosyakin SL, Robertson KR (2003) Amaranthus. Flora of North America North of Mexico. Edited by Committee FoNAE, vol. 4. New York: Oxford University Press: 410-435.
2. Délano-Frier JP, Avilés-Arnaut H, Casarrubias-Castillo K, Casique-Arroyo G, Castrillón-Arbeláez PA, et al. (2011) Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress. BMC genomics 12: 363.
3. Pal A, Swain SS, Das AB, Mukherjee AK, Chand PK (2013) Stable germ line transformation of a leafy vegetable crop amaranth (Amaranthus tricolor L.) mediated by Agrobacterium tumefaciens. In Vitro Cellular & Developmental Biology-Plant 49: 114-128.
4. Sanz-Penella JM, Laparra JM, Sanz Y, Haros M (2012) Bread supplemented with amaranth (Amaranthus cruentus): effect of phytates on in vitro iron absorption. Plant foods for human nutrition 67: 50-56.
5. Cruz-Garcia GS, Price LL (2012) Weeds as important vegetables for farmers. Acta Societatis Botanicorum Poloniae 81: 397-403.
6. Maroyi A (2013) Use of weeds as traditional vegetables in Shurugwi District, Zimbabwe. Journal of ethnobiology and ethnomedicine 9: 60.
7. Misra S, Misra MK (2013) Leafy vegetable plants of South Odisha, India. International Journal of Agricultural and Food Science 3(4): 131-137
8. Sinha R, Lakra V (2007) Edible weeds of tribals of Jharkhand, Orissa and West Bengal. Indian J Tradit Know 6: 217-222.
9. Rastogi A, Shukla S (2013) Amaranth: A New Millennium Crop of Nutraceutical Values. Critical reviews in food science and nutrition 53: 109-125.
10. Biswas M, Das SS, Dey S (2013) Establishment of a stable Amaranthus tricolor callus line for production of food colorant. Food Science and Biotechnology 22: 1-8.
11. Andini R, Yoshida S, Ohsawa R (2013) Variation in protein content and amino acids in the leaves of grain, vegetable and weedy types of Amaranths. Agronomy 3: 391-403.
12. Yaacob J, Hwei L, Taha R, Mat Nor N, Aziz N (2011) Pigment analysis and tissue culture of Amaranthus cruentus L. In: I International Symposium on Sustainable Vegetable Production in Southeast Asia 958: 171-178.
13. Yang WW, Liu SC, Lai ZX (2011) Preliminary study on in vitro flowering of amaranth. Journal of Fujian Agriculture and Forestry University(Natural Science Edition) 4: 360-364.
14. Samach A (2011) Control of flowering. In: Plant biotechnology and agriculture: prospects for the 21st century. Edited by Altman A, Hasegawa PM, vol. 495. New York: Academic Press 387-404.
15. Meng XQ, Hou ZX, Zhang L (2013) Progress on molecular and genetic mechanisms of floral control in higher plants. Current Biotechnology (1):1-6.
16. Sun CH, Deng XJ, Fang J, Chu CC (2007) An overview of flowering transition in higher plants. Heredity (Beijing). 29(10):1182-1190.
17. Song Y, Gao Z, Luan W (2012) Interaction between temperature and photoperiod in regulation of flowering time in rice. Science China Life Sciences 55: 241-249.
18. Borner R, Kampmann G, Chandler J, Gleibner R, Wisman E, et al. (2000) A MADS domain gene involved in the transition to flowering in Arabidopsis. The Plant Journal 24: 591-599. (Pubitemid 32040059)
19. Zhang G, Guo G, Hu X, Zhang Y, Li Q, et al. (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome research 20: 646-654.
20. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods 5: 621-628. (Pubitemid 351911867)
21. Rowland LJ, Alkharouf N, Darwish O, Ogden EL, Polashock JJ, et al. (2012)Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC plant biology 12: 46.
22. Singh VK, Garg R, Jain M (2013) A global view of transcriptome dynamics during flower development in chickpea by deep sequencing. Plant biotechnology journal 11(6): 691-701.
23. Kim J, Park JH, Lim CJ, Lim JY, Ryu J-Y, et al. (2012) Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC genomics 13(1): 657.
24. Bai S, Saito T, Sakamoto D, Fujii H, Moriguchi T (2013) Transcriptome analysis of Japanese Pear (Pyrus pyrifolia Nakai.) flower buds transitioning through endodormancy. Plant and Cell Physiology.
25. Huang YJ, Liu LL, Huang JQ, Wang ZJ, Chen FF, et al. (2013) Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.). BMC genomics 14: 691.
26. Yang N, Zhao KG, Chen LQ (2012) Deep sequencing-based transcriptome profiling analysis of Chimonanthus praecox reveals insights into secondary metabolites biosynthesis. Journal Of Beijing Forestry University (Suppl. 1):104-107.
27. Li TZ, Du HY, Hui-min L, Ta-na W, Lin W, et al. (2012) Transcriptome data assembly and gene function annotation of Eucommia mature fruits and young fruits. Journal of Central South University of Forestry & Technology 32(10): 9-17.
28. Cong H, Li Z, Xu L (2013) Characterizing developmental and inducible differentiation between juvenile and adult plants of Aechmea fasciata treated with ethylene by transcriptomic analysis. Plant Growth Regulation 69: 247-257.
29. Hsiao YY, Huang TH, Fu CH, Huang SC, Chen YJ, et al. (2013) Transcriptomic analysis of floral organs from Phalaenopsis orchid by using oligonucleotide microarray. Gene 518: 91-100.
30. Maughan PJ, Sisneros N, Luo M, Kudrna D, Ammiraju JS, Wing RA (2008) Construction of an bacterial artificial chromosome library and genomic sequencing of herbicide target genes. Crop Science 48: S-85-S-94.
31. Lee JR, Hong GY, Dixit A, Chung JW, Ma KH, et al. (2008) Characterization of microsatellite loci developed for Amaranthus hypochondriacus and their crossamplifications in wild species. Conservation genetics 9: 243-246.
32. Mallory MA, Hall RV, McNabb AR, Pratt DB, Jellen EN, et al. (2008) Development and characterization of microsatellite markers for the grain amaranths. Crop science 48: 1098-1106. (Pubitemid 351955479)
33. Horvath D (2010) Genomics for weed science. Current genomics 11: 47-51.
34. Lee RM, Thimmapuram J, Thinglum KA, Gong G, Hernandez AG, et al. (2009) Sampling the waterhemp (Amaranthus tuberculatus) genome using pyrosequencing technology. Weed Science 57: 463-469.
35. Riggins CW, Peng Y, Stewart CN, Tranel PJ (2010) Characterization of de novo transcriptome for waterhemp (Amaranthus tuberculatus) using GS-FLX 454 pyrosequencing and its application for studies of herbicide target-site genes. Pest management science 66: 1042-1052.
36. Maughan PJ, Yourstone SM, Jellen EN, Udall JA (2009) SNP discovery via genomic reduction, barcoding, and 454-pyrosequencing in amaranth. The plant genome 2: 260-270.
37. Liu SC, Lin YL, Chen XD, Lai ZX (2011) Novel and Conserved miRNAs Identification during in vitro Flowering of Amaranthus by Solexa Sequencing. Chin J Trop Crops (7):1296-1303.
38. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Fulllength transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29: 644-652.
39. Natale DA, Shankavaram UT, Galperin MY, Wolf YI, Aravind L, et al. (2000) Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol 1, research/0009.1-19.
40. Lulin H, Xiao Y, Pei S, Wen T, Shangqin H (2012) The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PloS one 7: e38653.
41. Armour CD, Castle JC, Chen R, Babak T, Loerch P, et al. (2009) Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nature methods 6(9):647-649.
42. Hao D, Ma P, Mu J, Chen S, Xiao P, et al. (2012) De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. Science China Life Sciences 55: 452-466.
43. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
44. de Montaigu A, Tóth R, Coupland G (2010) Plant development goes like clockwork. Trends in Genetics 26: 296-306.
45. Imaizumi T (2010) Arabidopsis circadian clock and photoperiodism: time to think about location. Current opinion in plant biology 13: 83-89.
46. Hicks KA, Millar AJ, Carré IA, Somers DE, Straume M, et al. (1996) Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant. Science 274: 790-792.
47. Hicks KA, Albertson TM, Wagner DR (2001) EARLY FLOWERING3 encodes a novel protein that regulates circadian clock function and flowering in Arabidopsis. The Plant Cell Online 13: 1281-1292. (Pubitemid 32592903)
48. Mizoguchi T, Wheatley K, Hanzawa Y, Wright L, Mizoguchi M, et al. (2002) LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Developmental cell 2: 629-641. (Pubitemid 34538143)
49. Lu SX, Webb CJ, Knowles SM, Kim SH, Wang Z, et al. (2012) CCA1 and ELF3 Interact in the control of hypocotyl length and flowering time in Arabidopsis. Plant physiology 158: 1079-1088.
50. Lau OS, Huang X, Charron JB, Lee J-H, Li G, et al. (2011) Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock. Molecular Cell 43: 703-712.
51. Hyodo H, Yamakawa S, Takeda Y, Tsuduki M, Yokota A, et al. (2003) Active gene expression of a xyloglucan endotransglucosylase/hydrolase gene, XTH9, in inflorescence apices is related to cell elongation in Arabidopsis thaliana. Plant molecular biology 52: 473-482. (Pubitemid 36761659)
52. Tanaka N, Itoh H, Sentoku N, KojimaM, Sakakibara H, et al. (2011) The COP1 ortholog PPS regulates the juvenile-adult and vegetative-reproductive phase changes in rice. The Plant Cell Online 23: 2143-2154.
53. Cui X, Lu FL, Li Y, Xue YM, Kang YY, et al. (2013) Ubiquitin-Specific Proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis. Plant physiology 162: 897-906.
54. Bernier G, Havelange Ae, Houssa C, Petitjean A, Lejeune P (1993) Physiological signals that induce flowering. The Plant Cell 5: 1147.
55. Dunwell JM, Gibbings JG, Mahmood T, Saqlan Naqvi S (2008) Germin and germin-like proteins: evolution, structure, and function. Critical reviews in plant sciences 27: 342-375.
56. Ono M, Sage-Ono K, Inoue M, Kamada H, Harada H (1996) Transient increase in the level of mRNA for a germin-like protein in leaves of the short-day plant Pharbitis nil during the photoperiodic induction of flowering. Plant and cell physiology 37: 855-861. (Pubitemid 26405180)
57. Heintzen C, Fischer R, Melzer S, Kappeler S, Apel K, et al. (1994) Circadian oscillations of a transcript encoding a germin-like protein that is associated with cell walls in young leaves of the long-day plant Sinapis alba L. Plant physiology 106: 905-915. (Pubitemid 24986503)
58. Fan Z, Gu H, Chen X, Song H, Wang Q, et al. (2005) Cloning and expression analysis of Zmglp1, a new germin-like protein gene in maize. Biochemical and biophysical research communications 331: 1257-1263. (Pubitemid 40692492)
59. Chu TT, Xie H, Xu Y, Ma RC (2010) Research advanced of plant MADS box gene FRUITFULL (FUL). China Biotechnolog 30: 98-104.
60. Li ZQ, Shao HB (2004) The Gene Control of Flowering Time in Higher Plants (II). Life Science Research 8(4): 76-82
61. Kumar SV, Wigge PA (2010) H2A. Z-containing nucleosomes mediate the thermosensory response in Arabidopsis. Cell 140: 136-147.
62. Wang Z, Fang B, Chen J, Zhang X, Luo Z, et al. (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC genomics 11(1):726.
63. Fullwood MJ, Wei CL, Liu ET, Ruan Y (2009) Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome research 19: 521-532.
64. Lai ZX, Lin YL (2013) Analysis of the global transcriptome of longan (Dimocarpus longan Lour .) embryogenic callus using Illumina paired-end sequencing. BMC genomics 14: 561.
65. He CY, Cui K, Zhang JG, Duan AG, Zeng YF (2013) Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo. BMC plant biology 13: 119.
66. Wei W, Qi X, Wang L, Zhang Y, Hua W, et al. (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC genomics 12(1):451.
67. Ge G, Xiao P, Zhang Y, Yang L (2011) The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing. PLoS One 6: e21220.
68. Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, et al. (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC genomics 12(1):131.
69. Wang QQ, Liu F, Chen XS, Ma XJ, Zeng HQ, et al. (2010) Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 96(6):369-376.
70. Natarajan P, Parani M (2011) De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing. BMC genomics 12: 191.
71. Logacheva M, Kasianov A, Vinogradov D, Samigullin T, Gelfand M, et al. (2011) De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC genomics 12(1):30.
72. Xiong Y, Li QB, Kang BH, Chourey PS (2011) Discovery of genes expressed in basal endosperm transfer cells in maize using 454 transcriptome sequencing. Plant Molecular Biology Reporter 29: 835-847.
73. Jarillo JA, Piñeiro M (2011) Timing is everything in plant development. The central role of floral repressors. Plant Science 181: 364-378.
74. Andrés F, Coupland G (2012) The genetic basis of flowering responses to seasonal cues. Nature Reviews Genetics 13: 627-639.
75. Wilczek AM, Roe JL, Knapp MC, Cooper MD, Lopez-Gallego C, et al. (2009) Effects of genetic perturbation on seasonal life history plasticity. Science 323(5916):930-934.
76. Piñeiro M, Jarillo JA (2013) Ubiquitination in the control of photoperiodic flowering. Plant Science 198: 98-109.
77. Li W, Ahn I-P, Ning Y, Park C-H, Zeng L, et al. (2012) The U-Box/ARM E3 ligase PUB13 regulates cell death, defense, and flowering time in Arabidopsis. Plant Physiol 159(1):239-250.
78. Pacín M, Legris M, Casal JJ (2014) Rapid decline in nuclear COP1 abundance anticipates the stabilisation of its target HY5 in the light. Plant physiology: pp. 113.234245.
79. Kobayashi M, Takato H, Fujita K, Suzuki S (2012) HSG1, a grape Bcl-2-associated athanogene, promotes floral transition by activating CONSTANS expression in transgenic Arabidopsis plant. Molecular biology reports 39: 4367-4374.
80. Takayama S, Xie Z, Reed JC (1999) An evolutionarily conserved family of Hsp70/Hsc70 molecular chaperone regulators. Journal of Biological Chemistry 274: 781-786.
81. Kobayashi M, Katoh H, Takayanagi T, Suzuki S (2010) Characterization of thermotolerance-related genes in grapevine (Vitis vinifera). Journal of plant physiology 167: 812-819.